qpix 420 colony picking system user guide -...

QPix 420 Colony Picking System

User Guide

5026152 A March 2013

This document is provided to customers who have purchased Molecular Devices®, LLC (“Molecular Devices”) equipment, software, reagents, and consumables to use in the operation of such Molecular Devices equipment, software, reagents, and consumables. This document is copyright protected and any reproduction of this document, in whole or any part, is strictly prohibited, except as Molecular Devices may authorize in writing.

Software that may be described in this document is furnished under a license agreement. It is against the law to copy, modify, or distribute the software on any medium, except as specifically allowed in the license agreement. Furthermore, the license agreement may prohibit the software from being disassembled, reverse engineered, or decompiled for any purpose.

Portions of this document may make reference to other manufacturers and/or their products, which may contain parts whose names are registered as trademarks and/or function as trademarks of their respective owners. Any such usage is intended only to designate those manufacturers’ products as supplied by Molecular Devices for incorporation into its equipment and does not imply any right and/or license to use or permit others to use such manufacturers’ and/or their product names as trademarks.

Molecular Devices makes no warranties or representations as to the fitness of this equipment for any particular purpose and assumes no responsibility or contingent liability, including indirect or consequential damages, for any use to which the purchaser may put the equipment described herein, or for any adverse circumstances arising therefrom.

For research use only. Not for use in diagnostic procedures.

The trademarks mentioned herein are the property of Molecular Devices, LLC or their respective owners. These trademarks cannot be used in any type of promotion or advertising without the prior written permission of Molecular Devices, LLC.

Patents: http://www.moleculardevices.com/productpatents

Product manufactured by Molecular Devices, LLC.

1311 Orleans Drive, Sunnyvale, California, United States of America 94089.

Molecular Devices, LLC is ISO 9001 registered.

© 2013 Molecular Devices, LLC.

All rights reserved.

http://www.moleculardevices.com/productpatents

http://www.moleculardevices.com/productpatents

Contents

Safety Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9Warning and Caution Definitions . . . . . . . . . . . . . . . . . . . . . . . . 9Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9General Precautions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9Health and Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10External or implanted medical device risk. . . . . . . . . . . . . . . . 10Transport and Storage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10Lifting Points. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10External Covers. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

Electrical Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11Electrical Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11High Voltage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11Disposal of Electronic Equipment . . . . . . . . . . . . . . . . . . . . . . 11

Chemical and Biological Safety . . . . . . . . . . . . . . . . . . . . . . . . 12Moving Parts. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12Cleaning. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12Safety Features. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13Door . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13UV Light . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13Emergency Stop Button . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13Drive Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13Hot Air/Halogen Dryer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13Noise Levels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13Biohazard . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

Chapter 1: Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15Using the QPix 420 Colony Picking System . . . . . . . . . . . . . . . 15

Functionality of the QPix 420 System. . . . . . . . . . . . . . . . . . . . 15Picking . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

Chapter 2: Software Overview . . . . . . . . . . . . . . . . . . . . . . . . 17The QPix 420 Colony Picking Software . . . . . . . . . . . . . . . . . . . 17Navigation Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17Menu Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18File Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18View Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18Tools Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18Help Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

Right Menu Column - Current and New Processes . . . . . . . . . . 18Gridding Processes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19Routines Window. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19Barcodes Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19Head Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20Microplates and Filters Window . . . . . . . . . . . . . . . . . . . . . . . 20

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Filter Design Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21Filter Layout Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21Substrate Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21Holder Layout Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22Load Plates Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22Settings Summary Window . . . . . . . . . . . . . . . . . . . . . . . . . . 23

Standard and Regional Picking Processes . . . . . . . . . . . . . . . . . 24Routines Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24Filter Pairs List. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24Barcodes Window. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25Destination Options Window . . . . . . . . . . . . . . . . . . . . . . . . . 25Destination/Source Options Window (Regional Picking). . . . . . . 26Head/Sanitise Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26Source Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27Settings Summary Window . . . . . . . . . . . . . . . . . . . . . . . . . . 27Holder Layout Summary Window . . . . . . . . . . . . . . . . . . . . . . 28Test Image Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28FL Test Image Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29Feature Selection Window . . . . . . . . . . . . . . . . . . . . . . . . . . . 29Feature Counts Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30Display Options Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30

Load Plates Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30Control Plate Creation Processes . . . . . . . . . . . . . . . . . . . . . . . 31Routines Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31Barcodes Window. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31Destination Options Window . . . . . . . . . . . . . . . . . . . . . . . . . 31Head/Sanitise Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32Source Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32Control Plate Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32Settings Summary Window . . . . . . . . . . . . . . . . . . . . . . . . . . 33Holder Layout Summary Window . . . . . . . . . . . . . . . . . . . . . . 34Test Image Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34Feature Selection Window . . . . . . . . . . . . . . . . . . . . . . . . . . . 34Load Plates Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

Replication Processes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35Routines Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35Barcodes Window. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35Microplates/Sanitise Window . . . . . . . . . . . . . . . . . . . . . . . . . 35Head Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36Holder Layout Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36Load Plates Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36Settings Summary Window . . . . . . . . . . . . . . . . . . . . . . . . . . 37

Rearraying Processes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38Routines Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38Barcodes Window. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38Source Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38Destination Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39Head and Sanitise Window . . . . . . . . . . . . . . . . . . . . . . . . . . 39Holder Layout Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40Load Plates Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

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Settings Summary Window. . . . . . . . . . . . . . . . . . . . . . . . . . 41Data Viewer Processes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42Data Viewer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42Database Management. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42

Manage Sanitise Profiles. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43Camera Alignment Process . . . . . . . . . . . . . . . . . . . . . . . . . . . 44Instrument Utilities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45Change Head . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45Pin Fire Test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45UV Sanitise Window. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46Sanitise . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46

Chapter 3: Instrument Maintenance . . . . . . . . . . . . . . . . . . . . 47Aligning the Camera . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47Changing the Head . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48Performing a Pin Fire Test . . . . . . . . . . . . . . . . . . . . . . . . . . . 49

Chapter 4: Instrument Overview . . . . . . . . . . . . . . . . . . . . . . 51Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51Pre-Power-Up Checklist . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51Power-Up Procedures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51Shutdown procedure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52

Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52Mounting the Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . 52

Instrument Layout. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53Front Panel Display . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54Display Icons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55Service and Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55General Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55Weekly Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56Bi-annual Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56

Cleaning Procedures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56Cleaning the Instrument Interior . . . . . . . . . . . . . . . . . . . . . 56Incoming Compressed Air Supply . . . . . . . . . . . . . . . . . . . . 56Automated Pin Cleaning . . . . . . . . . . . . . . . . . . . . . . . . . . . 56

Removable Parts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57The Head . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57

Chapter 5: Preparations for Running a Routine . . . . . . . . . . . 59Preparing your Wash Baths. . . . . . . . . . . . . . . . . . . . . . . . . . . 59Conducting a Sanitise . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60Conducting a UV Sanitise . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60Creating and Editing Sanitise Profiles. . . . . . . . . . . . . . . . . . . . 61Editing a Sanitise Profile. . . . . . . . . . . . . . . . . . . . . . . . . . . . 62Deleting a Sanitise Profile . . . . . . . . . . . . . . . . . . . . . . . . . . . 63

Chapter 6: Conducting a Picking Routine . . . . . . . . . . . . . . . . 65Preparing for a Picking Routine . . . . . . . . . . . . . . . . . . . . . . . . 65Creating and Editing a Picking Routine . . . . . . . . . . . . . . . . . . . 66Selecting Barcode Reading Options . . . . . . . . . . . . . . . . . . . . 67Setting Filter Pairs (Fluorescent Light only). . . . . . . . . . . . . . . 69

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Setting Destination Options . . . . . . . . . . . . . . . . . . . . . . . . . . 69Selecting Head and Sanitise Options. . . . . . . . . . . . . . . . . . . . 71Setting your Picking Source. . . . . . . . . . . . . . . . . . . . . . . . . . 72Viewing the Settings Summary . . . . . . . . . . . . . . . . . . . . . . . 73

Running a Picking Routine. . . . . . . . . . . . . . . . . . . . . . . . . . . . 74Arranging the Layout of the Holders . . . . . . . . . . . . . . . . . . . . 74Creating a White Light Test Image . . . . . . . . . . . . . . . . . . . . . 75Creating a Fluorescent Test Image (Fluorescent light only) . . . . 77Selecting Colonies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78Viewing a Summary of Selected Colonies . . . . . . . . . . . . . . . . 80Viewing Additional Display Options. . . . . . . . . . . . . . . . . . . . . 81Continuing or Saving Your Routine . . . . . . . . . . . . . . . . . . . . . 81Loading the Plate Holders . . . . . . . . . . . . . . . . . . . . . . . . . . . 82Viewing the Picking Progress . . . . . . . . . . . . . . . . . . . . . . . . . 82Completing or Running Another Routine . . . . . . . . . . . . . . . . . 83

Chapter 7: Conducting a Regional Picking Routine . . . . . . . . . 85Preparing for a Regional Picking Routine . . . . . . . . . . . . . . . . . . 85Creating and Editing a Regional Picking Routine. . . . . . . . . . . . . 86Selecting Barcode Reading Options . . . . . . . . . . . . . . . . . . . . 87Setting Filter Pairs (Fluorescent Light only) . . . . . . . . . . . . . . . 89Configuring Destination Microplates . . . . . . . . . . . . . . . . . . . . 89Setting your Regional Picking Source . . . . . . . . . . . . . . . . . . . 90Defining Destination/Source Options . . . . . . . . . . . . . . . . . . . 91Selecting Head and Sanitise Options. . . . . . . . . . . . . . . . . . . . 92Viewing the Settings Summary . . . . . . . . . . . . . . . . . . . . . . . 94

Running a Regional Picking Routine . . . . . . . . . . . . . . . . . . . . . 95Arranging the Layout of the Holders . . . . . . . . . . . . . . . . . . . . 95Creating a White Light Test Image . . . . . . . . . . . . . . . . . . . . . 96Creating a Fluorescent Test Image (Fluorescent light only) . . . . 98Selecting Colonies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98Viewing a Summary of Selected Regional Colonies . . . . . . . . . 101Viewing Additional Display Options. . . . . . . . . . . . . . . . . . . . 102Continuing or Saving Your Routine . . . . . . . . . . . . . . . . . . . . 103Loading the Plates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103Viewing Regional Picking Progress . . . . . . . . . . . . . . . . . . . . 104Completing or Running Another Routine . . . . . . . . . . . . . . . . 105

Chapter 8: Control Plate Creation Processes. . . . . . . . . . . . . 107Preparing for a Control Plate Creation Routine . . . . . . . . . . . . . 107Creating and Editing a Control Plate Creation Routine. . . . . . . . 108Selecting Barcode Reading Options . . . . . . . . . . . . . . . . . . . 109Setting Destination Options . . . . . . . . . . . . . . . . . . . . . . . . . 109Selecting Head and Sanitise Options. . . . . . . . . . . . . . . . . . . 110Setting your Source Receptacle . . . . . . . . . . . . . . . . . . . . . . 111Designating the Control Plate Layout . . . . . . . . . . . . . . . . . . 111Viewing the Settings Summary . . . . . . . . . . . . . . . . . . . . . . 112

Running a Control Plate Creation Routine . . . . . . . . . . . . . . . . 113Arranging the Layout of the Holders . . . . . . . . . . . . . . . . . . . 113Loading Source Receptacles . . . . . . . . . . . . . . . . . . . . . . . . 114Creating a Test Image . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114

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Selecting Colonies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116Viewing a Summary of Selected Colonies . . . . . . . . . . . . . . . 118Viewing Additional Display Options . . . . . . . . . . . . . . . . . . . 118Continuing or Saving Your Routine . . . . . . . . . . . . . . . . . . . 119Loading the Plate Holders . . . . . . . . . . . . . . . . . . . . . . . . . . 119Viewing the Picking Progress. . . . . . . . . . . . . . . . . . . . . . . . 120Viewing the Summary of Your Routine . . . . . . . . . . . . . . . . . 120

Chapter 9: Replication Processes . . . . . . . . . . . . . . . . . . . . . 123Preparing for a Replicating Routine . . . . . . . . . . . . . . . . . . . . 123Creating and Editing a Replicating Routine . . . . . . . . . . . . . . . 124Selecting Barcode Reading Options . . . . . . . . . . . . . . . . . . . 124Setting Microplate and Sanitise Options . . . . . . . . . . . . . . . . 127Setting Head Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128

Running a Replicating Routine. . . . . . . . . . . . . . . . . . . . . . . . 128Arranging the Layout for the Routine . . . . . . . . . . . . . . . . . . 128Viewing the Settings Summary . . . . . . . . . . . . . . . . . . . . . . 130Continuing or Saving Your Routine . . . . . . . . . . . . . . . . . . . 130Viewing the Replication Progress . . . . . . . . . . . . . . . . . . . . . 131Viewing the Replicating Process Summary . . . . . . . . . . . . . . 131

Chapter 10: Conducting a Rearraying Routine . . . . . . . . . . . 133Performing Rearraying Procedures. . . . . . . . . . . . . . . . . . . . . 133Preparing for a Rearraying Routine . . . . . . . . . . . . . . . . . . . . 133Creating and Editing a Rearraying Routine . . . . . . . . . . . . . . . 133Selecting Barcode Reading Options . . . . . . . . . . . . . . . . . . . 134Identifying your Source Receptacle . . . . . . . . . . . . . . . . . . . 135Defining your Destination Receptacle . . . . . . . . . . . . . . . . . . 137Selecting Head and Sanitise Options . . . . . . . . . . . . . . . . . . 138

Running a Rearraying Routine. . . . . . . . . . . . . . . . . . . . . . . . 138Confirming the Layout for the Routine . . . . . . . . . . . . . . . . . 139Viewing the Settings Summary . . . . . . . . . . . . . . . . . . . . . . 140Viewing the Rearraying Progress . . . . . . . . . . . . . . . . . . . . . 141Viewing the Rearraying Process Summary . . . . . . . . . . . . . . 141

Chapter 11: Gridding Processes . . . . . . . . . . . . . . . . . . . . . . 143Preparing for a Gridding Routine . . . . . . . . . . . . . . . . . . . . . . 143Creating and Editing a Gridding Routine . . . . . . . . . . . . . . . . . 143Selecting Barcode Reading Options . . . . . . . . . . . . . . . . . . . 144Selecting Head and Sanitise Options . . . . . . . . . . . . . . . . . . 146Setting Source and Destination Receptacles . . . . . . . . . . . . . 146Creating a Filter Design Layout . . . . . . . . . . . . . . . . . . . . . . 147Selecting the Destination Tray . . . . . . . . . . . . . . . . . . . . . . 152Selecting Stamping and Inking Options . . . . . . . . . . . . . . . . 153

Running a Gridding Routine . . . . . . . . . . . . . . . . . . . . . . . . . 154Arranging the Layout for the Routine . . . . . . . . . . . . . . . . . . 154Viewing the Settings Summary . . . . . . . . . . . . . . . . . . . . . . 155Continuing or Saving Your Routine . . . . . . . . . . . . . . . . . . . 156Viewing the Gridding Progress. . . . . . . . . . . . . . . . . . . . . . . 157Viewing the Summary of Your Routine . . . . . . . . . . . . . . . . . 157

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Contents

Chapter 12: Data Viewer Processes. . . . . . . . . . . . . . . . . . . . 159Conducting a Data Search. . . . . . . . . . . . . . . . . . . . . . . . . . . 159Searching by Tag . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160Searching by Barcode. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160Searching by Date . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161Searching by User . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161Searching by Location. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161Viewing and Printing Settings Details . . . . . . . . . . . . . . . . . . 161

Working with Tags . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162Creating a Tag. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162Adding Tags to a Receptacle, Location, or Routine . . . . . . . . . 162Removing a Tag. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163

Adding Annotations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164Exporting Processes or Routines . . . . . . . . . . . . . . . . . . . . . . 165Adding or Deleting Properties for Microplates . . . . . . . . . . . . . 165Adding Properties. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165Deleting a Property . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 166

Viewing a Map of the Locations . . . . . . . . . . . . . . . . . . . . . . . 167Working with Sample Trails . . . . . . . . . . . . . . . . . . . . . . . . . . 168Adding and Removing Sample Trails. . . . . . . . . . . . . . . . . . . 168Viewing and Clearing Sample Trails . . . . . . . . . . . . . . . . . . . 169

Appendix A: Replacement Parts and Optional Extras . . . . . . 171Replacement Fuses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171

Appendix B: Technical Specifications . . . . . . . . . . . . . . . . . . 173Technical Specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173Electrical Connections. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 174Dimensions of the QPix 420 System. . . . . . . . . . . . . . . . . . . . 175

Appendix C: Electromagnetic Compatibility (EMC) . . . . . . . . 177REGULATORY INFORMATION FOR CANADA (ICES/NMB-001:2006) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 177ISM EQUIPMENT CLASSIFICATION (Group 1, Class A) . . . . . . . 177INFORMATION FOR THE USER (FCC NOTICE) . . . . . . . . . . . . . 177

Appendix D: Technical Assistance and Troubleshooting . . . . 179Technical Assistance. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179

Global Customer Support Center . . . . . . . . . . . . . . . . . . 179To Inquire About a Service Plan . . . . . . . . . . . . . . . . . . . . . . 179North America . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179Europe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179

Key Service and Support Offices . . . . . . . . . . . . . . . . . . . . . 179North America . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179Europe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179

Troubleshooting. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180

Glossary of Terms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183

8 5026152 A

Safety Information

Warning and Caution DefinitionsAll Warning and Cautions in this document include an exclamation point, a lightning bolt, or a light burst symbol framed within a triangle.The exclamation point symbol is an international symbol which serves as a reminder that all safety instructions should be read and understood before installation, use, maintenance, and servicing is attempted.

CAUTION! A CAUTION calls attention to a condition or possible situation that could damage or destroy the product or the operator’s work.

When warnings and cautions appear in this guide, pay special attention to the specific safety information associated with them.Please read and observe all warnings, cautions, and instructions. remember, the most important key to safety is to operate the QPix 420 System with care.

MaintenancePerform only the maintenance described in this guide. Maintenance other than that specified in this guide should be performed only by Molecular Devices service engineers.

General PrecautionsAll wastes, for example ethanol, must be disposed of according to local regulation. Ethanol is flammable and should be handled accordingly.Do not use in explosive environments.For safety reasons, never interfere with or override the front door switch.

WARNING! If the equipment is used in a manner not specified by Molecular Devices®, the protection provided by the equipment can be impaired.

WARNING! A WARNING calls attention to a condition or possible situation that could cause injury to the operator.

Note: It is your responsibility to decontaminate components of the QPix 420 System before requesting service by a service engineer or returning parts to Molecular Devices for repair. Please contact Molecular Devices for the relevant decontamination certificate. Molecular Devices will NOT accept any items which have not been decontaminated where it is appropriate to do so. If any parts are returned, they must be enclosed in a sealed plastic bag stating that the contents are safe to handle and are not contaminated.

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Safety Information

Health and Safety

External or implanted medical device risk

Transport and StorageThe QPix 420 System must be stored and transported in temperatures within the range of -25°C to +55°C.

Lifting PointsThe QPix 420 System should not be moved after installation. If relocation is necessary, standard lifting gear is adequate but should be undertaken only in the presence of a Molecular Devices approved engineer.The instrument should be moved into position using appropriate handling equipment such as forklift trucks or dolly trucks, and it should be properly balanced on the forks prior to lifting.

CAUTION! Do not use any part of the QPix 420 System exterior body to lift it, as this can cause irreparable damage.

External Covers

Note: Before using the QPix 420 System, Molecular Devices recommends you read this guide to understand all safety instructions.

Prior to using the instrument, confirm all tasks listed in the Pre-Power-Up Checklist on page 51, to ensure all moving parts are correctly positioned.

Molecular Devices also recommends you follow all steps in Power-Up Procedures on page 51.

WARNING! Motors and their associated drives and cabling are sources of electromagnetic fields. Persons with external or implanted medical devices need to evaluate the risks associated with these devices before entering an area where they are in use.

WARNING! High magnetic field. If you have an external or implanted medical device fitted, keep 300 mm away from drive magnets.

WARNING! If any of the external covers on the QPix 420 System are removed, the power supply does not automatically stop. If you must remove any of the external covers, you must ensure that the power is switched off first. Do not attempt to use the instrument again until all covers are replaced.

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Electrical SafetyTo prevent electrically related injuries and property damage, properly inspect all electrical equipment prior to use and immediately report any electrical deficiencies. For any servicing of equipment requiring the removal of covers or panels, contact a service engineer.

Electrical Safety

High Voltage

Do not remove instrument covers. To avoid electrical shock, use only supplied power cords and connect to properly grounded (three-holed) wall outlets.

Disposal of Electronic EquipmentIt is important to understand and follow all laws regarding the safe and proper disposal of electrical instrumentation.The symbol of a crossed-out wheeled bin on the product is required in accordance with the Waste Electrical and Electronic Equipment (WEEE) Directive of the European Union. The presence of this marking on the product indicates that:

• the device was put on the European Market after August 13, 2005.• the device is not to be disposed via the municipal waste collection

System of any member state of the European Union.For products under the requirement of WEEE directive, please contact your dealer or local Molecular Devices office for the proper decontamination information and take back program, which will facilitate the proper collection, treatment, recovery, recycling, and safe disposal of the device.

WARNING! The QPix 420 System must be connected to a properly earthed power outlet to protect users from the risk of electric shock. The main chassis of the instrument is earthed together with all associated electrical components. Do not remove any of the fixed covers, as there are no user serviceable parts inside. All electrical work should be referred to Molecular Devices approved service personnel.In the event of a liquid spillage into the base cavity of the instrument, disconnect the mains power supply before attempting to clean up.

WARNING! This symbol indicates the potential of an electrical shock hazard existing from a high voltage source and that all safety instructions should be read and understood before proceeding with the installation, maintenance, and servicing of all modules.

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Safety Information

Chemical and Biological SafetyNormal operation of the instrument can involve the use of materials that are toxic, flammable, or otherwise biologically harmful. When using such materials, observe the following precautions:

• Handle infectious samples according to good laboratory procedures and methods to prevent the spread of disease.

• Observe all cautionary information printed on the original solutions containers prior to their use.

• Dispose of all waste solutions according to your facility’s waste disposal procedures.

• Operate the instrument in accordance with the instructions outlined in this guide, and take all the necessary precautions when using pathological, toxic, or radioactive materials.

• Splashing of liquids can occur; therefore, take appropriate safety precautions, such as using safety glasses and wearing protective clothing, when working with potentially hazardous liquids.

• Use an appropriately contained environment when using hazardous materials.

• Observe the appropriate cautionary procedures as defined by your safety officer when using flammable solvents in or near a powered-up instrument.

• Observe the appropriate cautionary procedures as defined by your safety officer when using toxic, pathological, or radioactive materials.

Moving PartsTo avoid injury due to moving parts, observe the following:

• Never attempt to exchange labware, reagents, or tools while the instrument is operating.

• Never attempt to physically restrict any of the moving components of the QPix 420 System.

• Keep the QPix 420 System interior clear to prevent obstruction of the movement.

Cleaning

Observe the cleaning procedures outlined in this user guide for the instrument. Prior to cleaning equipment that has been exposed to hazardous material:

• Appropriate Chemical and Biological Safety personnel should be contacted.

• The Chemical and Biological Safety information contained in this user guide should be reviewed.

Note: Observe all warnings and cautions listed for any external devices attached to or in use during the operation of the instrument. See the applicable user guides for operating and safety procedures of that device.

Note: Molecular Devices recommends you always use ethanol for cleaning, because autoclaving is not compatible with anodized parts.

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Safety Features

DoorThe QPix 420 System is equipped with an automatically locking door which locks whenever you run any routine. The door is made from acrylic, and so prevents UV light from passing through during operation.As a safety measure, if the door is open, an electromagnetic switch prevents the instrument from running. This switch should never be tampered with, as it serves two purposes:

• It prevents the motors from running and therefore the potential of any physical damage.

• It disables the UV light therefore preventing the risk of damage from UV radiation.

UV LightThe QPix 420 System is fitted with a UV germicidal lamp and timer. It is a 30W linear discharge lamp with a sharply defined output at 253.7 nm, making it an efficient source of germicidal radiation.

Emergency Stop ButtonThe location of the Emergency Stop button is shown in Front Panel Display on page 54. Pressing the Emergency Stop button immediately stops all motion and turns off the instrument. Before you can restart the instrument, you must pull the button out and also press the Start button.Be sure to not block or obstruct this button.

Drive Safety

CAUTION! Be aware that the motors use high-powered magnets.The linear drive units and encoders are delicate, so take great care with them. Follow the Pre-Power-Up Checklist on page 51 before every routine, to prevent serious damage to the QPix 420 System or any of its constituent parts. All power ceases to the drives when the doors are open.

Hot Air/Halogen DryerThe QPix 420 System is fitted with high temperature halogen dryer. The casing can become hot during the drying cycle.

Noise LevelsDuring normal operation the level of airborne noise emitted by the QPix 420 System will not exceed 70db(A) measured at a distance of 1 metre.

Biohazard

WARNING! The casing can become hot during the drying cycle.

WARNING! If any biohazard is introduced to the instrument during operation the area needs to be clearly marked with an appropriate biohazard sign.

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Safety Information

14 5026152 A

1
Introduction
OverviewThe QPix 420 Colony Picking System allows you to control selective microbial colony picking. It allows multiple users to select and collect microbial colonies from various receptacles.

Using the QPix 420 Colony Picking SystemThis user guide contains all the information you will need to fully understand and use the QPix 420 System. Please refer to the related chapters for important setup, maintenance and safety information.

• Safety Information on page 9• Software Overview on page 17• Instrument Maintenance on page 47• Instrument Overview on page 51• Preparations for Running a Routine on page 59• Data Viewer Processes on page 159

Functionality of the QPix 420 SystemThe QPix 420 instrument is part of the QPix 400 series, which also includes the QPix 450 and QPix 460. The QPix 420 System offers available features to suit a whole range of needs, including fluorescent imaging, regional picking, rearraying, and compression and expansion replicating.The QPix 420 System is available both with transmitted White Light only and Fluorescent And White Light functionality. Multiple fluorescent filters ensure compatibility with a wide range of fluorescent cloning dyes and proteins, and enables both systems to reveal unique information about individual colonies. Fluorescent imaging is available as an option on all systems.After colonies are located using a CCD camera, they are picked at high speed from source plates and then inoculated into pre-filled 96 or 384 well microplates. Selected colonies of interest can then be rearrayed from a library into new microplates.In order to optimize these systems, Molecular Devices® has developed a range of plastic consumables for use with the instrument. The destination microplate bed allows for versatile use of shallow, standard, and deep well microplates in various combinations.You can log all your processes such as picking, replicating, and re-arraying with the software, which allows you to tag important samples to enhance the history, location, and extra details of sample-specific data.

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Introduction

PickingThe QPix 420 System is capable of automatically picking in excess of 3000 colonies per hour. This is achieved with an integrated vision, detection, and analysis hardware and software System and a 96-pin head assembly, both custom designed by Molecular Devices.After you have identified potential colonies, the source plate is then imaged in multiple frames using a CCD camera. These images are processed to produce a single, large image of the colonies on the source plate. Specific colonies are then selected for picking using feature selection parameters, such as size, shape, and proximity.The instrument picks from a range of source plates including large QTrays, Omni Trays, and standard Petri dishes using the optional source plate holders.A fluorescent imaging head is also available. This comprises an LED-based light source that enables different excitation wavelengths to be selected using preset filter pairs, a filter for selecting appropriate fluorescence emission wavelengths, and a sensitive monochrome CCD camera for image acquisition. When fitted, this fluorescence head can also be used for white light imaging using the transmitted light source fitted below the source plate holder.The fluorescent imaging system allows for the addition of fluorescent intensity parameters in the selection criteria.

Note: The QPix 420 System is strictly for research use only and is not intended or recommended for the diagnosis of disease in humans or animals. If the System is used in a manner not specified in this manual, the protection provided by the equipment could become impaired.

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2
Software Overview
The QPix 420 Colony Picking SoftwareThe QPix 420 software controls the QPix 420 Colony Picking System. You access all processes and other functionality from the Navigation window, which opens after you launch the software. The following tabs are found at the top of the window:

• New Process allows you to create a new routine. It contains existing QPix 420 software processes, as well as Maintenance and Utility processes.

• Recent Processes allows you to use a previously saved routine.The following processes can be performed using the QPix 420 software.

• Gridding Processes on page 19• Standard and Regional Picking Processes on page 24• Control Plate Creation Processes on page 31• Replication Processes on page 35• Rearraying Processes on page 38• Data Viewer Processes on page 42• Manage Sanitise Profiles on page 43• Camera Alignment Process on page 44• Instrument Utilities on page 45

This chapter describes the functionality of these various processes. Subsequent chapters describe how to perform the various routines that are possible within each process.Once all systems have been correctly powered up and initialized, start the software and connect to the QPix 420 System by double-clicking the QPix 420 icon.

Navigation WindowThe Navigation window displays all processes for the QPix 420 System.

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Software Overview

Menu OptionsThe same menu is displayed in all windows, but available items will vary.

File Menu

The only menu option that is usable under the File menu is the following:• Exit closes the QPix 420 software.

View Menu

• Properties displays the routine properties being set prior to starting the routine.

• Progress displays the progress of a running routine.• Administrative Properties allows you to change the Properties view

and default values.

Tools Menu

• Configuration opens the QPix 420 software configuration settings.

• Prepare Error Report launches a wizard that creates a data file containing the configuration and recent log files to help Molecular Devices troubleshoot your problem.

Help Menu

• About displays the version numbers of the QPix 420 software modules. If asked to provide the software version number, give this number unless otherwise directed.

• Online Support opens the online support web page if the QPix 420 System has an active internet connection.

Right Menu Column - Current and New ProcessesThese menus are applicable to other Molecular Devices products using the same software platform. They are not applicable to the QPix 420 System.

Note: Molecular Devices® recommends only trained personnel configure these settings.

18 5026152 A


Gridding ProcessesThe gridding process allows you to deposit liquid samples from one or more source microplates to one or more destination surfaces (either agar filled QTrays or filters).For information on conducting a gridding routine, see Gridding Processes on page 143.As with other processes, you must start with creating your routine.

Routines WindowThe QPix 420 software allows you to run a new or existing routine using various pre-configured routines from the Routines window.

Barcodes WindowThe QPix 420 software lets you read barcodes in various ways.Source barcodes can be listed in any order. The QPix 420 System searches the list to validate that the source barcode is present. If it is not, a message appears describing the erroneous receptacle.

Note: Validation barcodes are an option for source receptacles only. Barcodes compatible with the barcode reader are code 39, code 93, and code 128.

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Software Overview

Head WindowUse the Head window for setting the gridding head and wash cycle you want for the routine.

Microplates and Filters WindowUse the Microplates and Filters window to set up the source receptacles and destination surface, as well as control the number of times the head dips into the source receptacle or stirs the source solution.

Note: If the stacker icons are greyed out and unselectable in the next window, it is because you chose an unsuitable microplate in the current window. The software knows the specifics of the stacker lane configuration for your instrument, and allows you to choose only suitable microplates. Return to this current window to select a suitable microplate.

20 5026152 A


Filter Design WindowUse the Filter Design window to create and arrange the gridding spot patterns and the fields they will be stamped onto.

Filter Layout WindowThe Filter Layout window selection options are greyed out, because you have only the option of using one QTray.

Substrate WindowUse the Substrate window to select stamping and inking options for your routine.

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Software Overview

Holder Layout WindowThe Holder Layout window shows you how to correctly arrange the microplate holders in the instrument for your routine dictated by the selections made at the Source/Destination step earlier. You must click the Checked? box to continue from this window.

Load Plates WindowThe Load Plates window displays how many and what type of microplates you need to load for your routine. You must click the Checked? box to continue from this window.

22 5026152 A


Settings Summary WindowUse the Settings Summary window to view the settings for your gridding routine.

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Software Overview

Standard and Regional Picking ProcessesThe QPix 420 software allows you to pick colonies from receptacles using either the standard or regional process. These can be performed with both white light and fluorescent imaging capabilities if your System has been suitably configured. Both processes are described in this section.If you want to perform a regional colony pick, it must be done using a 48-region divided Bioassay tray (for example the Molecular Devices QTray (X6029)). For more information on additional available spares, see the table, QPix 420 Colony Picking System Replacement Parts on page 171.

For information on performing a standard picking routine, see Conducting a Picking Routine on page 65.For information on performing a regional picking routine, see Conducting a Regional Picking Routine on page 85.

Routines WindowThe QPix 420 software allows you to run a new or existing routine using various pre-configured routines from the Routines window.

Filter Pairs List

If you have purchased the fluorescent imaging option, you can make imaging adjustments with various supplied filter pairs using the Filter Pair list.

Note: If fluorescent picking is required, you need to have a specific imaging head based on fluorescent detection installed on the instrument. For more information, contact technical support [email protected].

Note: Filter Pairs are available only if Fluorescent Imaging is installed. If the Barcodes window does not display a filter pairs list, it means your System has only White Light functionality installed.

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Barcodes WindowThe QPix 420 software lets you read barcodes in various ways.Source barcodes can be listed in any order. The QPix 420 System searches the list to validate that the source barcode is present. If it is not, a message appears describing the erroneous receptacle.

Destination Options WindowUse the Destination Options window to configure your destination microplate settings.

Note: Validation barcodes are an option for source receptacles only. Barcodes compatible with the barcode reader are code 39, code 93, and code 128.

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Software Overview

Destination/Source Options Window (Regional Picking)The Destination/Source Options window is configured especially for regional picking. It will only appear when you are performing a regional pick. Use it to control your regional picking source and destination deposit options.

Head/Sanitise WindowChoose head and sanitise options for your routine from the Head/Sanitise window.The top of the window allows you to select the relevant head for your routine.The lower section of this window allows you to choose your sanitise options for your routine from this section. The Sanitise Profile list displays all sanitise profiles created using Manage Sanitise Profiles. Select the desired sanitise profile and its related wash routine displays in the Wash Cycle table. You cannot change sanitise profile settings from here. For information on how to perform this task, see Creating and Editing Sanitise Profiles on page 61.

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Source WindowUse the Source window to choose your source Holder, Receptacle type, and positioning, and picking depth.

Settings Summary WindowThe Settings Summary window displays a list of all settings configured for a routine. This window will display different information based on the settings you just made.

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Software Overview

Holder Layout Summary WindowThe Holder Layout Summary window shows you how to correctly arrange the microplate holders in the instrument for your routine dictated by the selections made earlier. You must click the Checked? box to continue from this window.

Test Image WindowUse the Test Image window to optimise your imaging settings for detecting colonies.

28 5026152 A


FL Test Image WindowA fluorescent test image is also created if you have chosen to perform fluorescent imaging. This test image is similar to the standard white light test image, but the only Acquisition settings for use are exposure and gain.

Feature Selection WindowUse the Feature Selection window to detect colonies you want to pick that match a desired shape, size and proximity.To perform both white light and fluorescent picking, toggle between the White Light and fluorescent image tabs.

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Software Overview

Feature Counts Tab

The Feature Counts tab shows the number of feature counts detected on a source receptacle. The barcode for the source receptacle is listed, the number of features found is displayed, as well as the number of features to pick as determined by the selection criteria.

Display Options Tab

The Display Options tab allows you to view additional information about the receptacle image.


Note: This tab contains some Regional Picking specific options.

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Control Plate Creation ProcessesUse the Control Plate Creation process to create a batch of microplates containing specified control samples. These can be created by picking colonies from specified source receptacles into specified destination wells.For information on conducting a control plate creation routine, see Control Plate Creation Processes on page 107.As with other processes, you must start with creating your routine.

Routines WindowFor details of elements in the Routines windows, see Routines Window on page 24.

Barcodes WindowThe Control Plate Creation Barcodes window is simpler than the usual Barcodes window. You have the option of choosing either Use Barcode Reader or Generate Random Barcodes.

Destination Options WindowUse the Destination Options window to set your destination microplate options. You can create up to 70 control microplates.

Note: If the stacker icons are greyed out and unselectable in the next window, it is because you chose an unsuitable microplate in the current window. The software knows the specifics of the stacker lane configuration for your instrument, and allows you to choose only suitable microplates. Return to this current window to select a suitable microplate.

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Software Overview

Head/Sanitise WindowThe Head/Sanitise window allows you to choose a head and select a sanitise profile. For more information on sanitise profiles, see Creating and Editing Sanitise Profiles on page 61.

Source WindowThe Source window allows you to configure your source holder and receptacle, as well as set the picking depth into the agar.

Control Plate WindowThe Control Plate window allows you to designate where the control samples are placed on the destination receptacle.

32 5026152 A


Settings Summary WindowThe Settings Summary window contains a full summary of the routine settings you just configured.

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Software Overview

Holder Layout Summary WindowThe Holder Layout Summary window shows you how to correctly arrange the microplate holders in the instrument for your routine dictated by the selections made at the Source/Destination step earlier. You must click the Checked? box to continue from this window.

Test Image WindowThe Test Image window is described in the Standard and Regional Picking Processes section. For more information, see Test Image Window on page 28.

Feature Selection WindowThe Feature Selection window is described in the Standard and Regional Picking Processes section. For more information, see Feature Selection Window on page 29.


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Replication ProcessesThe QPix 420 software allows you to replicate your picked colony samples in the following ways:

• Library Replication duplicates samples from one microplate to another of the same format. You can create several copies of the original microplate.

• Library Compression replicates samples from 96-well microplates to 384-well microplates. You can create several copies of the original microplate.

• Library Expansion replicates samples from a 384-well microplate to a 96-well microplate. You can create several copies of the original microplate.

All three tasks follow similar routine steps, so the differences only will be highlighted. For information on conducting a replicating routine, For information on performing a replicating routine, see Replication Processes on page 123.

Routines WindowFor details of elements in the Routines windows, see Routines Window on page 24.

Barcodes WindowFor details of elements in the Barcodes windows, see Barcodes Window on page 25.

Microplates/Sanitise WindowSelect your replicating source and destination microplates, dipping, stirring, and copying options, and your sanitise profile from the Microplates/Sanitise window.

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Software Overview

Head WindowThe Head window allows you to set the head type and inoculation dipping height options of both the source and destination microplate.

Holder Layout WindowFor information on the Holder Layout window, see Holder Layout Window on page 22.

Load Plates WindowThe Load Plates window displays the required layout and positioning for your source, destination, and copy microplates (if you chose to make copies). You must click the Checked? box to continue from this window.

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Settings Summary WindowThe Settings Summary window contains a full summary of the routine settings you just configured. You can print a copy of the settings by clicking Print.

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Software Overview

Rearraying ProcessesRearraying allows you to re-deposit liquid samples between one or more source and destination microplates. You can, therefore, consolidate chosen wells into microplates in an ordered fashion.For information on performing a rearraying routine, see Conducting a Rearraying Routine on page 133.As with other processes, you must start with creating your routine and barcodes.

Routines WindowFor details on routines, see Routines Window on page 24.

Barcodes WindowUse the Barcodes window to read barcodes in various ways.

Source WindowUse the Source window to rearray (transfer) selected colonies from existing source receptacles into new destination receptacles.

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Destination WindowUse the Destination window to configure destination microplate settings.

Head and Sanitise WindowChoose head and sanitise options from the Head and Sanitise window.The top of the window allows you to select the relevant head for your routine.The lower section of this window allows you to choose your sanitise options for your routine from this section. The Sanitise Profile list displays all sanitise profiles created using Manage Sanitise Profiles. Select the desired sanitise profile and its related wash routine displays in the Wash Cycle table. You cannot change sanitise profile settings from here. For information on how to perform this task, see Creating and Editing Sanitise Profiles on page 61.

Note: You cannot make a copy of a destination microplate during rearraying, but you can make a copy within both picking and replicating processes.

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Software Overview

Holder Layout WindowThe Holder Layout Summary window shows you how to correctly arrange the microplate holders in the instrument for your routine dictated by the selections made at the Source/Destination step earlier. You must click the Checked? box to continue from this window.

Load Plates WindowThe Load Plates window displays the required layout and positioning for your source, destination, and copy microplates (if you chose to make copies). You must click the Checked? box to continue from this window.

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Settings Summary WindowThe Settings Summary window contains a full summary of the routine settings you just configured. You can print a copy of the settings by clicking Print.

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Software Overview

Data Viewer ProcessesThe QPix 420 System allows you to view data and manage the data of previous routines run on the instrument. For information on performing a data viewer processes, see Data Viewer Processes on page 159.

Data ViewerThe Data Viewer window allows you to search and view any previously-run routine on the instrument. The routines are searchable in multiple ways, for example by process or by tag, barcode, date, user, and location.

Database ManagementIn this window, Molecular Devices engineers or trained customers only can update the database or perform an automatic backup of the database.

The process also allows engineers and trained customer to set options for backup and restore and versioning the software database.You will need to run a versioning program following an install which also contains a database upgrade.

Note: Trained people only should perform this task.

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QPix Utility Processes can be run at any time and are an important part of the ongoing maintenance of the QPix 420 System.

Manage Sanitise ProfilesManage Sanitise Profiles allows you to set up various sanitise profiles as required by various experimental needs. You will need to have at least one sanitise profile created before you can successfully conduct a picking routine. For more information on using sanitise profiles, see Creating and Editing Sanitise Profiles on page 61.

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Software Overview

Camera Alignment ProcessTo ensure the most accurate picking, the camera must be calibrated and aligned correctly to achieve pin-to-spot accuracy, relating the image pixel co-ordinates with the instrument x and y coordinates. If the actuator is knocked, picking accuracy might be affected. Calibration and alignment are performed before the instrument is dispatched and are checked by a Molecular Devices approved engineer during installation.For more information on how to conduct camera alignment, see Aligning the Camera on page 47.

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Instrument Utilities Instrument Utilities allow you to perform the following maintenance and cleaning activities.

Change HeadChange Head allows you to safely move the head of the instrument so you can change it. For more information on changing the head, see Changing the Head on page 48.

Pin Fire TestPin Fire Test allows you to fire all pins to ensure they are obstruction-free before use. You can control the speed of the pin firing by moving the speed slider at the bottom of the window. For more information how to conduct a pin fire test, see Performing a Pin Fire Test on page 49.

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Software Overview

UV Sanitise WindowYou can use the UV Sanitise window to sanitise the QPix 420 System interior for a designated period of time (up to 600 seconds). For more information on conducting a UV sanitise, see Conducting a UV Sanitise on page 60.

SanitiseThe Sanitise window allows you to wash the head outside of a routine (for example, if the System had been unused for a long period of time). For more information on conducting a sanitise, see Conducting a Sanitise on page 60.

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3
Instrument Maintenance
Molecular Devices® recommends regular and thorough maintenance of the QPix 420 Colony Picking System to ensure it continues to function correctly.The following maintenance tasks are available for the QPix 420 System:

• Aligning the Camera on page 47• Changing the Head on page 48• Performing a Pin Fire Test on page 49

For information on how to clean the instrument, see:• Conducting a Sanitise on page 60• Conducting a UV Sanitise on page 60• Creating and Editing Sanitise Profiles on page 61

Aligning the CameraTo ensure the most accurate picking, the camera must be calibrated and aligned correctly to achieve pin-to-spot accuracy, relating the image pixel co-ordinates with the instrument x and y coordinates.

1. From the Navigation window, double-click the Camera Alignment Process icon. Ensure you are using a 96 pin head.

2. Place a QTray with agar onto the light table holder, and then click Next.3. Click Goto Pos to move the head over the QTray.4. Use the settings in the Acquisition section to sharpen and focus the

image you are working with.5. Click Fire Pin A1 and, using the blue jogger arrows, jog the pin

down until it just touches the agar. You can adjust the increment for each jog using the Dist (mm) field next to the arrows.

6. Click Retract Pin, and using the camera settings (Visit Position and Set Position), align the camera to the hole in the agar.

7. Click Goto Camera and using the Vertical blue jogger arrows, zoom into the hole in the agar. Adjust camera settings as necessary.

8. Using the Lateral red and green jogger arrows, jog the camera until the centre of the hole aligns with the red crosshairs. You can adjust the increment for each jog using the Move Size list.

9. Click Set when you are satisfied with your camera alignment settings.10. Click Next to complete this process.

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Changing the HeadTo remove the head from the instrument, Molecular Devices recommends you use the QPix 420 software to help you safely perform this task.

1. From the Navigation window, double-click Instrument Utilities, and then double-click the Change Head icon. The Change Head window appears.

1. Select one of the following: Change Head allows you to safely move and change the head. Park Head allows you to home the head to its starting location.

A warning message appears, telling you to ensure the bed is clear.2. Click OK.

If you clicked Park Head, the head homes to its starting location and the process is complete. If you clicked Change Head, the head moves to the front of the instrument. You can now safely remove the head.

3. To remove the head, unscrew and remove the thumbscrew, which secures the head to the actuator assembly, taking care not to lose the washer. Be careful not to touch the camera.

4. Grab the head handle and slide it out of the actuator. 5. If you have finished using the head, slide it into the metal cover (pins

facing inwards) and securing it in place with the thumbscrew.6. Click Next to return to the Instrument Utilities window.

WARNING! If moving head manually, use handle to avoid pinching.

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Performing a Pin Fire TestThe Pin Fire Test checks that pins are obstruction-free and can move freely.

1. From the Navigation window, double-click Instrument Utilities, and then double-click the Pin Fire Test icon.The Pin Fire Test dialog opens stating that once you click OK, the head will move to the Change Head position.

2. Click OK.

The Pin Fire Test window appears.

3. Select the various parameters for your test from the following options: Select Head allows you to select the head to be tested. No of rows displays the number of rows of pins on the head. No of columns displays the number of columns on the head. Fire Pins In Sequence test fires the pins in the order you select

from the following check boxes (default is by column order). This test continues until you click Stop or all the pins have been fired.

X Row First fires the pins one by one in row order. Rearray Valve activates pin dampening as they retract. Fire All Pins test fires all the pins at once. Fire Pins Randomly randomly test fires the pins. The pin map

shows which pins are firing by temporarily changing the colour of the fired pin. This test continues until you click Stop or all the pins have been fired.

Click Next. The Pin Fire Test dialog opens, telling you to move the head to a safe parking position.

4. Click OK to start the test.

CAUTION! Wait for all firing to stop before opening the door.

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4
Instrument Overview
IntroductionThe QPix 420 Colony Picking System is constructed within a welded steel framework. All working parts are located within the interior of the instrument.Before operating the instrument or performing maintenance operations, make sure that you are familiar with the safety information in this user guide. For more information on safety, see Safety Information on page 9.The door on the front of the instrument, is fitted with an electro-mechanical lock, allowing it to operate only when the door is correctly closed and locked. The bed of the instrument contains source and destination plate holders, and wash baths, making it easier to clean pins both before and during routines. For more information on cleaning and preparing the instrument, see Preparations for Running a Routine on page 59.For more information on regular instrument maintenance, see Instrument Maintenance on page 47.

Pre-Power-Up Checklist1. Check the Emergency Stop button (see Figure 4-2 on page 54) is

pulled out. The instrument will not start if the button is pushed in.2. Confirm the instrument bed is clear of obstructions and loose items. 3. Confirm that all motor tracks are free of obstruction.4. Confirm there are no obstructions to movement of the head.

Power-Up Procedures1. Turn on the power supply to the compressor.2. Push the Start button on the front panel (see Figure 4-2 on page 54).

The Power On icon displays on the front panel. If the power to the QPix 420 System does not turn on, it is likely that the door is open or the Emergency Stop button is pushed in (see Figure 4-2 on page 54). The instrument cycles through various processes which is indicated in the LCD Indicator panel. When initialization is complete, this message will disappear, and the display icons will appear. For more information about display icons, see Display Icons for QPix 400 Series of Colony Picking Instruments on page 55.

3. Check that the Air Pressure OK icon on front panel is displayed. 4. Switch on the computer and wait for it to discover the QPix 420 Colony

Picking System local network.

5. Once you are certain the computer has finished its initialization, from the Desktop, double-click the QPix 420 Colony Picking System icon. Every time the instrument is used, the three axes will sequentially run through their “Initialize drives” routine. This enables the drives to find their respective home positions. The QPix 420 System must be allowed

Note: A common mistake at this point, is trying to launch the software before the network has been discovered. If this happens, an error message will appear, notifying you that it cannot find the instrument.

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Instrument Overview

to complete this routine without interference to ensure that there is no damage to the instrument or its ancillary equipment.

Shutdown procedure1. Click Exit from the File menu in the Navigation window. The QPix 420

System closes down.2. Click Start at the bottom of your computer screen, and then click Shut

Down. Wait for the computer to switch off completely.3. Switch off the instrument by pushing the STOP button on the front

panel.4. Switch off the power at the mains.

InstallationInstallation is to be undertaken only by Molecular Devices® approved personnel. The QPix 420 System must be located in a well ventilated area. For more information on installation, see Technical Specifications on page 173.

Mounting the InstrumentBe sure to install the instrument on a suitably strong and firm surface. Because of the weight of the instrument and the movement of the head during most processes, some vibration and wobble can occur. This can reduce performance effectiveness, most notably a reduction in the quality of imaging results.Molecular Devices supplies a suitable table for purchase, but if you choose to not purchase this table, be sure that the table on which you mount the instrument is stable enough to minimize vibration and wobble.

Note: The instrument is supplied with four adjustable leveling feet. Once the instrument is mounted on a table, be sure to adjust these feet accordingly in order to maximize performance.

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Instrument Layout

Figure 4-1: Angled Front View Showing a Three-Holder Layout

Item Description

1 Plate Holders

2 Imaging Table with Source Tray loaded

3 Wash Baths

1

3

2

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Instrument Overview

Front Panel Display

Figure 4-2: The QPix 420 System Front Panel Display

Item Description

1 LCD Indicator Panel

2 START Button

3 STOP Button

4 Emergency Stop Button

1

2

3

4

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Display Icons

Figure 4-3: Display Icons for QPix 400 Series of Colony Picking Instruments

Service and MaintenanceYou are responsible for day-to-day maintenance, details of which are explained in the following pages.In addition, Molecular Devices strongly recommends that a complete instrument maintenance be carried out every 6 months by a Molecular Devices approved service engineer. Maintenance contracts or one-off visits can be obtained from your regional Molecular Devices office.For more information on service and maintenance processes, see Instrument Maintenance on page 47.

General Maintenance1. Ensure that the QPix 420 System interior is free from dirt and dust (for

more information on cleaning, see Cleaning Procedures on page 56). In particular, check the surface of the x-axis drag-chain support bracket. Dust and debris accumulated here can be swept onto the QPix 420 System bed during operation.

2. Remove, clean, and sanitise wash bath(s) and brushes.

Item Description

1 Power is on

2 Air pressure is low

3 Air pressure is correct

4 The instrument is running a process (not applicable for Instrument Utilities).

5 The interior light is switched on

6 The UV light is switched on

1 3 4

5 6

2

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Instrument Overview

3. Check the air regulator for signs of moisture. If necessary, twist the drain clockwise approximately half a turn to force moisture out. Some types of regulator might require the drain purge to be pushed up towards the regulator bowl.

Weekly Maintenance1. Dismantle head completely and thoroughly clean all component parts.2. Check operation of the Emergency Stop button.3. If the QPix 420 System door shows any signs of damage you need to

request a replacement door from Molecular Devices.

Bi-annual MaintenanceMaintenance performed by Molecular Devices approved personnel.

Cleaning Procedures

Cleaning the Instrument Interior

For efficient decontamination of pathogenic micro-organisms, all non-removable parts within the QPix 420 System should be wiped with a cloth using 70% ethanol. Abrasive cleaners should not be used, as they will damage the surface of the bed.The QPix 420 System can be left in a laboratory during formaldehyde vapor fumigation at an appropriate concentration.For more information on cleaning, see Preparing your Wash Baths on page 59, Conducting a Sanitise on page 60 and Conducting a UV Sanitise on page 60.

Incoming Compressed Air Supply

Compressed air is required for the picking action of the picking pins. The oil-free compressed air unit draws air from the local environment and delivers it to the instrument through the regulator set to 100 psi.

Automated Pin Cleaning

The reusable picking pins are subject to repeated pin cleaning during a routine. Specifically, they are cleaned prior to the first pick, between each cycle of picking, and at the end of the run. The cleaning routine consists of the following configurable tasks:

• Brushing of the pins in the three baths. • Halogen dryer heats the picking pins and removes residual ethanol.•

Note: Excessive formaldehyde treatment will damage sensitive electrical and optical components.

Note: To avoid damaging the instrument or any of its components, if a solution spill occurs in the instrument interior, especially if it is 1% sodium hypochlorite (bleach), be sure to conduct an immediate clean up using your standard cleaning practices.

Note: Automated cleaning should not replace the sanitisation of picking pins by sonication.

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Removable PartsYou can clean and remove all parts of the QPix 420 System components that come into close contact with biological materials.

The Head

The Z ball-screw drive carries a unique actuator System that accommodates the head. This allows for easy exchange and set-up of the head. Although it is possible to move the head manually, Molecular Devices recommends using the QPix 420 System to safely remove the head. For more information on removing the head, see Changing the Head on page 48.

Note: Molecular Devices recommends you always use ethanol for cleaning, because autoclaving is not compatible with anodized parts.

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Instrument Overview

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5
Preparations for Running a Routine
Molecular Devices® recommends regular and thorough preparation of the QPix 420 Colony Picking System to ensure it continues to function correctly.This chapter describes the preparation of the instrument you should conduct before running any routine. Before starting any new routine, Molecular Devices recommends you perform a manual clean (using 70% ethanol) and UV sanitise of the interior of the instrument. For more information, see Conducting a UV Sanitise on page 60.It is also important that the sanitise profiles are edited prior to starting a new routine. For more information, see Creating and Editing Sanitise Profiles on page 61.

Preparing your Wash BathsThe QPix 420 System contains three wash baths which you will use when running various routines. It is important that these baths are filled with a suitable amount of solutions and they are arranged correctly. For a typical picking routine, Molecular Devices recommends the following solutions are put in the following wash baths:

• Wash Bath 1 (furthest from front) - 70% ethanol• Wash Bath 2 (middle wash bath) - sterile water• Wash Bath 3 (closest to the front) - 1% sodium hypochlorite (bleach)

For other routines, follow their relevant designated procedures.

Note: Bleach can cause corrosion if left in the instrument for too long. It should be removed from the instrument immediately after use. Bleach is typically required for difficult-to-sterilise organisms, such as yeast and Streptomyces.

Note: Be sure to validate the wash baths and cycles that are required for their application.

Note: Before starting any sanitise routine, remove loose items from the interior of the instrument.

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Conducting a Sanitise1. In the Navigation window, double-click Instrument Utilities, and then

double-click Sanitise.2. From the Sanitise window, select a Sanitise Profile from the list and

select a Wash Cycle tab.

3. Click Wash. The System will run the displayed wash cycle.4. Click Next to return to the Navigation window.

Conducting a UV Sanitise1. In the Navigation window, double-click Instrument Utilities, and then

double-click UV Sanitise.2. From the UV Sanitise window, either accept the default (600 seconds)

or change the duration of the sanitise in the Duration of Ultra Violet Exposure field.

3. Click Begin. The UV light switches on for the assigned time (unless you get an error message, which will state the problem). When the sanitise is complete the light goes out, and a Completed message appears above the Begin button.After the routine starts, stop the UV sanitise any time by clicking Stop.

Note: If you want a different wash cycle to what is available, you will need to cancel this routine and create a new sanitise profile. For more information, see Creating and Editing Sanitise Profiles on page 61.

Note: As a final step, remember to top up your wash baths with relevant cleaning fluids and wipe down the surfaces of the interior.

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Creating and Editing Sanitise ProfilesThe QPix 420 Colony Picking Software comes with one default sanitise profiles. If this is the first time performing any routine, Molecular Devices recommends you open Manage Sanitise Profiles to edit the supplied default profile to suit your specific needs. Sanitise profiles consists of two types of wash cycles - Multi Stage and Single Stage. Wash cycles can contain any number of wash bath steps, all of which have to be created in the Manage Sanitise Profiles window.

1. In the Navigation window, double-click the Manage Sanitise Profiles icon. The Manage Sanitise Profiles window appears.

2. In the Manage Sanitise Profiles window, click New. To edit a profile, skip to Editing a Sanitise Profile on page 62.To delete a profile, skip to Deleting a Sanitise Profile on page 63.

3. In the Add Profile dialog, type the profile name in the Name field and then select one of the following options for your wash profile:Single Stage means you plan to use the same wash cycle before and during a routine.Multi Stage means you want different wash cycles before and during a routine.

Note: You cannot edit sanitise profiles when running a routine, so while you are working in the Manage Sanitise Profiles window, it is worth creating a range of various profiles that you think you might need for future routines.

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4. Click Add. The sanitise profile now appears in the Profiles table along with all other sanitise profiles.Although you have created a sanitise profile, it needs at least one wash bath step to make it useful in a routine.

5. To add wash bath steps to a sanitise profile, in the Manage Sanitise Profile window, click Edit.

Editing a Sanitise Profile1. From the Profiles table, highlight a sanitise profile, then select one of

the following wash cycle options from the Stages list:First and Main Wash Cycle (displays only if you selected Single Stage in the Add New Profile dialog) creates one wash cycle to be used both before and during a routine.

First Wash Cycle creates the pre-routine wash cycle of a Multi Stage sanitise profile.Main Wash Cycle creates the wash cycle to be used during the routine of a Multi Stage sanitise profile.

2. Click Edit. This activates the Add and Remove buttons related to each wash bath step in the Steps table, and deactivates all other buttons.

3. From the Bath Name list, select a wash bath (1, 2 or 3), and then type relevant amounts into the following fields:Bath Cycles sets the number of times to wash pins in that wash bath. Dry Time (seconds) sets the number of seconds for the pins to be dried in the halogen dryer.Wait After Drying (seconds) sets the number of seconds you want to wait before continuing.

4. Click Add if you want to add another wash bath step to the wash cycle.5. Click Remove if you want to remove an existing wash bath step.6. Repeat the previous steps until you have created all wash bath steps

you want to associate with this wash cycle.7. Click Save. This sanitise profile is now available for all processes. 8. If you are creating a sanitise profile with Multi Stage cycles, select the

other wash cycle from the Stages list and repeat the previous steps.9. When you have finished adding wash bath steps to your wash cycles,

Click Next to return to the Navigation window.

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Deleting a Sanitise Profile1. In the Manage Sanitise Profiles window, select a profile, and then

click Delete. A confirmation dialog appears.

2. Click Yes. The profile is removed from the Profiles table.Now that you have edited at least one sanitise profile, you can perform the following routines:

• Conducting a Picking Routine on page 65• Conducting a Regional Picking Routine on page 85• Replication Processes on page 123• Running a Rearraying Routine on page 138

Note: Now you have edited at least one sanitise profile, as you prepare the instrument for a routine, remember to install correct cleaning fluids in the correct number of wash baths.

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Preparations for Running a RoutinePreparations for Running a Routine

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6
Conducting a Picking Routine
The QPix 420 Colony Picking Software allows you to pick colonies from receptacles using either the standard or regional process. Both processes have white light and fluorescent picking capabilities.

This chapter contains the following sections:• Preparing for a Picking Routine on page 65• Creating and Editing a Picking Routine on page 66• Running a Picking Routine on page 74

Preparing for a Picking RoutineYou need to perform some preliminary steps before successfully conducting a picking routine. For more information on these steps, see Preparations for Running a Routine on page 59.If this is your first picking routine on the QPix 420 System, you must edit the supplied sanitise profile to suit your needs. For more information on sanitise profiles, see Creating and Editing Sanitise Profiles on page 61.If you have made any adjustments to the instrument, such as changing the head, you will have to align the camera again. For more information on camera alignment, see Aligning the Camera on page 47.Before you begin any new picking routine, Molecular Devices® recommends you perform a sanitise, UV sanitise, and a manual clean of the interior of the instrument with ethanol. For more information on these tasks:

• See Conducting a Sanitise on page 60.• See Conducting a UV Sanitise on page 60.

Remove any loose items from the interior of the instrument and remember to top up your wash baths with relevant cleaning fluids.

Note: If you want fluorescent picking on your instrument, the QPix 420 Colony Picking System must be configured with a specific fluorescent imaging head. For more information, contact technical support at [email protected].

Note: If you have the fluorescence imaging module, a picking routine just using white light imaging will take longer because more images are taken.

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Creating and Editing a Picking RoutineNow that you have created and edited at least one sanitise profile, performed both sanitise routines, and given the instrument interior a manual clean, you are ready to create a picking routine. This consists of the following steps:

• Selecting Barcode Reading Options on page 67• Setting Filter Pairs (Fluorescent Light only) on page 69• Setting Destination Options on page 69• Selecting Head and Sanitise Options on page 71• Setting your Picking Source on page 72• Viewing the Settings Summary on page 73

1. In the Navigation window, double-click the Picking icon.2. In the Picking window, click Picking Type and select one of the

following: White Light indicates you want to use only white light to illuminate

and identify colonies to pick. White Light And Fluorescent (optional feature) indicates you

want white light to illuminate and identify colonies, and fluorescent light for determining the desired colonies to pick.

3. Click Apply, and then click Start.The System “homes” the drives, and then the Routines window opens. This allows you to create or edit existing routines.

4. In the Routines window select New Routine, and then click Next. To run an existing routine, select Run Existing Routine. This saves you time by allowing you to choose an existing routine from the Select Routine list and either editing it, or using it in its exact configuration (Select Skip Steps for this option). Select Skip Steps if you want to keep all existing parameters for

the routine and skip directly to the Settings Summary window. Delete routines from the Select Routine list by clicking Delete.

Note: Not all steps in this chapter will be available on your instrument. This will depend on which additional features you purchased. Optional features will be identified as appropriate.

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If you selected White Light earlier, the Barcodes window appears. If you selected White Light and Fluorescent The Filter Pair and Barcodes window appears.

Selecting Barcode Reading OptionsThe Barcodes window allows you to select barcode reading options.The Filter Pair and Barcodes window allows you to select filter pair and barcode reading options. For more information on filter pairs, see Setting Filter Pairs (Fluorescent Light only) on page 69.

1. If using the barcode reader, leave the Use Barcode Reader check box selected (default), and then select a Read Failure Action option.Use Barcode Reader means the barcode reader will automatically scan receptacles for barcodes (both source and destination).

2. Select one of the following options from the Read Failure Action section, in case a barcode cannot be read correctly: Manual prompt launches a dialog where you can manually type a

barcode or microplate name (both source and destination receptacles).

Skip Receptacle tells the instrument to cease looking for a barcode and look for a barcode on the next receptacle (both source and destination receptacles).

Note: Molecular Devices recommends you always use barcodes for accurate data tracking.

Note: If you choose to create validation or manual barcodes they will only be applied to your source microplates.

Note: If the instrument fails to identify a barcode for the source receptacle, the routine will end, as the source needs a valid barcode.

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3. Enter your full range of barcodes for this routine in the Validation Barcode table using the following options. This helps you to check barcodes on source receptacles as they are scanned by the barcode reader. You can list the barcodes in any order. The instrument scans the Validation Barcode list to confirm the source barcode is present. If it is missing, a message appears describing the erroneous receptacle. Insert means you need to type each bar code manually into the

Insert field, and then click Insert. Import means you can import barcodes from a text or .csv file. From Database means you can import barcodes from a database.

4. If you are not using barcodes, and you have cleared the Use Barcode Reader check box, select one of the following:Generate Random Barcodes generates a random and unique barcode for every receptacle used (both source and destination), with prefix Auto. This option prohibits manually typing barcodes.

Clicking the Generate List button, allows you to create your own receptacle identifiers. The Generate Barcode List window opens. Type relevant information into the following fields: Prefix creates a text label for your microplate identifiers. Start Number sets the starting identifier number. Digit Padding adds zeros before the identifier number. Number to Generate sets amount of identifiers for this routine.

To preview your manually generated barcodes, click Generate. A list of these barcodes displays in the Manual Barcodes table.

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5. After choosing your barcode reading option, click Next. The Destination Options window opens. For more information, see Setting Destination Options on page 69.

Setting Filter Pairs (Fluorescent Light only)If you have selected the fluorescent light option, the Filter Pair Selection feature is contained within the Barcodes window. In this case, the window is called Filter Pair And Barcodes.

1. Choose a suitable filter pair from the Filter Pair list.

2. After you have selected your filter pair for this routine, click Next. The Destination Options window appears.

Setting Destination OptionsThe Destination Options window allows you to configure your destination microplate settings.

Setting your Picking Source

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1. In the Destination Options window, choose a destination microplate from the Select Destination Microplate list. If you do not see a microplate that you use on this list, please contact Molecular Devices to see if we can add it to the list.

2. Choose from the following additional options: Multi Dip indicates you want the instrument to dip the pins into the

receptacle multiple times per dip. Number of Dips tells the instrument how many dips per deposit

you want it to make. Stir Destination stirs the pins in the destination receptacle wells.

If you choose this option, you cannot multi-dip.3. Click Make Copy if you want to create a copy of the destination

microplate. If you choose this option, you must also select the other destination microplate to copy using the Select Copy Microplate list.

4. Choose between By Columns or By Rows as the Deposit Order for the destination microplate.

5. Decide your Deposit Strategy between the following options: Fill All Microplates tells the instrument to fill every well of the

destination microplates. New Microplate For Each Position indicates one QTray or Petri

dish is considered one position. Clicking this means a new destination microplate will be used when picking begins in a new position.

New Microplate For Each Batch indicates two omni trays are considered as one batch. Clicking this means a new destination microplate will be used when a new batch of source microplates are loaded onto the System bed.

6. To edit the Destination Microplate Template, click Edit. This template allows you to clear various wells so that they are not picked, for example when control wells are desired. The Edit Destination Microplate Template dialog appears.

Cleared wells are displayed in light blue and selected wells are pink. 7. Click any well you want to leave empty, and right-click and drag your

mouse over multiple wells you want to remain empty. Click a well again to re-select it.

8. Click Exit, and then click Next. The Head/Sanitise window appears.

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Selecting Head and Sanitise OptionsThe Head/Sanitise window allows you to choose a head and select a sanitise profile. For more information on sanitise profiles, see Creating and Editing Sanitise Profiles on page 61.

1. In the Head/Sanitise window, choose from the following Picking Head Options: Picking Head allows you to choose various short or long heads. Pin Columns Before Inoculation allows you to set the number of

pins available to pick with before inoculation into the destination microplate. This helps inoculate colonies faster into the destination microplate (without having to wait until all pins have been used).

Wash between Partial Inoculation allows you to wash pins between shorter inoculations.

2. Use the Inoculation Heights (mm above well bottom) fields to set the depth (in millimeters) the pin travels to above the bottom of a well for both your Destination and Copy receptacles. The Copy field appears here if you chose Make Copy in the Destination Options window. Default values are displayed for each microplate type chosen earlier.

3. Select a sanitise profile from the Sanitise Profile list.

4. Click Next. The Source window appears.

Note: In the Destination Options window, if you selected By Rows earlier, you can select 1 to 7 rows, and if you selected By Columns, you can select 1 to 11 columns.

Note: If none of the sanitise profiles suit your routine, you will need to exit the routine at this point and create a sanitise profile. For more information, see Creating and Editing Sanitise Profiles on page 61.

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Setting your Picking SourceThe Source window allows you to configure your picking source microplate.

1. In the Source window, choose your source holder, receptacle type and positioning, and picking depth.

Holder selects the source plate holder layout. When using QTrays, this is the default.

Receptacle displays possible receptacles for the holder selected. Positions describes receptacle quantity and displays their

positions. For example two QTrays.

Picking Depth Into Agar (mm) sets the travel depth for the picking pin into the agar in the source tray.

Limit Max. Number Of Features Per Position limits the number of colonies (Features) per Position (QTray or Petri dish). If you select this, the Max. Number Of Features Per Position check box becomes editable.

2. Click Next. The Settings Summary window appears.

Note: When using Validation barcodes, if you are using only one source barcode, one source receptacle position will only display here. Also, the positions number is automatically greyed out. For more information, see Selecting Barcode Reading Options on page 67.

Note: Selecting this option makes it impossible to change this number in the Feature Selection section. The number per region will be set and cannot be changed. For more information on limiting features per position, see Selecting Colonies on page 78.

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Viewing the Settings SummaryThe Settings Summary window contains a full summary of the picking routine settings you just configured.

Print a copy of the settings by clicking Print, or click Next to continue. The Holder Layout Summary window appears.

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Running a Picking RoutineNow that you have configured your parameters, you are ready to prepare the instrument and run the routine. This consists of the following steps:

• Arranging the Layout of the Holders on page 74• Creating a White Light Test Image on page 75• Creating a Fluorescent Test Image (Fluorescent light only) on page 77• Selecting Colonies on page 78• Viewing a Summary of Selected Colonies on page 80• Viewing Additional Display Options on page 81• Continuing or Saving Your Routine on page 81• Loading the Plate Holders on page 82• Viewing the Picking Progress on page 82• Completing or Running Another Routine on page 83

Arranging the Layout of the HoldersThe Holder Layout Summary window shows you how to correctly arrange the microplate holders in the instrument for your picking routine. This is defined by the selections you made earlier in this routine.

1. Follow the holder layout instructions on the screen, and after you are certain you have loaded everything correctly, click Checked?If you do not select Checked? you cannot continue the process.

Note: The instrument door now locks. The only way to over-ride this is to click Cancel or press the Stop button on the front of the instrument.

Note: After clicking Next here, you can no longer click Back.

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2. Click Next. The Please load source window appears.

3. After you have loaded the source tray in its correct location, click Next. The instrument now takes a white light test image of the source tray.The Test Image window appears.

Creating a White Light Test ImageThe Test Image window contains the test image and an image adjustment pane. Use these settings to optimize white light settings for picking colonies.

As well as detecting desired colonies, you can also discard debris or detected objects that are not colonies from here.

1. Adjust Acquisition, Detection, and Remove Debris settings here. The Receptacle list displays the number of source receptacles to

view.2. In the Acquisition section, adjust the following. To apply these

settings, you must click Grab Image.

Note: When you are also conducting fluorescent imaging, this window is labelled WL Test Image in the left menu column to distinguish between the white light and fluorescent test images.

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Exposure (ms) allows you to control the amount of light exposed to the sample (10ms to 1000ms).

Gain allows you to increase the image signal without increasing the amount of light exposed to the sample.

3. In the Detection section, adjust the following:Use Auto Thresholding automatically detects colonies (check box is selected as a default). Deselect this check box to manually edit these settings and move the slider to the position where all the desired colonies are colored green.

4. In the Display section, view three different images to detect colonies. To change views, select one of the following from the Display list: Image And Overlay displays both green threshold color and

yellow rings for detected colonies. Image Only displays only the yellow rings. No threshold green is

displayed. Overlay Only displays only a black and white image of the

detected colonies with yellow detection rings.

Figure 6-1: Various Image Types based on Display List Selection

5. In the Remove Debris section, adjust the following. Use these settings to discard detected debris from the images. When excluding debris, any object that is excluded will not have the yellow line circling the detected object. Diameter (mm) discards detected objects smaller than the defined

measurement. Axis Ratio discards detected objects smaller than the defined

measurement (in a percentage).

Features Found displays the number of features (colonies) detected after excluding the debris. This dynamically updates with your changes.

6. Click Next. The System begins “Imaging and Image Processing.” After the imaging, the Feature Selection window appears.

Note: When discarding debris, be sure to discard only debris smaller than the desired colonies, otherwise this will affect the detection of colonies and what you can pick. Excluding larger colonies will be explained in the next step.

Note: If you selected White Light and Fluorescent at the start of this routine, clicking Next here starts the fluorescent imaging.

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Creating a Fluorescent Test Image (Fluorescent light only)The Fluorescent Test Image window contains the test image and an imaging adjustment pane.

Use these settings to optimize fluorescent light settings for picking colonies.1. Under the Acquisition section, adjust the following:

Exposure (ms) allows you to control the amount of light exposed to the sample (10ms to 1000ms).


2. Click Grab Image to save your settings.3. Click Next.

The System begins “Imaging and Image Processing.” After the image processing is completed, the Feature Selection window appears.

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Selecting ColoniesWhen the imaging is completed, the Feature Selection window appears, allowing you to pick colonies of a desired shape, size and proximity.

The source receptacle with its detected colonies displays in the center and the barcode for that receptacle is displayed to the right.Pickable colonies display in yellow, while unpickable colonies (those that are too close to the edge of the receptacle or do not match your selection criteria) are displayed in red. Any colony not circled has been excluded from the selection either at the test image stage, or because it was discarded using the remove debris settings.

If you are performing both fluorescent and white light imaging, the Feature Selection window contains the following tabs:

• White Light displays everything captured using white light.• Fluorescent Filter Pair Name (Fluorescent light only) displays

everything captured with the filter pair chosen earlier. Toggle between the tabs to select colonies.

1. In the Feature Selection window, use the slider bars beneath the imaged source receptacle to zoom in for a closer look at the colonies or adjust the image contrast as required.

2. In the Selection section, adjust the following parameters to control and optimize the size and shape of desired colonies as well as exclude those colonies that are too close together:

Note: If your routine consists of both fluorescent and white light imaging, the Feature Selection window will contain two tabs. Toggle between the two to select colonies.

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Compactness sets the level of irregularity for picking colonies. The value is a ratio of the perimeter divided by the area of the colony, so irregular shaped colonies will be closer to 0 and regular shaped colonies will be closer to 1. The System default value is that any colony equal to or less than 0.65 and will not be picked.

Axis Ratio measures how oval the colony is. The value is a ratio of the longest diameter divided by the shortest diameter, so oval shaped colonies will be closer to 0 and round colonies will be closer to 1. The System default value is that any colony equal to or less than 0.65 will not be picked.

Min Diameter (mm) sets the minimum diameter of colonies for picking. Any colony equal to or smaller than the value stated in the adjacent field will not be picked.

Max Diameter (mm) sets the maximum diameter of colonies for picking. Any colony equal to or greater than the value stated in the adjacent field will not be picked.

Min Proximity (mm) sets the distance between colonies to be picked, so that when picking one colony another adjacent colony will not be picked. The System default value is 0.45mm.

3. If required, manually select your desired colonies by right clicking on them, and either picking or discarding them, as shown in the following image:

4. View details of any displayed colony by holding your cursor over that colony. Properties of that colony display in a popup. If a colony has not been selected, the reason for this will be highlighted in red.

5. (Fluorescent imaging only) Adjust the histogram to obtain the optimal selection of colonies. The Histogram displays the level of colony intensity within a selected image. The peaks show the distribution of the intensity of the colonies.

6. Set intensity measurements with the following settings:

Note: Min Diameter (mm) cannot be lower than the diameter value set in the Debris Discard section of Test Image.

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Mean Intensity is the average fluorescence of the detected colony (the fluorescence of all the pixels within the colony perimeter divided by the number of pixels within the colony perimeter).

Median Intensity is the middle fluorescence value of all the pixels within the detected colony perimeter.

Geometric Intensity is the geometric intensity of the detect colony (the fluorescence of all the pixels with the colony perimeter).

Centre Mean Intensity is the average fluorescence value of the middle 9 pixels within the detected colony perimeter.

7. Adjust your colony totals with the following settings:

Total Feature Count is the total features available to pick based on your criteria. This number resets as you adjust these criteria.

Limit Colonies limits the total number of pickable colonies. If Limit Max. Number of Feature Per Region was selected in the Setting your Picking Source section, this option will be grayed out and the total number of colonies for picking will display. You cannot change this number.

8. Click the Export Image button to save the image in any of the following formats: .bmp, .jpg, or .png file.

Viewing a Summary of Selected ColoniesThe Feature Counts tab shows the number of colonies detected on a source receptacle. The barcode (identifier) for the source receptacle is displayed, along with the number of found colonies, as well as the number of colonies to pick as determined by the selection criteria.

1. Click the Feature Counts tab to view a summary of pick information.

2. Export colony data to a .csv file by right-clicking in the table and selecting Export.

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Viewing Additional Display OptionsThe Display Options tab allows you to view additional information about the source receptacle image.

1. Click the Display Options tab to adjust the display options of the colony selection.

Display Detected Features displays all detected colonies with a yellow circle when the check box is selected. When not selected, detected features are not displayed (selected by default). Shade Features gives the detected colonies some shading for

clearer visualization. (cleared by default). Display Proximity Indicators displays connecting red lines

between one detected colony to its closest neighbor.Shade Exclusion Zone creates an exclusion zone (red shading on the image) where the System is not able to pick. When not selected, the red hatching is removed from the image (selected by default).After you have made all your feature selections and adjustments, you are almost ready to begin your picking routine.

2. Click Next. The Continue Or Save New Routine dialog appears.

Continuing or Saving Your Routine1. In the Continue or Save New Routine dialog, choose one of the

following: Routine Without Saving means you do not want to save the

settings for this routine for future use. Save Routine means you want to save the settings for this routine.

2. To continue the routine without saving, click OK.To save this routine, select Save Routine, type a name in the Name field, and then click Save.

The Load Plates window appears.

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Loading the Plate HoldersThe Load Plates window displays how many and what type of microplates you need to load for your picking routine.

1. Based on the layout of the plate holders shown in the Arranging the Layout of the Holders section, load the plate holders with the correct destination microplates (numbers 1 through 12).

2. In the Load Plates window, after you are satisfied you have loaded the plate holders correctly and complied with all items in the onscreen checklist, click Checked?

3. Click Next. The Please load 4. The picking routine begins, and the Picking Progress window

appears.

Viewing the Picking ProgressThe Picking Progress window displays a summary of this picking routine, including a timeline to tell you how long to completion.

The Picking Progress window displays the following information:

• Start Time shows the time the picking of the colonies began.• Source Barcode shows the barcode of the source receptacle being

picked from.• Pin is the picking pin being used.

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• Copy Plate No is the barcode of the copy receptacle that is being picked into (if selected in the setup).

• Destination Barcode is the barcode of the destination receptacle that is currently being picked into.

• Destination Offset is the well into which the pins will be lowered. This will change if using a 384 well microplate.

• Colonies Picked is the number of colonies picked so far.• Colonies To Pick is the total number of colonies to be picked.• Estimated Time Remaining indicates remaining time.• Current Action displays the current action of the System, for example

Pick, when the System is picking.• Pause allows you to safely pause the routine.

Completing or Running Another RoutineWhen all source micropates have been loaded, the routine is complete. At this point, the Finished Picking Current Batch dialog appears.

1. In the Finished Picking Current Batch dialog, select one of the following options: Finish Picking ends this picking routine. Continue With Image Review allows you to review and edit the

colony selection settings again before running the same routine with another source tray.

Continue Without Image Review allows you to run the same routine again with a difference source tray, but without reviewing and editing colony selection settings.

2. Click OK. If you selected Finish Picking, the Picking Summary window

appears. Export the picking data for this routine by clicking Export. If you selected Continue With Image Review, the Test Image

window appears. See Creating a White Light Test Image on page 75 and Creating a Fluorescent Test Image (Fluorescent light only) on page 77 for a reminder of the necessary steps.

If you selected Continue Without Image Review, the Please load source dialog appears. See Running a Picking Routine on page 74 for a reminder of the necessary steps.

After all picking routines are completed, the Picking Summary dialog appears, showing the number of source colonies picked, along with the number of destination microplates used, and any missing source receptacles. You can export this information into a table by clicking Export.

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3. Click Next. The Process Completed window appears.4. Click Finish to return to the Navigation window.

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7
Conducting a Regional Picking Routine
The QPix 420 Colony Picking Software allows you to pick colonies from receptacles using either the standard or regional process. Both processes have white light and fluorescent picking capabilities. There are some additional viewing and selection options with a regional picking routine compared to standard picking. For more information on regional feature selection, see Viewing Additional Display Options on page 102

This chapter contains the following sections:• Preparing for a Regional Picking Routine on page 85• Creating and Editing a Regional Picking Routine on page 86• Running a Regional Picking Routine on page 95

Preparing for a Regional Picking RoutineYou need to perform some preliminary steps before successfully conducting a picking routine. For more information on these steps, see Preparations for Running a Routine on page 59.If this is your first picking routine on the QPix 420 System, you must edit the supplied sanitise profile to suit your needs. For more information on sanitise profiles, see Creating and Editing Sanitise Profiles on page 61.If you have made any adjustments to the instrument, such as changing the head, you will have to align the camera again. For more information on camera alignment, see Aligning the Camera on page 47.Before you begin any new picking routine, Molecular Devices® recommends you perform a sanitise, UV sanitise, and a manual clean of the interior of the instrument with ethanol. For more information on these tasks:


Remove any loose items from the interior of the instrument and remember to top up your wash baths with relevant cleaning fluids.

Note: If you want fluorescent picking on your instrument, the QPix 420 Colony Picking System must be configured with a specific fluorescent imaging head. For more information, contact technical support at [email protected].

Note: If you have the fluorescence imaging module, a picking routine just using white light imaging will take longer because more images are taken.

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Creating and Editing a Regional Picking RoutineNow that you have created and edited at least one sanitise profile, performed both sanitise routines, and given the instrument interior a manual clean, you are ready to create a regional picking routine. This consists of the following steps:

• Selecting Barcode Reading Options on page 87• Setting Filter Pairs (Fluorescent Light only) on page 89• Configuring Destination Microplates on page 89• Setting your Regional Picking Source on page 90• Defining Destination/Source Options on page 91• Selecting Head and Sanitise Options on page 92• Viewing the Settings Summary on page 94

1. In the Navigation window, double-click the Picking icon.2. In the Picking window, click Picking Type and select one of the

following: White Light indicates you want to use only white light to illuminate

and identify colonies to pick. White Light And Fluorescent (optional feature) indicates you

want white light to illuminate and identify colonies, and fluorescent light for determining the desired colonies to pick.

3. Click Apply, and then click Start.The System “homes” the drives, and then the Routines window opens. This allows you to create or edit existing routines.

4. In the Routines window select New Routine, and then click Next. To run an existing routine, select Run Existing Routine. This saves you time by allowing you to choose an existing routine from the Select Routine list and either editing it, or using it in its exact configuration (Select Skip Steps for this option).


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Select Skip Steps if you want to keep all existing parameters for the routine and skip directly to the Settings Summary window.

Delete routines from the Select Routine list by clicking Delete.If you selected White Light earlier, the Barcodes window appears. If you selected White Light and Fluorescent The Filter Pair and Barcodes window appears.

Selecting Barcode Reading OptionsThe Barcodes window allows you to select barcode reading options.The Filter Pair and Barcodes window allows you to select filter pair and barcode reading options. For more information on filter pairs, see Setting Filter Pairs (Fluorescent Light only) on page 89.

1. If you are using the barcode reader, leave the Use Barcode Reader check box selected (this is the default), and then select a Read Failure Action option.Use Barcode Reader means the barcode reader will automatically search receptacles for barcodes (both source and destination).

2. Select one of the following options from the Read Failure Action section, in case a barcode cannot being read correctly: Manual prompt launches a dialog where you can manually type a



Note: If you choose to create validation or manual barcodes they will only be applied to your source microplates.

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Skip Receptacle tells the System to cease looking for a barcode and look for a barcode on the next receptacle (both source and destination receptacles).

3. Enter your full range of barcodes for this routine in the Validation Barcode table using the following options. This helps you to check barcodes on source receptacles as they are scanned by the barcode reader. You can list the barcodes in any order. The instrument scans the Validation Barcode list to confirm the source barcode is present. If it is missing, a message appears describing the erroneous receptacle. Insert means you need to type each bar code manually into the

Insert field, and then click Insert. Import means you can import barcodes from a text or .csv file. From Database means you can import barcodes from a database.





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5. After choosing your barcode reading option, click Next. The Destination Options window opens. For more information, see Defining Destination/Source Options on page 91.

Setting Filter Pairs (Fluorescent Light only)If you have selected the fluorescent light option, the Filter Pairs feature is contained within the Barcodes window. In this case, the window is called Filter Pairs and Barcodes.The Filter Pairs section allows you to choose a filter pair.

1. In the Filter Pair Selection section, choose a filter pair from the Filter Pair list.

2. After you have selected your filter pairs for this routine, click Next. The Destination Plates window appears.

Configuring Destination MicroplatesThe Destination Plates window allows you to configure your destination microplate.

Note: For additional destination options, see Defining Destination/Source Options on page 91.

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1. In the Destination Plates window, choose a destination microplate from the Select Destination Microplate list. If you would like to add a microplate to this list, please contact Molecular Devices to see if we can add it.


receptacle multiple times per dip. Number of Dips tells the instrument how many dips per deposit


If you choose this option, you cannot multi-dip.3. Click Make Copy if you want to create a copy of the destination

microplate. If you choose this option, you must also select the other destination microplate to copy using the Select Copy Microplate list.


Setting your Regional Picking SourceThe Source window allows you to configure your source microplate.

1. In the Regional Source window, configure the picking depth.

Holder displays the default QTray option only, because this is the only microplate that is designed for regional picking.

Receptacle is greyed out because as you are doing regional picking, you have no choice but to use the 48-region QTray.

Picking Depth Into Agar (mm) sets the travel depth for the picking pin into the agar in the source tray.

2. Click Next. The Destination/Source Options window appears.

Note: Because you are regional picking, you can only select a QTray.

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Defining Destination/Source OptionsThe Destination/Source Options window is specific to regional picking, and appears only when you are creating a regional picking routine. Use it to control your regional picking source and destination options.

1. In the Destination/Source Options window, set your Source Region Options to limit the number of features (colonies) to be selected from each region. Limit Max. Number Of Features Per Position limits the number

of colonies (Features) per Position (QTray or Petri dish). If you select this, the Max. Number Of Features Per Position check box becomes editable.

If you select this box, you also need to type a number in the following field:

Number of Features Per Region allows you to set the limit of colonies to be selected per region.

Reserve Wells For Regions allows you to request wells to be left empty if the number of colonies per region is not reached. For example, if you had selected 8 colonies per region, but only 6 colonies were eligible for picking, wells 7 and 8 would be left blank.

2. Choose between By Columns or By Rows as the Deposit Order for the destination microplate.

3. Decide your Deposit Strategy between the following options: Fill All Microplates tells the instrument to fill every well of the

destination microplates. New Microplate For Each Position indicates one QTray or Petri

dish is considered one position. Clicking this means a new destination microplate will be used when picking begins in a new position.

Note: Selecting this option makes it impossible to change this number in the Feature Selection section. The number per region will be set and cannot be changed. For more information on limiting features per position, see Selecting Colonies on page 98.

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4. To edit the Destination Microplate Template, click Edit. This template allows you to clear various wells so that they are not picked, for example when control wells are desired. The Edit Destination Microplate Template dialog appears. Cleared wells are displayed in light blue and selected wells are pink.

5. Click any well you want to leave empty, and right-click and drag your mouse over multiple wells you want to remain empty. Click a well again to re-select it.


Selecting Head and Sanitise OptionsThe Head/Sanitise window allows you to choose a head and select a sanitise profile. For more information on sanitise profiles, see Creating and Editing Sanitise Profiles on page 61.

1. In the Head/Sanitise window, choose from the following Picking Head Options: Picking Head allows you to choose various heads. Pin Columns Before Inoculation allows you to set the number of

pins available to pick with before inoculation into the destination microplate. This helps inoculate colonies faster into the destination microplate (without having to wait until all pins have been used).

Wash between Partial Inoculation allows you to wash pins between shorter inoculations.

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2. Use the Inoculation Heights (mm above well bottom) fields to set the depth (in millimeters) the pin travels to above the bottom of a well for both your Destination and Copy receptacles. The Copy field appears here if you chose Make Copy in the Destination Plates window. Default values are displayed for each microplate type chosen earlier.



Note: If you selected By Rows earlier in the Destination Options window, you can select 1 to 11 rows, and if you selected By Columns, you can select 1 to 7 columns.


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Viewing the Settings SummaryThe Settings Summary window contains a full summary of the regional picking routine settings you just configured.

Print a copy of your settings by clicking Print, or click Next. The Holder Layout Summary window appears.

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Running a Regional Picking RoutineNow that you have configured your parameters, you are ready to prepare the instrument and run the routine. This consists of the following steps:

• Arranging the Layout of the Holders on page 95• Creating a White Light Test Image on page 96• Selecting Colonies on page 98• Viewing a Summary of Selected Regional Colonies on page 101• Viewing Additional Display Options on page 102• Continuing or Saving Your Routine on page 103• Loading the Plates on page 103• Viewing Regional Picking Progress on page 104• Completing or Running Another Routine on page 105


1. Follow the holder layout instructions on the screen, and after you are certain you have loaded everything correctly, click Checked?

Note: If you do not select Checked? you cannot continue the process.


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2. Click Next. A dialog appears asking you to Please load source.

C

3. After you have loaded the source tray in its correct location, click Next. The instrument now takes a white light test image of the source tray.The Test Image window appears.

Creating a White Light Test ImageThe Test Image window contains the test image and an imaging adjustment pane. Use these settings to optimize white light settings for picking colonies.


Note: When you are also conducting fluorescent imaging, this window is labelled WL Test Image in the left menu column to distinguish between the white light and fluorescent test images.

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settings, you must click Grab Image. Exposure (ms) allows you to control the amount of light exposed

to the sample (10ms to 1000ms). Gain allows you to increase the image signal without increasing the

amount of light exposed to the sample. 3. In the Detection section, adjust the following:

Use Auto Thresholding automatically detects colonies (check box is selected as a default).

Use Auto Thresholding adjusts image threshold and colony detection. Select this check box to manually edit these settings and move the slider to the position where all the desired colonies are colored green.






5. In the Remove Debris section, adjust the following. Use these settings to discard detected debris from the images. When excluding debris, anything excluded will not have a yellow line around it. Diameter (mm) discards detected objects smaller than the defined


measurement (in a percentage).

Features Found displays the number of features (colonies) detected after excluding the debris. This dynamically updates.

6. Click Next. The System begins “Imaging and Image Processing.” After this processing is completed, the Feature Selection window appears.


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Creating a Fluorescent Test Image (Fluorescent light only)The Fluorescent Test Image window contains the test image and an imaging adjustment pane. Use these settings to optimize fluorescent light settings for picking colonies.

1. Under the Acquisition section, adjust the following: Exposure (ms) allows you to control the amount of light exposed

to the sample (10ms to 1000ms). Gain allows you to increase the image signal without increasing the

amount of light exposed to the sample. 2. Click Grab Image to save your settings.3. Click Next.

The System begins “Imaging and Image Processing.” After the image processing is completed, the Feature Selection window appears.

Selecting ColoniesWhen the imaging is completed, the Feature Selection window appears, allowing you to pick colonies of a desired shape, size and proximity. The primary difference between a standard picking routine and a regional picking routine is the selection grid overlaid on the imaged colonies with each region displaying the total number of eligible colonies for picking. This number is dynamic and will change depending on the selection criteria you set for your routine.

The source receptacle with its grid of detected colonies displays in the center and the barcode for that receptacle is displayed to the right.

Note: If you selected White Light and Fluorescent at the start of this routine, clicking Next here starts the fluorescent imaging.

Note: If your routine consists of both fluorescent and white light imaging, the Feature Selection window will contain two tabs. Toggle between the two to select colonies.

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Pickable colonies display in yellow with the total for that region showing as a number in green. Unpickable colonies (those that are too close to the edge of the receptacle or do not match your selection criteria) is displayed in red. Any colony not circled has been excluded from the selection either at the test image stage, or because it was discarded using the remove debris settings.

If you are performing both fluorescent and white light imaging, the Feature Selection window contains the following tabs:

• White Light displays everything captured using white light.• Fluorescent Filter Pair Name (Fluorescent light only) displays

everything captured with the filter pair chosen earlier. Toggle between the tabs to select colonies.


2. In the Selection section, adjust the following parameters to control and optimize the size and shape of desired colonies as well as exclude those colonies that are too close together: Compactness sets the level of irregularity for picking colonies. The

value is a ratio of the perimeter divided by the area of the colony, so irregular shaped colonies will be closer to 0 and regular shaped colonies will be closer to 1. The System default value is that any colony equal to or less than 0.65 and will not be picked.



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5. (Fluorescent imaging only) Adjust the histogram to obtain the optimal selection of colonies. The Histogram displays the level of colony intensity within a selected image. The peaks show the distribution of the intensity of the colonies.

6. Set intensity measurements with the following settings:

Mean Intensity is the average fluorescence of the detected colony (the fluorescence of all the pixels within the colony perimeter divided by the number of pixels within the colony perimeter).

Median Intensity is the middle fluorescence value of all the pixels within the detected colony perimeter.


Note: Even though the histogram and setting controls are visible on the White Light tab, they will have no impact on the image. You can make histogram adjustments only on the Fluorescent tab.

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Geometric Intensity is the geometric intensity of the detect colony (the fluorescence of all the pixels with the colony perimeter).

Centre Mean Intensity is the average fluorescence value of the middle 9 pixels within the detected colony perimeter.

7. Adjust your colony totals with the following settings.


Limit Colonies limits the total number of pickable colonies. If Limit Max. Number of Feature Per Region was selected in the Defining Destination/Source Options section, this option will be grayed out and the total number of colonies for picking will display. You cannot change this number.


Viewing a Summary of Selected Regional ColoniesThe Feature Counts tab shows the number of colonies detected on a source receptacle. The barcode (identifier) for the source receptacle is displayed, along with the number of found colonies, the location of the well (region), as well as the number of colonies to pick as determined by the selection criteria.

1. Click the Feature Counts tab to view a summary of pick information. Because you are running a regional pick, the Feature Counts tab displays information different to a standard picking routine. This tab displays the following regional picking information:Well (Regional Picking only) identifies the source tray region based on its X-Y grid location.Found states the number of colonies found in that region.Pickable states number of pickable colonies in that region, based on your selection criteria.Picking states number of colonies in that region that will be picked, based on your selection criteria.


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Viewing Additional Display OptionsThe Display Options tab allows you to view additional regional picking information about the source receptacle image.


Display Detected Features displays all detected colonies with a yellow circle when the check box is selected. When not selected, detected features are not displayed (selected by default).

Shade Features gives the detected colonies some shading for clearer visualization. (cleared by default).

Display Numbers Per Region (Regional Picking only) displays the number of features for each region on the receptacle image. If you have not placed a limit on the number of features (colonies) detected per region, all the numbers will display in green. If you

Note: Because you are conducting a regional pick, there are additional picking options under the Display Options tab.

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have created a limit on detectable colonies, the number will display in green if the criteria are acceptable and red if they are not.

Display Proximity Indicators displays connecting red lines between one detected colony to its closest neighbor.

Shade Exclusion Zone creates an exclusion zone (red shading on the image) where the System is not able to pick. When not selected, the red hatching is removed from the image (selected by default).After you have made all your feature selections and adjustments, you are almost ready to begin your picking routine.

2. Click Next. The Continue or Save New Routine dialog appears.

Continuing or Saving Your Routine1. In the Continue or Save New Routine dialog, choose either:

Routine Without Saving means you do not want to save the settings for this routine for future use.

Save Routine means you want to save the settings for this routine.2. To continue the routine without saving, click OK.

To save this routine, select Save Routine, type a name in the Name field, and then click Save.


Loading the PlatesThe Load Plates window displays how many and what type of microplates you need to load for your picking routine.


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3. Click Next. The picking routine begins, and the Picking Progress window appears.

Viewing Regional Picking ProgressThe Regional Picking Progress window displays a summary of this regional picking routine, including a timeline to tell you how long to completion.

During the picking routine, the Regional Picking Progress window displays the following information:

• StartTime shows the time the picking of the colonies began.• Source Barcode shows the barcode of the source receptacle being

picked from.• Source Region shows the specific region of the source receptacle

being picked from.• Pin is the picking pin being used.• Copy Plate No is the barcode of the copy receptacle that is being

picked into (if selected in the setup).• Destination Barcode is the barcode of the destination receptacle that

is currently being picked into.• Destination Offset is the well into which the pins will be lowered. This

will change if using a 384 well microplate.• Colonies Picked is the number of colonies picked so far.• Colonies To Pick is the total number of colonies to be picked.• Calculate Remaining Time...indicates how far along the routine is.• Current Action displays the current action of the System, for example

Pick, when the System is picking.• Pause allows you to safely pause the routine.

Note: Remember you can pause the routine by clicking Pause.

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Completing or Running Another RoutineWhen all source micropates have been loaded, the routine is complete. At this point, the Finished Picking Current Batch dialog appears.

1. In the Finished Picking Current Batch dialog, select one of the following options: Finish Picking ends this picking routine. Continue With Image Review allows you to review and edit the

colony selection settings again before running the same routine with another source tray.

Continue Without Image Review allows you to run the same routine again with a difference source tray, but without reviewing and editing colony selection settings.

2. Click OK. If you selected Finish Picking, the Regional Picking Summary

window appears. You can export the information for this routine by clicking Export.

If you selected Continue With Image Review, the Test Image window appears. See Creating a White Light Test Image on page 96 and Creating a Fluorescent Test Image (Fluorescent light only) on page 98 for a reminder of the necessary steps.

If you selected Continue Without Image Review, the Please load source dialog appears. See Running a Regional Picking Routine on page 95 for a reminder of the necessary steps.

After all picking routines are completed, the Regional Picking Summary dialog appears, showing the number of source colonies picked, along with the number of destination microplates used, and any missing source receptacles. You can export this information into a table by clicking Export.

3. Click Next. The Process Completed window appears.4. Click Finish to return to the Navigation window.

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8
Control Plate Creation Processes
The QPix 420 Colony Picking System allows you to create a batch of well microplates that contain one or more positive control samples, before being picked into during a standard picking routine. This process is called Control Plate Creation.

This chapter contains the following sections:• Preparing for a Control Plate Creation Routine on page 107• Creating and Editing a Control Plate Creation Routine on page 108• Running a Control Plate Creation Routine on page 113

Preparing for a Control Plate Creation RoutineYou need to conduct some preliminary steps before successfully conducting a control plate creation routine. For more information on these steps, see Preparations for Running a Routine on page 59.Remove any loose items from the interior of the instrument and remember to top up your wash baths with relevant cleaning fluids.If this is your first control plate creation routine on the QPix 420 System, you must edit the supplied sanitise profile to suit your needs. For more information on sanitise profiles, see Creating and Editing Sanitise Profiles on page 61.If you have made any adjustments to the instrument, such as changing the head, you will have to align the camera again. For more information on camera alignment, see Aligning the Camera on page 47.Before you begin any new routine, Molecular Devices® recommends you perform a manual clean of the instrument interior (using 70% ethanol), and then conduct a sanitise and UV sanitise. For more information on these tasks:



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Creating and Editing a Control Plate Creation RoutineNow that you have created and edited at least one sanitise profile, conducted both sanitise routines, and given the instrument interior a manual clean, you are ready to create a control plate creation routine. This consists of the following steps:

• Selecting Barcode Reading Options on page 109• Setting Destination Options on page 109• Selecting Head and Sanitise Options on page 110• Setting your Source Receptacle on page 111• Designating the Control Plate Layout on page 111• Viewing the Settings Summary on page 112

1. In the Navigation window, double-click the Control Plate Creation icon.

2. In the Control Plate Creation window, click Start. The System “homes” the drives, and then the Routines window opens. This allows you to create or edit existing routines.

3. In the Routines window select New Routine, and then click Next. You can also choose the following editing options for routines from here: Run Existing Routine saves you time by allowing you to choose

an existing routine from the Select Routine list and either editing it or using it in its exact configuration (Select Skip Steps for this option).

Select Skip Steps if you want to keep all existing parameters for the chosen routine and skip directly to the Settings Summary window.

The Barcodes window appears.


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Selecting Barcode Reading OptionsThe Barcodes window allows you to select barcode reading options.

1. From the Barcodes window, choose one of the following: Use Barcode Reader means the barcode reader will automatically

scan receptacles for barcodes (both source and destination). Generate Random Barcodes means the instrument generates a

random and unique barcode for every receptacle used (both source and destination), with prefix Auto. This option prohibits manually typing barcodes.

2. After choosing your barcode reading option, click Next. The Destination Options window opens.

Setting Destination OptionsThe Destination Options window allows you to configure your destination microplate settings.

1. In the Destination Options window, choose a destination microplate from the Select Destination Microplate list. If you do not see a microplate that you use on this list, please contact Molecular Devices to see if we can add it to the list.


receptacle multiple times per dip.


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Number of Dips tells the instrument how many dips per deposit you want it to make.

Stir Destination stirs the pins in the destination receptacle wells. If you choose this option, you cannot multi-dip.

Number of Control Microplates allows you to make duplicates of the destination microplate (up to 70).

3. To edit the Destination Microplate Template, click Edit. This template allows you to clear various wells so that they are not picked into, for example when control wells are desired. The Edit Destination Microplate Template dialog appears.

Cleared wells are displayed in light blue and selected wells are pink. 4. Click any well you want to leave empty, and right-click and drag your

mouse over multiple wells you want to remain empty. Click a well again to re-select it.


Selecting Head and Sanitise OptionsThe Head/Sanitise window allows you to choose a head and select a sanitise profile. For more information on creating sanitise profiles, see Creating and Editing Sanitise Profiles on page 61.

1. In the Head/Sanitise window, choose a head from the Picking Head list.

2. Use the Destination field to set the depth (in millimeters) the pin travels into the bottom of a well of a destination receptacle.


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Setting your Source ReceptacleThe Source window allows you to configure your source receptacle type as well as set the picking depth into the agar.

1. In the Source window, choose from the following options related to the source receptacles for this routine:

Holder selects the source receptacle type. Receptacle (greyed out) displays source receptacle dimensions. Picking Depth Into Agar (mm) sets the travel depth for the

picking pin into the agar in the receptacle.2. Click Next. The Control Plate window appears.

Designating the Control Plate LayoutThe Control Plate window allows you to designate where the control samples are placed on the destination receptacle.

1. From the Control Plate window, click the location of the desired wells in the destination receptacle map (on the right).

Note: You cannot edit a sanitise profile from this window. If none of the sanitise profiles suit your routine, you will need to exit the routine at this point and create a sanitise profile. For more information, see Creating and Editing Sanitise Profiles on page 61.

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For a multiple well selection, you can also left-click drag the cursor over multiple wells in the destination map.

2. When you are satisfied with the layout of the control samples in the destination receptacle map, click Next. The Settings Summary window appears.

Viewing the Settings SummaryThe Settings Summary window contains a full summary of the routine settings you just configured.

Print a copy of the settings by clicking Print, or click Next to continue.

The Holder Layout Summary window appears.

Note: Once you click Next here, you can no longer click the Back button to return to a previous window.

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Running a Control Plate Creation RoutineNow that you have configured your parameters, you are ready to prepare the instrument and run the routine. This consists of the following steps:

• Arranging the Layout of the Holders on page 113• Loading Source Receptacles on page 114• Creating a Test Image on page 114• Selecting Colonies on page 116• Viewing a Summary of Selected Colonies on page 118• Viewing Additional Display Options on page 118• Continuing or Saving Your Routine on page 119• Viewing the Picking Progress on page 120• Viewing the Summary of Your Routine on page 120



2. Click Next. The Please load source window appears.



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Loading Source ReceptaclesThe Please Load Source window is a visual aid for installing the source microplates correctly in the instrument.

1. Load the source receptacles in their correct location.2. Click Next. The instrument now takes a white light test image of the

source receptacle.The Test Image window appears.

Creating a Test ImageThe Test Image window contains the test image and an image adjustment pane. Use these settings to optimize your selection settings.




settings, you must click Grab Image. Exposure (ms) allows you to control the amount of light exposed

to the sample (10ms to 1000ms).

Note: All detected objects are viewed as features, so to ensure you are detecting colonies not debris, use Remove Debris in this part of the routine.

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3. In the Detection section, adjust the following:Use Auto Thresholding automatically detects colonies (check box is selected as a default). Deselect this check box to manually edit these settings and move the slider to the position where all the desired colonies are colored green.






5. In the Remove Debris section, adjust the following. Use these settings to discard detected debris from the images. When excluding debris, any object that is excluded will not have the yellow line circling the detected object. Diameter (mm) discards detected objects smaller than the defined


measurement (in a ratio of roundness).

Features Found displays the number of features (colonies) detected after excluding the debris. This dynamically updates with your changes.

6. Click Next. The System begins “Imaging and Image Processing.” After the imaging, the Feature Selection window appears.


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Selecting ColoniesWhen the imaging is completed, the Feature Selection window appears, allowing you to pick colonies of a desired shape, size and proximity, and fluorescent intensity.An image of the source receptacle with its detected colonies is displayed in the center and the barcode for that receptacle is displayed to the right.Pickable colonies are displayed in yellow, while unpickable colonies (those that are too close to the edge of the receptacle or do not match your selection criteria) are displayed in red. Any colonies with no circle were excluded in the test image stage because they fell within the remove debris settings.


2. In the Selection section, adjust the following parameters to control and optimize the size and shape of desired colonies as well as exclude those colonies that are too close together: Compactness sets the level of irregularity for picking colonies. The

value is a ratio of the perimeter divided by the area of the colony, so irregular shaped colonies will be closer to 0 and colonies that are more of a perfect circle are closer to 1. The System default value is that any colony equal to or less than 0.65 and will not be picked.



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5. Adjust your colony totals with the following settings:


Limit Colonies (not applicable for Control Plate Creation, and as such this remains greyed out).



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Viewing a Summary of Selected ColoniesThe Feature Counts tab shows the number of found features on a source receptacle. The barcode (identifier) for the source receptacle is displayed, along with the number of found colonies, as well as the number of colonies to pick as determined by the selection criteria.

1. Click the Feature Counts tab to view a summary of pick information.


Viewing Additional Display OptionsThe Display Options tab allows you to view additional information about the source receptacle image.


Display Detected Features displays all detected features with a yellow circle when the check box is selected (default). When not selected, detected features are not displayed. Shade Features gives the detected colonies some shading for

clearer visualization (unselected by default). Display Proximity Indicators displays connecting red lines

between one detected colony to its closest neighbor.Shade Exclusion Zone creates an exclusion zone (red shading on the image) where the System decides it is not safe to pick (default). When not selected, the shading is removed from the image.After you have made all your feature selections and adjustments, you are almost ready to begin your picking routine.

2. Click Next. The Continue Or Save New Routine dialog appears.

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Loading the Plate HoldersThe Load Plates window displays how many and what type of microplates you need to load for your picking routine.



3. Click Next. The picking routine begins, and the Picking Progress window appears.

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Viewing the Picking ProgressThe Picking Progress window displays a summary of this routine, including a timeline to tell you how long to completion.


• Start Time shows the time the picking of the colonies began.• Source Barcode shows the barcode of the source receptacle being

picked from.• Pin is the picking pin being used.• Copy Plate No is the barcode of the copy receptacle that is being

picked into (if selected in the setup).• Destination Barcode is the barcode of the destination receptacle that


will change if using a 384 well microplate.• Colonies Picked is the number of colonies picked so far.• Colonies To Pick is the total number of colonies to be picked.• Estimated Time Remaining indicates remaining time.• Current Action displays the current action of the System, for example

Pick, when the instrument is picking.• Light Table Off allows you to switch off the light table light in the

instrument.• Pause allows you to safely pause the routine.

When your routine is finished, the Picking Summary window appears.

Viewing the Summary of Your RoutineAfter your routine is complete, the Picking Summary dialog appears, showing the number of source colonies picked, along with the number of destination microplates used, and any missing source receptacles.

1. Choose from one of the following options: Click Export to save this information into a .csv file.

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Click Details to open the Picking Details dialog and view full information of all activities related to the source and destination receptacles. Click Export from here to save the information to a .csv file. Click Close to return to the Picking Summary window.

2. Click Next, and then click Finish to return to the Navigation window.

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9
Replication Processes
The QPix 420 Colony Picking Software gives you the following three options to replicate your samples from one microplate to another:

• Library Replication replicates between microplates with the same number of wells.

• Library Compression replicates from 96-well microplates to 384 well-microplates (compresses the samples).

• Library Expansion replicates from 384-well microplates to 96 well-microplates (expands the samples).

This chapter contains the following sections:• Preparing for a Replicating Routine on page 123• Creating and Editing a Replicating Routine on page 124 • Running a Replicating Routine on page 128

Preparing for a Replicating RoutineYou need to conduct some preliminary steps before being able to successfully replicate your colonies. If this is the first time you have ever conducted a replicate on the QPix 420 Colony Picking System, you must edit the supplied sanitise profile to suit your needs.

• For more information on completing this task, see Creating and Editing Sanitise Profiles on page 61.

If you have made any adjustments to the instrument, such as changing the head, you will have to align the camera again. For more information on camera alignment, see Aligning the Camera on page 47.Before you begin any new routine, Molecular Devices® recommends you perform a manual clean of the instrument interior (using 70% ethanol), and then conduct a sanitise and UV sanitise. For more information on these tasks:


Remove any loose items from the interior of the instrument, and wipe them down too. Finally, remember to top up your wash baths with relevant cleaning fluids.

Note: The process for conducting all three replication routines are very similar, so they will all be covered in this chapter. Differences and exceptions will be clearly identified and explained.

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Creating and Editing a Replicating RoutineNow that you have conducted both sanitise routines and given the instrument interior a manual clean, you are ready to create a replicating routine. This consists of the following steps:

• Selecting Barcode Reading Options on page 124• Setting Microplate and Sanitise Options on page 127• Setting Head Options on page 128• Viewing the Settings Summary on page 130• Continuing or Saving Your Routine on page 130• Viewing the Replication Progress on page 131• Viewing the Replicating Process Summary on page 131

conduct the following steps to create and edit a replicating routine:1. In the Navigation window, double-click the Library Replication icon,

then click Start.The System “homes” the drives, and then the Routines window opens. This allows you to create or edit existing routines.





Selecting Barcode Reading OptionsThe Barcodes window allows you to select your barcode reading options.


Note: If you choose to use validation or create manual barcodes they will only be applied to your source microplates, and the instrument will look only for the number of microplates listed to plate.

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1. If you are using the barcode reader, leave the Use Barcode Reader check box selected (this is the default), and then select a Read Failure Action option.Use Barcode Reader means the barcode reader will automatically scan receptacles for barcodes (both source and destination).




3. If validating barcodes, enter your full range of barcodes for this routine in the Validation Barcode table using the following options. This helps you to check barcodes on source receptacles as they are scanned by the barcode reader. You can list the barcodes in any order. The instrument scans the Validation Barcode list to confirm the source barcode is present. If it is missing, a message appears describing the erroneous receptacle. Insert means you need to type each bar code manually into the

Insert field, and then click Insert. Import means you can import barcodes from a text or .csv file. From Database allows you to import barcodes from the database.



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5. After choosing your barcode reading option, click Next. The Microplates/Sanitise window opens.

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Setting Microplate and Sanitise OptionsThe Microplates/Sanitise window allows you to define your source and destination microplate types, choose multi-dipping and stirring, create additional copies (Library Replication only), and replicate from multiple source microplates. You also choose your sanitise profile from this window.

1. In the Microplates window, select source and destination receptacles from the Source Microplate and Destination Microplate lists. With Library Replication, the two lists in the Microplate Options

section allow you to select only microplates with the same number of wells (the other list changes its microplate selection options based on your most recent selection).

With Library Compression, the two lists in the Microplate Options section allow you to select only relevant microplates related to compression (96-well to 384-well). The Source Microplate list contains only a selection of 96-well microplate options, and the Destination Microplate list contains only 384-well microplate options.

With Library Expansion, the two lists in the Microplate Options section allow you to select only relevant microplates related to expansion (384-well to 96-well). The Source Microplate list contains a selection of 384-well microplate options, and the Destination Microplate list contains 96-well microplate options.

2. From the Microplate Options section, choose from the following additional options for your source, destination or both microplates: Multi Dip indicates you want the instrument to dip the pins into the

microplate well multiple times. Number of Dips tells the instrument how many dips per microplate

well you want it to make. Stir Source stirs the pins in the source microplate wells. If you

choose this option, you cannot multi-dip.3. With Library Replication, if you want to make additional copies during

this routine, set a number (up to two) in the Additional Copies field.The Sanitise Between Copies check box becomes ungreyed if you select this option, allowing you to set additional wash cycles.

4. Use the Number of Source Microplates list if you are using multiple source receptacles (maximum 100). The Number of Source Per Bed field automatically updates (maximum 10) and notifies you how many source receptacles you can place on QPix 420 interior bed based on how many source receptacles you are using for the routine.

5. Choose a sanitise profile from the Sanitise Profile list. For more information on creating or editing sanitise profiles, see Creating and Editing Sanitise Profiles on page 61.

6. Click Next. The Head window opens.

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Setting Head OptionsThe Head window allows you to select the head type, and set inoculation dipping heights for both Source and Destination microplates.

1. In the Head window, select a head type from the Select Head list.2. Set your inoculation heights in the Source and Destination fields.

These set the depth above the bottom of a well that the pin travels to. 3. Click Next. The Holder Layout window appears.

Running a Replicating RoutineNow that you have configured your parameters, you are ready to prepare the instrument and run the routine. This consists of the following steps:

• Arranging the Layout for the Routine on page 128• Arranging the Layout for the Routine on page 128• Viewing the Settings Summary on page 130• Continuing or Saving Your Routine on page 130• Viewing the Replication Progress on page 131• Viewing the Replicating Process Summary on page 131

Arranging the Layout for the RoutineThe Holder Layout Summary window shows you how to correctly arrange the microplate holders in the instrument for your picking routine. This is defined by the selections you made earlier.


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Click Next. The Load Plates window appears with instructions on where to place the source and destination microplates on the plate holders. If you do not select Checked? you cannot continue the process.

2. Follow the layout instructions in the Load Plates window (including removing all microplate lids), and after you are certain you have loaded everything correctly, click Checked?



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Viewing the Settings SummaryThe Settings Summary window contains a summary of the routine settings you just configured. You can print a copy of these by clicking Print.

From the Settings Summary window, click Next. The Continue or Save New Routine dialog appears.





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2. To continue the routine without saving, click OK.To save this routine, select Save Routine, type a Name and Description in the relevant fields, and then click Save. The replication routine begins. The instrument reads the barcodes, and the Library Replication Progress window appears.

Viewing the Replication ProgressThe Library Replication Progress window displays the following details:

• Start Time displays the time the replicating of samples began.• Source Plate No shows the source microplate being replicated.• Source Barcode shows the barcode of the source receptacle being

replicated.• Source Offset displays the source well into which the pins will be

lowered. This changes if using a 384-well microplate.• Depositing into displays the well or microplate the sample will be

deposited into.• Destination Plate No displays the current destination microplate

number that is being replicated into.• Destination Barcode displays the current destination microplate

barcode that is being replicated into.• Destination Offset shows the destination well into which the pins will

be lowered. This will change if using a 384-well microplate.• Calculate Remaining Time...indicates how far along the routine is.

Note: The QPix 420 System will ask for more source microplates to replicate.

Viewing the Replicating Process SummaryAfter the replicating routine has been completed, the Replicating Process dialog appears, showing the number of source wells replicated, along with the number of destination microplates used, and any missing source microplates.

You have the following options from this window:• Click Export to save this information into a .csv file.

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• Click Details to open the Replicating Details dialog and view full information of all activities related to the source and destination receptacles. Click Export from here to save the information to a .csv file. Click Close to return to the Replicating Process window.

• Click Next, and then click Finish to return to the Navigation window.

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10
Conducting a Rearraying Routine
Performing Rearraying ProceduresThe QPix 420 Colony Picking Software allows you to re-deposit (rearray) colonies between one or more source and destination microplates. You would do this if you wanted to organize (cherry-pick) your picked source colonies into destination subsets of a more specific and orderly layout.The following sections are described here:

• Preparing for a Rearraying Routine on page 133• Creating and Editing a Rearraying Routine on page 133• Running a Rearraying Routine on page 138

Preparing for a Rearraying RoutineYou need to perform some preliminary steps before being able to successfully rearray your picked colonies. If this is the first time you have ever performed a rearray on the QPix 420 Colony Picking System, you must edit the supplied sanitise profile to suit your needs.

• For more information on completing this task, see Creating and Editing Sanitise Profiles on page 61.

If you have made any adjustments to the instrument, such as changing the head, you will have to align the camera again. For more information on camera alignment, see Aligning the Camera on page 47.Before you begin any new replicating routine, Molecular Devices® recommends you perform a sanitise, UV sanitise, and a manual clean of the interior of the instrument with ethanol. For more information on these tasks:


Remove any loose items from the interior of the instrument, and wipe them down too. Finally, remember to top up your wash baths with relevant cleaning fluids.

Creating and Editing a Rearraying RoutineNow that you have performed both sanitise routines and given the instrument interior a manual clean, you are ready to create a rearraying routine. This consists of the following steps:

• Selecting Barcode Reading Options on page 134• Identifying your Source Receptacle on page 135• Defining your Destination Receptacle on page 137• Selecting Head and Sanitise Options on page 138

Perform the following steps to create and edit a rearraying routine:1. In the Navigation window, double-click the Rearraying Icon, and then

click Start.The System “homes” the drives, and then the Routines window opens. This allows you to create or edit existing routines.

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Delete routines from the Select Routine list by clicking Delete.The Barcodes window appears.

Selecting Barcode Reading OptionsThe Barcodes window allows you to select your barcode reading options.

1. If you are using the barcode reader, leave the Use Barcode Reader check box selected (this is the default), and then select a Read Failure Action option.Use Barcode Reader means the barcode reader will automatically scan receptacles for barcodes (both source and destination).





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3. After choosing your barcode reading option, click Next. The Source window opens.

Identifying your Source ReceptacleThe Source window allows you choose source microplate details and head behaviour, and input receptacle identifier information.

1. From the Source window, select a receptacle from the Source Microplate list, and select source microplate data in the following ways:Import inputs all source microplate data from a .txt or .csv file to the table. You can also use .frd (Fusion) and .imp (legacy QSoft) files.From Database imports source data from the software database. Clicking this button opens the Barcode Search window with the following tabs: By Tag conducts a tag search. Tags improve the ability to identify

and search for any routine, receptacle, or location (colony). For more information on tags, see Working with Tags on page 162.

By Process searches for barcodes from previous routines.


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Navigate to a completed routine in the table on the left, select a source barcode from the Barcode table on the right, and then click Add Barcode. That barcode now appears in the Selected Barcodes table.

2. Click Import or Remove Barcode to continue. Insert opens an editable image of the receptacle where you can

define the wells you want to pick from for your rearraying routine. Export allows you to export source microplate data to a .frd

(Fusion) or .imp (QSoft) file.

3. After you have added at least one microplate identifier to the Source window table, you can Edit, Remove, or Remove All the entries.

4. Select Stir Source if you want the head to stir the source before depositing it in a receptacle well.

5. Type a number in the Microplates to Process Before Depositing field to define the quantity of microplates to process before depositing.

6. Click Next.The Destination window appears.

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Defining your Destination ReceptacleThe Destination window allows you to define your destination receptacle.

1. In the Destination Microplate Options section, choose a destination microplate from the Select Microplate list. If you do not see a microplate that you use on this list, please contact Molecular Devices to see if we can add it to the list.

2. Choose from the following additional options for your destination microplates: Multi Dip indicates you want the instrument to dip the pins into the

source receptacle multiple times per dip. Number of Dips tells the instrument how many dips per deposit


If you choose this option, you cannot multi-dip.3. In the Deposit Order section, choose between By Columns or By

Rows as the Deposit Order for the destination receptacle.4. Click Edit to edit the Destination Microplate Template. This

template allows you to clear various wells so that they are not picked, for example when control wells are desired. The Edit Destination Microplate Template dialog appears.

Cleared wells are displayed in light blue and selected wells are displayed in pink.

5. Click any well you want to leave empty, and right-click and drag your mouse over multiple wells you want to remain empty. Click a well again to re-select it.

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6. Click Next. The Head and Sanitise window appears.

Selecting Head and Sanitise OptionsThe Head and Sanitise window allows you to pick a head and select a sanitise option. For more information on sanitise profiles, see Creating and Editing Sanitise Profiles on page 61.

1. In the Head and Sanitise window, choose a head from the Select Head list.


3. Use the Inoculation Heights (mm above well bottom) fields to set the depth (in millimeters) the pin travels to above the bottom of a well for both your Source and Destination microplates. Default values are displayed for each microplate type chosen earlier.

4. Click Next. The Holder Layout window appears.

Running a Rearraying RoutineNow that you have configured your parameters, you are ready to prepare the instrument and run the routine. This consists of the following steps:

• Confirming the Layout for the Routine on page 139• Viewing the Settings Summary on page 140• Viewing the Rearraying Progress on page 141• Viewing the Rearraying Process Summary on page 141


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Confirming the Layout for the RoutineThe Holder Layout window appears with instructions on setting the bed levels and loading the correct head and wash bath.

1. Follow the layout instructions in the Holder Layout window (including removing the imaging table).

2. After you are certain you have loaded everything correctly, click Checked?

3. Click Next. The Load Plates window appears with instructions on where you need to place the source and destination microplates on the plate holders.



Note: Because rearraying requires five plate holders, you must ensure the imaging table has been removed before continuing.

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Viewing the Settings SummaryThe Settings Summary window appears with a full summary of all the settings you have made for this routine.

1. Print a copy of your settings by clicking Print, or click Next to continue.

Note: The instrument door now locks. The only way to over-ride this is to press the Stop button on the front of the instrument.

WARNING! After clicking Next here, you can no longer click Back.

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Viewing the Rearraying ProgressThe Picking Progress window displays the following information:

• Start Time shows the time the picking of the colonies began.• Source Plate No shows number of the source receptacle.• Source Barcode shows the barcode of source receptacle being picked.• Pin is the picking pin being used.• Destination Plate No shows the number of the destination receptacle. • Destination Barcode is the barcode of the destination receptacle that


will change if using a 384 well microplate.• Total Wells Rearrayed is the number of wells rearrayed so far.• Total Wells to Rearray is the total number of wells to be rearrayed.• Estimated Time Remaining indicates how far along the routine is.• Current Action displays the current action of the System, for example

Deposit, when the System is depositing.• Pause allows you to safely pause the routine.•

Viewing the Rearraying Process SummaryAfter the rearraying routine has been completed, the Rearraying Process dialog appears, showing the number of source wells rearrayed, along with the number of destination microplates used, and any missing source microplates. You can export this information into a table by clicking Export.

1. In the Rearraying window, click Next. The Process Completed window appears.

2. In the Process Completed window, click Finish to return to the Navigation window.

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11
Gridding Processes
Gridding allows you to deposit liquid samples from one or more source microplates to one or more destination surfaces (either agar filled QTrays or filters).This chapter contains the following sections:

• Preparing for a Gridding Routine on page 143• Creating and Editing a Gridding Routine on page 143• Running a Gridding Routine on page 154

Preparing for a Gridding RoutineYou need to conduct some preliminary steps before successfully conducting a gridding routine. For more information on these steps, see Preparations for Running a Routine on page 59.Remove any loose items from the interior of the instrument and remember to top up your wash baths with relevant cleaning fluids.If this is your first gridding routine on the QPix 420 Colony Picking System, you must edit the supplied sanitise profile to suit your needs. For more information on sanitise profiles, see Creating and Editing Sanitise Profiles on page 61.If you have made any adjustments to the instrument, such as changing the head, you will have to align the camera again. For more information on camera alignment, see Aligning the Camera on page 47.Before you begin any new routine, Molecular Devices® recommends you perform a manual clean of the instrument interior (using 70% ethanol), and then conduct a sanitise and UV sanitise. For more information on these tasks:


Creating and Editing a Gridding RoutineNow that you have created and edited at least one sanitise profile, conducted both sanitise routines, and given the instrument interior a manual clean, you are ready to create a gridding routine. This consists of the following steps:

• Selecting Barcode Reading Options on page 144• Selecting Head and Sanitise Options on page 146• Setting Source and Destination Receptacles on page 146• Creating a Filter Design Layout on page 147• Selecting the Destination Tray on page 152• Selecting Stamping and Inking Options on page 153• Arranging the Layout for the Routine on page 154• Viewing the Settings Summary on page 155• Continuing or Saving Your Routine on page 156• Viewing the Gridding Progress on page 157• Viewing the Summary of Your Routine on page 157

Conduct the following steps to create and edit a gridding routine:1. In the Navigation window, double-click the Gridding icon.2. In the Gridding window, click Start.

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Gridding Processes

The System “homes” the drives, and then the Routines window opens. This allows you to create or edit existing routines.





Selecting Barcode Reading OptionsThe Barcodes window allows you to select barcode reading options.

1. If using the barcode reader, leave the Use Barcode Reader check box selected (default), and then select a Read Failure Action option.Use Barcode Reader means the barcode reader will automatically scan receptacles for barcodes (both source and destination).

2. Select one of the following options from the Read Failure Action section, in case a barcode cannot be read correctly:


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Manual prompt launches a dialog where you can manually type a barcode or microplate name (both source and destination receptacles).

Skip Receptacle tells the instrument to cease looking for a barcode and look for a barcode on the next receptacle (both source and destination receptacles).

3. If validating barcodes, enter your full range of barcodes for this routine in the Validation Barcode table using the following options. This helps you to check barcodes on source receptacles as they are scanned by the barcode reader. You can list the barcodes in any order. The instrument scans the Validation Barcode list to confirm the source barcode is present. If it is missing, a message appears describing the erroneous receptacle. Insert means you need to type each bar code manually into the

Insert field, and then click Insert. Import means you can import barcodes from a text or .csv file. From Database allows you to import barcodes from the database.




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Gridding Processes


5. After choosing your barcode reading option, click Next. The Head window opens.

Selecting Head and Sanitise OptionsThe Head window allows you to select a relevant gridding head and choose a sanitise profile. For more information on sanitise profiles, see Creating and Editing Sanitise Profiles on page 61.

1. In the Head window, choose a head from the Gridding Head list.2. Select a sanitise profile from the Sanitise Profile list.

3. Click Next. The Microplates and Filters window appears.

Setting Source and Destination ReceptaclesThe Microplates and Filters window allows you to set up the source receptacles and destination surface, as well as control the number of times the head dips into the source receptacle or stirs the source solution.

Note: You cannot edit a sanitise profile from this window. If none of the sanitise profiles suit your routine, you will need to exit the routine at this point and create a sanitise profile. For more information, see Creating and Editing Sanitise Profiles on page 61.

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1. From the Select Microplate list, select the appropriate microplate to suit the stacker configuration of your instrument.Choose from the following additional options: Multi Dip indicates you want the instrument to dip the pins into the

receptacle multiple times. Number of Dips tells the instrument how many dips you want it to

make. Stir Source stirs the pins in the source receptacle wells. If you

choose this option, you cannot multi-dip. Inoculation Heights (mm) allows you to set the depth the pin

travels to above the bottom of the receptacle well. By default, the pin drops as low as possible into the well.

2. From the Select Receptacle list, choose either QTray or Filter.3. Click Next. The Filter Design window appears.

Creating a Filter Design LayoutThe Filter Design window allows you to arrange how spot and field patterns can be stamped (gridded) onto destination receptacles - QTray or filter.You can choose existing spot patterns from the Reuse list, but only if some spot patterns have been previously created and saved. If there are no existing spot patterns (if the Reuse list, and Load and Delete buttons are greyed out), you will need to create a new spot pattern. Spot Patterns refer to the pattern and number of times that one pin will stamp onto the destination QTray.Field Patterns refer to the way that the QTray is divided up into sections. The fields match the dimensions of a 96-pin head. One field equals one head.

There is a great amount of flexibility with the Filter Design options.The default setting is to be able to fill your QTray with a maximum of 14,400 different samples (6 fields times 25 spots per pin times 96 pins) originating from 150 different 96-well source microplates (see image below).

Note: There is no visual correlation between Spot Pattern and Field Pattern, despite both patterns using the same colouring and numbering formats.

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Gridding Processes

o

At the other end of the range, assuming you were using 1 filled 96-well source microplate, the minimum number of samples being stamped onto your QTray would be 96 different samples (1 field times 1 spot per pin times 96 pins) (see image below).

You can create any number of different filter designs (field and spot patterns) within this range.

1. From the Reuse section of the Filter Design window, If there is at least one existing spot pattern in the Reuse list, you can make a selection from the Reuse list, and click Load. The Load Gridding Pattern? dialog appears, and notifies you that loading this pattern will overwrite the current spot pattern. Click Yes to confirm. Click Save to save a customized spot pattern separately from the

whole routine (field pattern is not saved). The Save New Gridding Pattern? dialog appears. Type a name in the Name field and click OK. The new name is instantly available from the Reuse list.

Note: The Filter Design window defaults to the maximum possible settings for the Field Pattern (6 fields) and Spot Pattern (25 spots per pin). You can change all of these settings to whatever you want.

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Click Delete to remove a spot pattern from the Reuse list. The Delete Gridding Pattern? dialog appears. Click Yes to delete.

If there are no spot patterns in the Reuse list, or if none of the existing spot patterns match your needs, you will need to create one.

2. From the Structure section, set the number of Rows and Columns to be stamped for each pin, and create the Spot Pattern per pin. Your spot pattern must have a logical numerical sequence to it (for example: 1,2,3,4 or 1,2,2,4). If you create an illogical sequence to the Rows or Columns fields (for example: 1,3,4,3 or 1,4,1,2), an error message at the bottom of the window displays “Can’t Calculate” in red text, a No Sequence button displays in red, and the Spot Pattern is cleared (blank yellow circles) until you select your Fill options to set your spot pattern automatically. The Next button also becomes greyed out, making it impossible to progress from this page.

3. From the Fill section, select a Replicate (copy) quantity (between 1 and 4), and click one of the eight direction buttons to confirm where you want the number 1 pin to start, along with the gridding direction you want the spot pattern to follow. The Spot Pattern displays the layout of the new spot pattern in coloured circles (n rows, n columns, n replicates), and the Sequence Complete button changes colour from red to green. Spots with the same colour and number indicate that the same sample will be spotted in those positions within the spot pattern, and spots with different numbers and colours indicate that different samples will be spotted in those positions within the spot pattern.Click Clear Spots, and then click OK in the Clear Pattern? dialog to clear the current spot pattern while keeping the same pattern structure.

Note: The Structure and Spot Pattern sections of the Filter Design window are highlighted and other sections removed in the following two images, to highlight the effects of changing numbers in the Rows and Columns fields.

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The higher the number in the Rows and Columns fields, the more spots per pin for the spot pattern, and the smaller the Row Pitch and Column Pitch (maximum space between each spot in the spot pattern) will be. These numbers change dynamically depending on your Rows and Columns settings.You can reduce the Row Pitch and Column Pitch but you cannot exceed the displayed maximum measurements (ums) in these fields.

4. To create a spot pattern automatically, click any of the eight direction buttons, and then click OK in the Fill Pattern? dialog to change the current gridding direction.

5. You can make manual changes to the Spot Pattern (only in Layout View) by highlighting a circle and either typing a new number for that circle, or clicking the Clear Spots button or pressing the Delete key to clear the colour and number. However, if your subsequent sequence or pattern is incorrect, the Sequence button displays Sequence Incomplete in red text, an error message displays “Can’t Calculate” in red text at the bottom of the window, and the Spot Pattern Status dialog appears, describing the

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error and instructions on the necessary fix. Also, the Next button becomes greyed out, making it impossible to continue from this page.

6. From the View section, click Actual View to see a realistic representation of the layout and spot pattern of the pins.Type any number up to 1500 into the Estimated Spot Size field to change the representation of the spot size (default is 200 um) in the Actual View of the Spot Pattern section. (The Field Pattern and Fill sections have been excluded from this image to simplify the view).

7. From the Field Pattern section, select any field and type any number between 1 and 6 to create the desired layout of the destination surface.

Note: You can grid your samples on up to 2 QTrays or 6 filters. However, the software creates one field pattern per routine (printed onto either destination receptacle), so whatever pattern you choose will be replicated onto the chosen number of receptacles (QTrays or filters) used for that routine.

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Each field represents one head stamp. By default, 6 different fields display in the Field Pattern section, meaning that each field will contain different samples. The large green number in the lower section of the window (in this example, 12) indicates the number of microplates required to fulfill this gridding pattern (number of different spots in the Spot Pattern times the number of different field patterns in the Field Pattern).

8. To change the Field Pattern layout, click a field and type any sequentially logical number between 1 and 6. To create a blank field, click the field, and then hit the Delete key.If the layout contains two identical fields (same colour and number), this means the fields will be replicates (copies). If you create a numerically illogical field pattern (for example: 1,1,2,5,3,5), the Sequence button changes from green text (Sequence Complete) to red text (Sequence Incomplete).

For information about the error and how to fix it, click the Sequence Incomplete button, and view the Field Pattern Status dialog. Click OK and type in a sequentially logical number (in this example, 4).

9. Click Next. The Filter Layout window appears.

Selecting the Destination TrayThe Filter Layout window allows you to choose only the QTray as your destination receptacle. The other options are greyed out.Click Next. The Substrate window appears.

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Selecting Stamping and Inking OptionsThe Substrate window allows you to select stamping and inking options.

1. From the Substrate window, set a number (between 1 and 5) in the Stamps Per Spot field. This allows you to increase the amount of samples spotted in one location. If you set a number more than one here, the Re-Ink After #of Stamps check box becomes ungreyed.

2. Check the Re-Ink After # of Stamps box if you would like the head to return to the source plate to re-ink the pins before stamping the samples again, and choose the quantity of re-inks (between 1 and 10).

3. If you have chosen to re-ink the pins after stamping, select one of the following radio buttons to define what re-inking method you would like: Cyclic means stamp all sample spots once before re-inking. Immediate means re-ink right after the first spot is stamped.

4. Choose Stamp Time (ms) and Dwell Time (ms) settings for how long you want the pin pressed against the destination surface (Stamp Time), and how long you want the pins submerged in the source well (Dwell Time).

5. Choose a number (between 1 and 15) in the Overtravel Adjustment (mm) field for the pins to travel an extra distance and ensure they all touch a potentially uneven receptacle surface firmly enough for a good transfer of all samples.

6. Click Next. The Holder Layout window appears.

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Gridding Processes

Running a Gridding RoutineNow that you have configured your parameters, you are ready to prepare the instrument and run the routine. This consists of the following steps:

• Arranging the Layout for the Routine on page 154• Viewing the Settings Summary on page 155• Continuing or Saving Your Routine on page 156• Viewing the Gridding Progress on page 157• Viewing the Summary of Your Routine on page 157

Arranging the Layout for the RoutineThe Holder Layout Summary window shows you how to correctly arrange the microplate holders in the instrument for your picking routine. This is defined by the selections you made earlier.


o

2. Click Next. The Load Plates window appears with instructions on where to place the source and destination microplates.

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Viewing the Settings SummaryThe Settings Summary window contains a full summary of your routine.

1. Print a copy of the settings by clicking Print, or click Next to continue.

The Continue Or Save New Routine dialog appears.



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The Please Load Destination window appears.

After you have loaded your source receptacles in their correct location inside the instrument, click Next. The Gridding Progress window appears and the gridding routine begins.

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Viewing the Gridding ProgressThe Gridding Progress window displays a summary of this routine, including a timeline to tell you how long to completion.


• Start Time shows the time the gridding began.• Source Plate No shows the current source microplate that is being

gridded from.• Source Barcode shows the barcode of the source microplate being

picked from.• Destination Receptacle No is current destination surface being

gridded onto.• Destination Barcode is the barcode of the destination surface being

gridded onto.• Field is the current destination field being gridded.• Spot is the current destination spot being gridded.• Field Replicate is the current destination field replicate being gridded.• Spot Replicate is the current destination spot replicate being gridded.• Stamp is the current stamp being gridded.

When the routine is completely finished, the Gridding Summary window appears.

Viewing the Summary of Your RoutineAfter your routine is complete, the Gridding Summary dialog appears, showing the number of spots stamped, along with the number of source microplates reaped, and any missing source receptacles.

1. Choose from one of the following options: Click Export to save this information into a .csv file. Click Details to open the Gridding Details dialog and view full

information of all activities related to the source and destination barcodes and destination regions and locations. Click Export from

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here to save the information to a .csv file. Click Close to return to the Picking Summary window.

2. Click Next, and then click Finish to return to the Navigation window.

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12
Data Viewer Processes
The Data Viewer window allows you to view data details from the full set of previous routines run on the QPix 420 Colony Picking System. The following procedures are described here:

• Conducting a Data Search on page 159• Working with Tags on page 162• Adding Annotations on page 164• Exporting Processes or Routines on page 165• Adding or Deleting Properties for Microplates on page 165• Viewing a Map of the Locations on page 167• Working with Sample Trails on page 168

Conducting a Data Search1. In the Navigation window, double-click the Data Viewer icon. The

Data Viewer window opens.

2. Using the navigation menu on the left, choose the particular routine you want by either one of the processes (Picking, Regional Picking, Rearraying, or Replicating), or by selecting one of the following specific search parameters: By Tag. For more information on searching by tags, see Searching

by Tag on page 160. For more information on creating and editing tags, see Working with Tags on page 162.

By Barcode. For more information on searching by barcodes, see Searching by Barcode on page 160.

By Date. For more information on searching by date, see Searching by Date on page 161.

By User. For more information on searching by user, see Searching by User on page 161.

By Location. For more information on searching by location, see Searching by Location on page 161.

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3. Single-click any routine in the table to display related barcoded receptacle and annotation details at the bottom of the window.

Max

If necessary, click More in the Barcoded Receptacles window, to view additional receptacles in the Destination Receptacles window. Click Close to return to the Processes window.

Searching by TagThe Search by Tag window allows you to search receptacles based on any given tags. Select the required tag from the Available Tags field, and then click Add. Search results for the tag display at the bottom of the window. Double-clicking any of these results displays more details related to the item. For more information about tags, see Working with Tags on page 162.

Searching by BarcodeThe Search by Barcode window allows you to search receptacles by any barcode. If found, the search results display below. Double-clicking any of these results displays more details related to the item.

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Searching by DateThe Search by Date window allows you to search for a routine based on the date it was run. All data produced on that date displays in the table below. Double-clicking any of these results displays more details related to the item.

Searching by UserThe Search by User window allows you to search by user from the User list. Double-clicking any of these results displays more details related to the item.

Searching by LocationThe Search by Location window allows you to search by location of wells. Select the required Well or Barcode to search for the desired data set. Double-clicking any of these results displays more details related to the item.

Viewing and Printing Settings Details1. To view and print every setting configured for your chosen routine, click

a process from the Processes menu on the left, double-click a specific routine in the Processes table on the right, and then click Settings from the subsequent window.

The View Settings window appears. Items will be different in this window, based on whether you are looking at details of a picking, rearraying, or replicating routine.

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2. Click Print to print these settings, or Exit to return to the previous window.

Working with TagsA tag is a user-created identifier for a routine, receptacle, or location. Use tags to easily identify data of interest. You can create, add, or remove tags from the menu in the Data Viewer window. You can create a tag at any time, but can only add or remove a tag after selecting a routine from the Processes table. For information on searching by tags, see Searching by Tag on page 160.

Creating a TagTags can be created from anywhere within the Data Viewer window.

1. From the Data Viewer window, click Create Tag. The Create Tag dialog appears.

2. Type the tag name in the Tag field, and if relevant, type a description in the Description field.

3. Click Create Tag, to return to the Data Viewer window. This new tag will now be available to add to relevant data.

Adding Tags to a Receptacle, Location, or RoutineOnce you have created at least one tag, you can add it to any routine, receptacle, or location (well or position in a QTray or Petri dish).

1. From the Data Viewer window, navigate to the desired routine, receptacle, or location, and then click Add Tag in the navigation menu on the left. The Select Tags to Add dialog appears. Depending what level of detail you have navigated to, this dialog will display radio buttons for either Process, Process and Receptacle, or Process, Receptacle, and Location.

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2. Select the relevant radio button based on the level you want to tag, and select a tag name from the table.

3. Click Add Tags. The Data Viewer window appears, with the tag name (in this example: qtray) displayed in the right side menu.

Removing a TagYou can remove a tag from any process, receptacle, or location.

1. From the Data Viewer window, navigate to the desired routine, receptacle, or location. If the item has a tag associated with it, the tag name will appear in the right side menu.

2. Click Remove Tag in the navigation menu on the left. The Select Tags to Remove dialog appears.

3. Select the tag you wish to remove, and then click Remove. The tag is removed and the Data Viewer window appears.

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Adding AnnotationsYou can add annotations (notes) to any routine, receptacle, or location once you have selected a specific routine.

1. From the Data Viewer window, navigate to the desired routine, receptacle, or location, and then click and then click Add Annotation in the left navigation menu. The Add Annotation dialog appears.

2. Type the relevant annotation text, and then click the radio button for the level where you want the information added (Process, Receptacle or Location).

3. Click Add. The dialog closes and the annotation now displays in the Annotations table at the bottom of the window.

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Exporting Processes or RoutinesYou can export a full list of processes or routines to either a .csv file (Processes) or HTML file (Routine settings).

1. From the Data Viewer window, navigate to the desired process or routine, and then click one of the following:Export Process saves all data related to the selected process into an Excel .csv spreadsheet.Export Routine saves all data related to the routine in an HTML file.

2. Navigate to where you want to save the file, and then click Save.

Adding or Deleting Properties for MicroplatesYou can add or delete additional property information related to any microplate well in the Location Properties table.

Adding Properties

1. From the Data Viewer window, navigate to the relevant microplate level, and then click Add Property. The Add Property dialog appears.

2. Type a relevant name for the additional property you want to add to this microplate data in the Property Name field, and type a relevant value in the Property Value field.

3. Choose one of the following categories from the Property Type list: String holds text (for example: Positive Sample) Int holds integer values (for example: 5) Double holds decimal numbers (for example: 6.75) Bool holds a boolean value (for example: True)

4. Click Add. The Add Properties dialog disappears, and the new property information displays in the Location Properties table to the right of the microplate image.

Note: This task is performed only at the microplate well level.

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Deleting a Property1. From the Data Viewer window, navigate to the relevant microplate

level, and then select the specific property you wish to delete from the Location Properties table.

2. Click Delete Property. The Delete Property dialog appears.

3. Click Delete Property, and when you return to the previous window, that property will no longer display in the Location Properties table.

Note: You can only delete properties that have been added to the existing default properties. Default properties cannot be deleted.

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Viewing a Map of the LocationsYou can view the connections of colonies that have been mapped from one receptacle to another by clicking Show Locations Map.

1. From the Data Viewer window, navigate to the relevant microplate well level, and then select a well that you would like to map its location.

2. From the left navigation menu, click Show Locations Map. The Location Map dialog appears, showing the path that the well of interest has followed.

3. Click Close to return to the previous window.


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Working with Sample TrailsYou can view details on how one or more wells were used in a particular routine by using Sample Trails. Until you have added at least one sample trail, the Display Sample Trail and Clear Sample Trail options remain greyed out.


Adding and Removing Sample Trails1. From the Data Viewer window, navigate to the relevant microplate.

2. Click Add/Remove. The Edit Sample Trail dialog appears.

3. Select the desired wells. To de-select a well, click it again.4. Click OK to return to the previous window. The selected wells are now

displayed in the Sample Trail tail, and Display Sample Trail and Clear Sample Trail are now clickable.

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5. To remove the sample trail, click Add/Remove, and deselect the relevant wells.

Viewing and Clearing Sample Trails1. From the Data Viewer window, click Display Sample Trail. The Sample

Trail Locations dialog appears, with sample property and location details of all the sample wells selected in the Edit Sample Trail dialog.

2. Click Close to return to the previous window.To save the information as a .csv file, click Save and navigate to the relevant save location.

3. To clear the total sample trail click Clear Sample Trail. All information is immediately deleted and removed from the Sample Trail table.

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A
Replacement Parts and Optional Extras
Please refer to the Molecular Devices® website for the latest replacement parts and optional extras at: www.moleculardevices.com/genetix

Replacement FusesFuses should only be replaced with the correct type and rating as specified:

• Input - F1 - T10A/250V - QPix 420/Halogen Heater• Output - F2 - T5A/250V - Computer and Monitor

For more information, see Technical Specifications on page 173.

Table A-1: QPix 420 Colony Picking System Replacement Parts

Code Description

X4006J Phage picker+ picking head, 96 pin, tip diameter 1.6 mm, deep well

X4006K Yeast picker+ picking head, 96 pin, tip diameter 1.6 mm, deep well

X4300 Picking Head 96-pin

X4310A Re-arraying and replicating head, standard transfer, 96 pin for 96- & 384-well microplates, tip diameter 0.55 mm, pin length 49.5 mm

X4310B Re-arraying and replicating head, hi-capacity transfer, 96 pin for 96- & 384-well microplates, tip diameter 1.6 mm, pin length 49.5 mm

X4370 Picking pin for E.coli/phagemid, tip diameter 0.55 mm

X4371 Picking pin for phage plaque, tip diameter 1 mm

X4372 Picking pin for yeast, tip diameter 1.6 mm

X4373 Picking pin for streptomyces, tip diameter 1 mm

X4375 Picking pin for E.coli/phagemid, tip diameter 0.55 mm, deep well

X4376 Picking pin for Yeast picker+, tip diameter 1.6 mm

X4377 Picking pin for Yeast picker+, tip diameter 1.6 mm, deep well

X4378 Picking pin for yeast, tip diameter 1.6 mm, deep well

X4379 Picking pin for streptomyces, 1 mm, deep well

X4380 Picking pin for Phage picker+, tip diameter 1.6 mm, deep well

X4390 Picking Spring

X4451 Petri tray holder, 4 Hole

X4452 Petri Tray holder, 1 Hole

X4453 Petri Tray holder, 5 Hole

X4454 Omni Tray holder, 2 hole

X6023 Vented QTray with cover, 242 x 240 x 20 mm

X6029 Vented QTray with cover & 48 Well Divider, 242 x 240 x 20 mm

ME4541 Wash Bath

ME4542 Wash Brushes

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http://www.moleculardevices.com/genetix

http://www.moleculardevices.com/genetix

Replacement Parts and Optional ExtrasReplacement Parts and Optional Extras

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B
Technical Specifications

Table B-1: External Dimensions and Weight

Size 1440 mm (width)

790 mm (depth)

780 mm (height)

Weight QPix 420 System - 184 kg

Table (including compressor) - 165 kg

Table B-2: Compressed Air Supply

Minimum Pressure 100 psi

Maximum Pressure 120 psi

Minimum Volume 80 L/min

Table B-3: Operating Environment

Indoor Use Only

Temperature 10°C to 40°C

Humidity 20 to 80% non-condensing

Altitude Up to 2000M

Mains Supply +/- 10% Rated Voltage

Transient overvoltage Installation Category (Overvoltage category) II

Rated Pollution Pollution degree 2

Table B-4: European Electrical Supply

Voltage 230V AC 50 Hz single phase

Power QPix 420 System - 1250W

Connections IEC Input - QPix 420 Mains / Halogen Heater

IEC Output - PC and Monitor

Fuses Input F1 - T10A / 250V - QPix 420/Halogen Heater

Output F2 - T5A / 250V - Computer and Monitor

Compressor 230V AC 50Hz 3.4A

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Electrical Connections

Figure B-1: QPix 420 Instrument Electrical Connections Panel

Table B-5: North American Electrical Supply

Voltage 115V AC 60 Hz single phase

Power QPix 420 System - 1250W

Connections IEC Input - QPix 420 Mains

IEC Output - PC and Monitor

Fuses Input F1 - T10A / 250V - QPix 420/Halogen Heater

Output F2 - T5A / 250V - Computer and Monitor

Compressor 115V AC 60Hz 7.5A

Item Description

1 Mains Inlet

2 Robot (10A) & Monitor and PC (5A) Fuse holders

3 Computer and Monitor Outlets

3

2

1

WARNING! Ensure that all mains leads used by the QPix 420 System meet specified power requirements appropriate for country of use. Ensure that all equipment is suitably earthed. Ensure mains plug is easily accessible when installed as this is the disconnecting device.The mains lead must not exceed 3 metres in length.

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CAUTION! MAGNETIC DEVICE. Keep magnetic storage devices or strips, such as hard drives, credit cards, etc., away from the instrument covers.

Dimensions of the QPix 420 System

Figure B-2: Front View of the QPix 420 System

Figure B-3: Side View of the QPix 420 System

WARNING! Be careful of the drive magnets. Do not place metal or other items near the X and Y axis where the head moves.

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Technical SpecificationsTechnical Specifications

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C
Electromagnetic Compatibility (EMC)
REGULATORY INFORMATION FOR CANADA (ICES/NMB-001:2006)

This ISM device complies with Canadian ICES-001.Cet appareil ISM est confomre à la norme NMB-001 du Canada.

ISM EQUIPMENT CLASSIFICATION (Group 1, Class A)This equipment is designated as scientific equipment for laboratory use that intentionally generate and/or use conductively coupled radio-frequency energy for internal functioning, and are suitable for use in all establishments, other than domestic and those directly connected to a low voltage power supply network which supply buildings used for domestic purposes.

INFORMATION FOR THE USER (FCC NOTICE)This equipment has been tested and found to comply with the limits for non-consumer ISM equipment, pursuant to part 18 of the FCC Rules. These limits are designed to provide reasonable protection against harmful interference in a non-residential installation. This equipment generates, uses, and can radiate radio frequency energy and if not installed and used in accordance with the instructions, might cause harmful interference to radio communications. However, there is no guarantee that interference will not occur in a particular installation. If this equipment does cause harmful interference to radio or television reception, which can be determined by turning the equipment off and on, the user is encouraged to try to correct the interference by one or more of the following measures:

• Reorient or relocate the receiving antenna.• Increase the separation between the equipment and receiver.• Connect the equipment into an outlet on a circuit different from that to

which the receiver is connected.• Consult the dealer or an experienced radio/TV technician for help.

In order to maintain compliance with FCC regulations, shielded cables must be used with this equipment. Operation with non-approved equipment or unshielded cables is likely to result in interference to radio and TV reception. The user is cautioned that changes and modifications made to the equipment without the approval of the manufacturer could void the user's authority to operate this equipment.

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Electromagnetic Compatibility (EMC)

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D
Technical Assistance and Troubleshooting
This chapter contains information and guidance regarding issues that may need technical assistance or troubleshooting.

Technical AssistanceMolecular Devices® is a leading worldwide manufacturer and distributor of analytical instrumentation. We are committed to the quality of our products and to fully supporting our customers with the highest possible level of technical service.Our support web site, www.moleculardevices.com/support.html, has links to technical notes, software upgrades, and other resources. If you do not find the answers you are seeking, follow the links to the Technical Support Request Form to send an email message to a pool of technical support representatives.Please have the System ID number, System serial number, software version number, and the System owner’s name available when you call.For all service and support needs, please contact:

Global Customer Support Center

1-800-635-5577

To Inquire About a Service Plan

North America

1-408-747-3694 (fax)[email protected]

Europe

+44 118 944 8001 (fax)[email protected]

Key Service and Support Offices

North America

1-800-635-5577Technical Support: [email protected] Service: [email protected]

Europe

+44 (0) 118 944 8000Technical Support: [email protected] Service: [email protected] can also contact your local Molecular Devices office.

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Technical Assistance and Troubleshooting

Troubleshooting

Table D-1: Common Problems

Problem Possible Solution

Instrument will not start. System not functioning correctly

• Check that main power switch is turned on at the wall, the emergency stop button is pulled out, and the start button is pressed.

• Check fuses in mains input lead plug and instrument.• Power the System off and on again.

Computer will not start. • Check the power switch on the computer and the main power switched is turned on at the wall.

• Check fuse in electrical connections panel. For more information on fuses, see Electrical Connections on page 174.

One or more of the axes won’t move.

• Check the main power switch is turned on and the start button is pressed.

Drive System fails to home. • Ensure the door is closed. Manually move the head to the centre of the instrument and retry the process.

UV light won’t turn on. • Check that bulb is not burned out. • Ensure door is closed correctly.

Lamp failure. • Check whether halogen bulbs need replacing.

Picking alignment incorrect. • Align the picking pin, check for any bent pins on head.

Pins bend when inoculating in microplate wells.

• Ensure microplate is aligned correctly towards both arrows in plate holder. Ensure correct microplate, head, and spacer blocks are installed.

Poor picking results. • Run camera alignment process and check for bent pins in picking process.

• Check head is securely fastened. • Check picking height is correctly set. • Check wash bash routines and levels. • Check air pressure is at 100 psi. Ensure colonies of an adequate

size are being picked (97% pick efficiency is expected with colonies between 1-1.5mm).

• Check size, roundness, axis ratio, and threshold parameters.• Call technical support to discuss.

Crashes during destinaton well plates inoculation.

• Ensure microplates are positioned the right way round in holders, and with lids off.

Picking pins bending on edge of bioassay tray.

• Check the agar volume setting, bioassay tray positioning, tray holder positioning in the bed.

Door Open warning shows. • Check door is closed and locked.

Low air warning. • Check air pressure is at 100 psi.• Check air compressor is switched on.

Message indicating licence expiring soon.

• Send licence request file to Molecular Devices (.req) following the software instructions.

Failed to connect to devices error message.

• If you have recently disconnected the computer from the instrument, check Ethernet connections in both instrument and computer are correct.

• Check that the instrument is powered on. • Restart software.

Barcodes failing to be read correctly.

• Ensure barcodes are correctly positioned on the receptacle.• Ensure barcodes are of correct type (Barcodes compatible with

the barcode reader are code 39, code 93, and code 128).

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Glossary of Terms

Barcode: Unique label for source and destination microplates.

Datum Point: Series of X, Y, Z co-ordinates that define a set position on the QPix 420 System bed.

Destination Plate: 96-well or 384-well microplate pre-filled with liquid medium to collect picked colonies.

Halogen Dryer: Proprietary ultra-high temperature dryer used for the Pin Sanitise System.

Image Acquisition: Capturing of images using pre-defined acquisition options.

LED Intensity: QPix 420 System uses LEDs for consistent and reliable imaging. Adjust the intensity of the LEDs to control image exposure from the Acquisition tab.

Interior Light: Illuminates the interior of the instrument. Can be activated or deactivated at any time using the Interior Light icon in the bottom right corner of the screen. Interior Light is not used for imaging and will automatically switch off during imaging.

Picking Pins: Reusable stainless steel tools used to collect colonies.

Process: Standard program for QPix 420 System to carry out a task such as a series of similar experiments, or a maintenance task.

Proximity Indicators: Red lines between colonies on the image that show the nearest neighbour for each colony. Note: This feature is not the same as the colony exclusion feature in Groups.

Receptacle: QTray or Petri dishes containing colonies for picking.

Routine: QA specific type of process.

Transillumination: White light option normally used to detect colonies using LEDs positioned on the QPix 420 System head.

White Light: Full spectrum LED illumination, used for configuring the QPix 420 and for visualising colonies

during picking.

X Drive: QPix 420 axis running from right to left.

Y Drive: QPix 420 System axis running from back to front.

Z Drive: QPix 420 System axis running vertically from high to low on the QPix 420 bed

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Glossary of Terms

182 5026152 A

Index

Aadding and removing sample trails 168adding tags to a location 162adding tags to a receptacle 162adding tags to a routine 162additional display options - regional picking, viewing 102

aligning the camera 47annotations 164annotations, adding 164assistance, technical 179

Bbarcode list, generate 68, 145barcode reading options, selecting 67, 87, 109, 124, 134, 144

barcodes 67, 87, 109, 144, 160barcodes window 19, 25barcodes, generating random 68, 109, 145barcodes, reading 124barcodes, searching by 160biological safety 12

Ccamera alignment 44change head 45changing the head 48chemical safety 12cleaning 12

automated cleaning routine 56colonies 80, 118colonies, selecting 78, 98, 116

conducting a control plate creation routinecontrol plate creation settings summary 112edit destination microplate 110selecting barcode reading options 109selecting head and sanitise options 32, 110setting control plate creation source 111setting destination options 109

conducting a gridding routinecreating a filter design layout 147field patterns 147, 151gridding settings summary 155selecting barcode reading options 144selecting destination tray 152selecting head and sanitise options 146selecting stamping and inking options 153spot patterns 147

conducting a picking routinedeposit strategy 70edit destination microplate 70picking settings summary 73selecting barcode reading options 67selecting head and sanitise options 71setting destination options 69setting filter pairs 69setting picking source 72

conducting a rearraying routinecreating and editing a rearraying routine 133defining destination receptacle 137identifying source receptacle 135preparing for a rearraying routine 133selecting barcode reading options 134selecting head and sanitise options 138viewing rearraying progress 141viewing settings summary 41, 140

conducting a regional picking routineconfiguring destination microplates 89creating and editing a regional picking routine 86

defining destination and source options 91preparing for a regional picking routine 85selecting barcode reading options 87selecting head and sanitise options 92setting filter pairs 89setting your regional picking source 90viewing settings summary 94

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Index

conducting a sanitise 60conducting a UV sanitise 60confirming holder layout 138control plate creation progress, viewing 120control plate creation routine, conducting 108control plate creation routine, creating and editing 108

control plate creation settings summary, viewing 112

control plate creation source 111control plate creation source, setting 111control plate creation, preparing 107creating and editing a control plate creation routine 108

creating and editing a gridding routine 143creating and editing a picking routine 66creating sanitise profiles 61creating tags 162

Ddata search, conducting 159data viewer processes 42

adding annotations 164adding or deleting microplate properties 165conducting data search 159exporting processes 165exporting routines 165removing a tag 163search by barcode 160search by date 161search by location 161search by tag 160search by user 161viewing and printing settings details 161viewing locations maps 167working with sample trails 168working with tags 162

database management 42dates 161dates, searching by 161defining destination receptacle 137definitions

warning and wautions 9deleting a sanitise profile 63deposit strategy 70

destination microplate, editing 70, 110destination microplates, configuring 89destination options 91destination options window 25destination options, setting 109destination receptacle, defining 137destination tray, selecting 152destination window (rearraying) 39destination/source options window (regional picking only) 26

detination options, setting 69display icons 55display options tab 30, 81, 118display options, viewing 81, 118

Eediting sanitise profiles 61, 62electrical connections 174electrical safety 11electromagnetic compatibility 177EMC 177emergency stop 13

Ffeature counts tab 30, 80, 118feature selection window 29field patterns 147, 151filter design layout, creating 147filter layout window 152filter pair and barcodes 87filter pairs 67, 87filter pairs list 24filter pairs, setting 69, 89fluorescent light test image, creating

fluorescent light test image, regional picking 98

fluorescent only, filter pairs 89fluorescent test image window 29fluorescent test image, creating 77fluroescent light only 77

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Ggeneral precautions 9generate barcode list 68, 145generate random barcodes 68, 109, 145gridding progress, viewing 157gridding routine, creating and editing 143gridding settings summary, viewing 155gridding, conducting 143gridding, preparing 143

Hhead and sanitise options, selecting 138head and sanitise window 39head options 32, 71, 92, 110, 146head options, setting 128head window 36head/sanitise window 26health and safety 10holder layout - replicating, confirming 128, 154holder layout summary 74, 95holder layout summary window 22, 28, 34holder layout, confirming 138holders, arranging layout 74

Iinoculation heights 71, 110instrument dimensions 175instrument maintenance 9

Lload plates window 22, 30, 34, 36, 40loading plate holders 82, 119location 161location, adding tags 162location, searching by 161locations map, show 167locations maps, viewing 167

Mmaintenance

annual 55cleaning 12general 55general precautions 9instrument 9service 55weekly 55

manage sanitise profiles 43microplate and sanitise options 127microplate and sanitise options, setting 127microplate properties, adding and deleting 165microplates, loading 103microplates/sanitise window 35moving parts 12

Ppicking progress, viewing 82picking routine, completing 105picking routine, conducting 66picking routine, creating and editing 66picking routine, preparing 65picking settings summary, viewing 73picking source 72picking source, setting 72pin fire test 45, 49plate holders, loading 82, 119power-up procedures 51preparing for a control plate creation routine 107

preparing for a gridding routine 143preparing for a picking routine 65pre-power-up procedure 51procedures

power-up 51pre-power-up 51shutdown 52

processes, exporting 165

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Index

Rreading barcodes 134rearraying processes overview 38rearraying progress, viewing 141rearraying routine, creating and editing 133rearraying settings summary, viewing 41, 140rearraying source receptacle, identifying 135rearrraying routine, preparing 133receptacle, adding tags 162regional picking 85

display options tab 30regional picking destination and source options, defining 91

regional picking head and sanitise options, selecting 92

regional picking overview 24regional picking progress, viewing 104regional picking routine, creating and editing 86regional picking routine, preparing 85regional picking settings summary, viewing 94removable parts

head 57replicating process overview 35replicating routine, preparing 123replicating routine, saving 130replicating routing, creating and editing 124routine, adding tags 162routine, continuing or saving 81, 119, 156routine, rearraying 133routine, saving 103routines

aligning the camera 47changing the head 48pin fire test 49

routines window 19, 24routines, exporting 165running a control plate creation routine

continuing or saving routine 119control plate creation, running 113creating an image 114selecting colonies 116viewing display options 118viewing picking progress 120viewing selected colonies 118

running a gridding routinecontinuing or saving routine 156viewing picking progress 157

running a picking routinearranging layout of the holders 74completing routine 83continuing or saving routine 81creating a fluorescent test image 77creating a white light test image 75loading plate holders 82, 119selecting colonies 78viewing display options 81viewing picking progress 82viewing selected colonies 80

running a rearraying routineconfirming the holder layout 138

running a regional picking routine 95arranging holders 95completing picking routine 105creating fluorescent light test image 98creating white light test image 96loading microplates 103saving your routine 103selecting colonies 98viewing additional display options - regional picking 102

viewing progress 104viewing selected regional colonies 101

running a replicating routineconfirming holder layout 128, 154creating and editing a replicating routine 124preparing for replicating 123saving routine 130selecting barcode reading options 124setting head options 128setting microplate and sanitise options 127viewing settings summary 130

Ssafety

biological 12chemical 12electrical 11emergency stop button 13features 13health 10moving parts 12

186 5026152 A

Index

safety and health 10safety features 13sample trails, adding or removing 168sample trails, editing 168sample trails, viewing and deleting 168sample trails, working with 168sanitise options 32, 71, 92, 110, 146sanitise options, selecting 138sanitise profiles, creating 61sanitise profiles, deleting 63sanitise profiles, editing 61, 62sanitise window 46selected colonies, regional picking 101selected colonies, viewing 80, 118selected regional colonies, viewing 101selecting barcode reading options 124, 134selecting colonies 78, 98, 116selecting head and sanitise options, rearraying 138

service and maintenance 55setting head options 128setting source and destination receptacles 146setting summary window (replicating) 37setting up routines

conducting a sanitise 60conducting a UV sanitise 60creating and editing sanitise profiles 61deleting a sanitise profile 63editing a sanitise profile 62

settings details, viewing and printing 161settings summary - replicating, viewing 130settings summary window (picking) 27show locations map 167shutdown procedure 52single and multi-dipping, multi-dip, single and multi 70, 109

software overviewbarcodes window 19, 25camera alignment 44change head 45current and new processes 18data viewer processes 42database management 42destination options window 25destination window (rearraying) 39destination/source options window (regional picking only) 26

display options tab 30feature counts tab 30feature selection window 29filter pairs list 24fluorescent test image window 29head and sanitise window 39head window 36head/sanitise window 26holder layout summary 22, 28, 34instrument utilities 45load plates window 22, 30, 34, 36, 40manage sanitise profiles 43menu options 18micorplates/sanitise window 35navigation window 17pin fire test 45rearraying processes overview 38replicating process overview 35routines window 19, 24sanitise window 46settings summary (replicating) 37settings summary window (picking) 27source window 27source window (rearraying) 38standard and regional picking 24test image window 28UV santise window 46

source 90source and destination microplates and filters, setting 146

source options 91source receptacle, rearraying 135source window 27source window (rearraying) 38source, setting regional picking 90spot patterns 147stamping and inking options, selecting 153standard picking overview 24

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Index

substrate window 153

Ttags 160, 162, 163tags, creating 162tags, removing 163tags, searching by 160tags, working with 162technical assistance 179technical specifications 173

dimension of the instrument 175electrical connections 174

test image window 28test image, creating 114

Uusers 161users, searching by 161UV sanitise window 46

Vviewing and deleting sample trails 168viewing rearraying progress 141viewing rearraying settings summary 41, 140

Wwarning and caution definitions 9WEEE compliance 11white light test image, creating 75, 96white light test image, regional picking 96

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qpix 420 colony picking system user guide -...

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