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ONCORE™ Manual

Automated Slide Staining System

Biocare Medical

Technical Support: 800-799-9499 Option 3

Customer Service: 800-799-9499 Option 2

Fax: 925-603-8080

Corporate Office:60 Berry DrivePacheco, CA 94553

www.biocare.net

Introduction ............................................................................................................................................................................1

Intended Use ...................................................................................................................................................................1

About the ONCORE ..........................................................................................................................................................1

Instrument Specifications .................................................................................................................................................1

Warranty ..........................................................................................................................................................................1

Instrument Components ....................................................................................................................................................2

Description of Parts .................................................................................................................................................................4

Slide Chambers ................................................................................................................................................................4

System Door ....................................................................................................................................................................4

Reagent Rack and Reagent Vials ........................................................................................................................................4

Z-head ............................................................................................................................................................................5

Buffer and Waste Storage ..................................................................................................................................................5

Storage and Handling ...............................................................................................................................................................6

Reagents .........................................................................................................................................................................6

Instrument.......................................................................................................................................................................6

Waste Disposal .................................................................................................................................................................6

Instrument Disposal ........................................................................................................................................................6

Installation Site Requirements ..................................................................................................................................................7

Environmental Conditions .................................................................................................................................................7

Ventilation .......................................................................................................................................................................7

Venting (exhaust) ............................................................................................................................................................7

Humidity .........................................................................................................................................................................7

Temperature ....................................................................................................................................................................7

Support .................................................................................................................................................................................8

Safety Precautions ...........................................................................................................................................................8

Reagents and Chemicals ...................................................................................................................................................8

Instrument.......................................................................................................................................................................9

Programming Cautions ......................................................................................................................................................9

Warning Symbols ..............................................................................................................................................................9

System Installation ...............................................................................................................................................................11

Packing List ...................................................................................................................................................................11

Use after Installation ......................................................................................................................................................11

ONCORE System Software ......................................................................................................................................................13

Software Features & Functions .......................................................................................................................................13

Using the ONCORE Automated Slide Staining System Software ..........................................................................................13

Logging in to the ONCORE System Software .....................................................................................................................13

ONCORE System Software Home Screen ..........................................................................................................................13

Prepare Labels ...............................................................................................................................................................14

Load and Unload Slides ..................................................................................................................................................15

Auto Start ......................................................................................................................................................................15

Scan Slides ...................................................................................................................................................................16

Assign Protocols .............................................................................................................................................................16

Scan Reagents ...............................................................................................................................................................17

Clean Screen .................................................................................................................................................................18

Table of Contents

4

System Utilities - Tools .......................................................................................................................................................... 19

Baking Slides ................................................................................................................................................................ 20

Load Slide Map File ...................................................................................................................................................... 21

SP1-Z1 Calibration ........................................................................................................................................................ 22

SP1-Z2 Calibration ........................................................................................................................................................ 22

Barcode Calibration ....................................................................................................................................................... 22

Tubing Cleaning ............................................................................................................................................................ 23

Generate Reports .......................................................................................................................................................... 24

Initialize System ........................................................................................................................................................... 26

Check Heaters .............................................................................................................................................................. 26

Prime Pump Z1 ............................................................................................................................................................. 27

Prime Pump Z2 ............................................................................................................................................................. 27

Lock Door / Unlock Door ................................................................................................................................................ 27

Backup Report Data ..................................................................................................................................................... 27

System Utilities – Editors ...................................................................................................................................................... 28

Protocol Editor .............................................................................................................................................................. 28

DS2 (Dewax Solution 2) Option ..................................................................................................................................... 28

AR (Antigen Retrieval) Option ......................................................................................................................................... 29

Antigen Retrieval Temperature ....................................................................................................................................... 29

Antibody/Probe Incubation Time ..................................................................................................................................... 30

Antibody Incubation Temperature .................................................................................................................................... 30

Negative Control Editor .................................................................................................................................................. 30

Reagent Editor .............................................................................................................................................................. 32

RFID Editor .................................................................................................................................................................. 33

Custom Group Editor ..................................................................................................................................................... 36

Panel Editor .................................................................................................................................................................. 37

Change Protocol Template .............................................................................................................................................. 39

System Utilities - Security Tab ............................................................................................................................................... 39

System Utilities - Settings Tab ............................................................................................................................................... 41

Baking Slide Settings ................................................................................................................................................... 41

2D Barcode Format ..................................................................................................................................................... 42

Check Heater Settings ................................................................................................................................................... 44

Save All Customizations ................................................................................................................................................. 44

Get Device Version......................................................................................................................................................... 44

Baking Slides Before Staining ........................................................................................................................................ 44

Changing Software Text Language ................................................................................................................................... 44

System Utilities - Network Tab ....................................................................................................................................... 45

System utilities - LIM Tab .............................................................................................................................................. 45

ONCORE Maintenance .......................................................................................................................................................... 45

Recommended Tissue Placement Guidelines .................................................................................................................... 46

Daily Maintenance ......................................................................................................................................................... 46

Weekly Maintenance ...................................................................................................................................................... 47

Monthly Maintenance .................................................................................................................................................... 48

Quarterly Maintenance ................................................................................................................................................... 48

Semi-annual Maintenance .............................................................................................................................................. 48

Troubleshooting ................................................................................................................................................................... 49

Ordering Information ............................................................................................................................................................. 51

Terminology and Abbreviations ............................................................................................................................................... 52

1

IntroductionIntended Use

This manual is intended for laboratory personnel who utilize the ONCORE Automated Staining Instrument to perform immunohistochemistry

(IHC) or in situ Hybridization (ISH). The manual describes how to operate the instrument using the ONCORE System Software. This

manual assumes prior knowledge and training in basic IHC and ISH principles and procedures. For professional use only.

About the ONCORE

The ONCORE is Biocare Medical’s automated slide staining system designed to perform reliable and consistent IHC and ISH on

formalin-fixed paraffin-embedded (FFPE) samples attached to positively charged slides. This enables easy transfer of established

manual staining methods to an automated platform with minimal protocol optimization.

Instrument Specifications

Slide capacity 36 positions

Heating capacity Room temperature to 103° C

Reagent vial capacity 40 (15 or 7 mL vials)

Reagent dispense volume 200 μL

Waste separation 1 each of 2 liter containers for hazardous and non-hazardous waste

Slide compatibility

Thickness: 1mm ± 0.127 mm

Length: 75 mm maximum

Width: 25 mm ± 0.38 mm

LIS connectivity Compatible with XML and HL-7 messaging standards

Electrical requirements 100 - 240 VAC; 50/60 Hz; 875 W

Instrument dimensions (W x H x D)35 in x 22 in x 24 in / 84 cm x 56 cm x 61 cm (with door closed)

35 in x 36 in x 24 in / 89 cm x 91 cm x 61 cm (with door open)

Instrument weight 110 lbs / 50 kg

Not for use with flammable solvents or gases

WarrantyThe ONCORE warranty is for 12 months from the day of instrument installation and covers all parts and labor when system service is performed solely by

Biocare Medical. Warranty becomes invalid if equipment is abused, damaged, or improperly maintained by customer. The warranty is not transferable to

any other party should the equipment be resold or transferred to another party by the customer. To the extent permitted by law, Biocare Medical disclaims

any liability for any incidental or consequential damages related to this equipment or for any warranty related services performed by Biocare Medical.

2

Instrument Components

On Floor

1. System Door

2. Buffer Tubing and Carboy (on counter)

3. Hazardous Waste Tubing and Carboy (on floor)

4. Non-Hazardous Waste Tubing and Carboy (on floor)

5. On/Off Switch

6. Reagent Rack

7. RFID Reagent Vial Registration Position

8. Desktop Computer and Monitor

9. Label Printer

10. Report Printer

Not Shown: Keyboard, Mouse.

1. Instrument Label

2. Serial Number Label

3. Main Power Switch

4. Power Cord Receptacle

5. USB to Desktop Computer

3

Z - Head

1. Dispense Probe (Z1)

2. Extraction Probe (Z2)

3. Hazardous Station

4. Non-Hazardous Station

5. RFID System

6. 2D Matrix Scanner

2-Liter Waste Carboys

The 2-liter buffer carboy is positioned

on the left side of the instrument and is

connected using the quick disconnect

tubing connection included with the system.

The two 2-liter waste carboys are

positioned below the instrument in a

secondary waste container. Tubing is

color-coded: black for hazardous waste

and blue for non-hazardous waste.

1. Reagent Rack

2. RFID Reagent Vial Registration Position

3. Slide Chamber Module

4

Description of PartsSlide Chambers

The ONCORE Automated Staining System features heated slide modules and innovative staining chambers that secure the slides

firmly in a horizontal position at all times during the staining run. A total of 36 slide modules and staining chambers are present on

each ONCORE system. The staining chambers can be removed from the slide module lid for routine cleaning.

Each of the 36 Slide Chambers is comprised of a Slide Chamber Housing and a removable Slide Chamber. The Slide Chamber Port

is located in the top, center of the Slide Chamber. The Slide Chamber Housing sits on top of the black Slide Heater Plate. A flexible

silicone gasket seals the Slide Chamber Housing against the slide surface, preventing liquids from overflowing into the instrument.

During staining, the Slide Chambers agitate to ensure even distribution of reagent across the slide.

1. LED Indicators 2. Slide Chamber Module 3. Slide Chamber Housing4. Slide Chamber5. Slide Chamber Port 6. Slide Heater Plate (black)7. Slide Clips

System Door

The ONCORE System Door allows access to the work platform. The System Door locks at the start of staining run. It must remain closed

during the operation of the instrument as well as during any heating procedures such as Slide Baking or a Heater Check.

Reagent Rack and Reagent Vials

The instrument has one Reagent Rack that holds 40 Reagent Vials. Two sizes of Reagent Vials are available with capacities of 15 mLand 7 mL. The 15 mL ONCORE Reagent Vials are pre-filled with Biocare reagents (empty vials are not available for purchase).The 7 mL Improv™ Reagent Vials are available for purchase and can be used for primary antibodies obtained from an alternate vendor.

5

Z-head

The Z-head is mounted on the Y-arm that moves along the horizontal X and Y axes inside the work platform of the instrument.

The following are components of the Z-head:

1. Extraction Probe

The Extraction Probe, also known as Z2 in the ONCORE System Software, is a Teflon-coated stainless steel probe used to extract

reagents from the slide chamber. The probe is washed internally and externally before each new reagent is aspirated. There is no need

for disposable pipette tips.

2. Dispense Probe

The Dispense Probe, also known as Z1 in the ONCORE System Software, is a Teflon-coated stainless steel probe used to dispense

reagents and buffer into the slide chamber. The probe is washed internally and externally before each new reagent is aspirated. There

is no need for disposable pipette tips.

3. 2-D Matrix Scanner

The 2-D Matrix Scanner is an electrical device used for reading the 2-D Matrix Code on the Slide Label. The 2-D Matrix Scanner consists

of an LED that integrates the unique 2-D Matrix Code into the ONCORE System Software.

4. RFID System

The RFID System is responsible for reading and writing to the Reagent Vial RFID Tag. The RFID System reads the reagent vial RFID tag

during reagent check to confirm the reagent name as well as the number of tests remaining in the reagent vial. The RFID System writes

information to a new Improv Reagent Vial RFID tag while in the RFID Editor.

Buffer and Waste Storage

The ONCORE Buffer and Waste Carboys have volume estimation markings on the applied label. Use these markings to estimate the

amount of liquid currently inside of the carboys. Prior to the start of each run, the software will display estimates of the required volume

of wash buffer as well as the amount of waste the run is expected to generate. If there is insufficient wash buffer in the ONCORE

Buffer Carboy connected to the buffer inlet or insufficient space in the ONCORE Waste Carboys, please correct this condition before

continuing with the staining process. It is recommended to fill the ONCORE Buffer Carboy and empty the ONCORE Waste Carboys prior

to starting a staining run.

Two separate 2-liter carboys are provided for non-hazardous and hazardous waste. The actual amount of waste volume will depend on

the number of reagents used. Waste lines are attached to the Hazardous Station and the Non-Hazardous Station respectively and are

fed through the base of the instrument to the waste carboys. Waste flows to both waste carboys via gravity.

Warning! There is no alarm for waste overflow. Waste carboys should be checked before each run to ensure enough capacity is

available for the volume of waste potentially generated. Be sure to use the secondary waste container provided.

6

Storage and HandlingReagents

Always follow the manufacturer’s instructions for storage and handling of reagents. To prevent contamination, follow good laboratory

practices of sterile technique when opening, diluting, and decanting all solutions. Store Biocare reagents at 2-8°C unless otherwise

specified in the data sheets to maintain reagent stability.

Biocare offers pre-packaged kits, reagents and probes for the ONCORE Automated Slide Staining System.

See ‘Ordering Information’ section for materials and reagents required but not provided.

Instrument

Storage temperature: 10-40°C (50-104°F)

Transportation temperature: 0-50°C (32-122°F)

Waste Disposal

Some of the reagents used on the ONCORE Automated Slide Stainer may be hazardous, and must be disposed of properly in accordance

with local regulations. For a given reagent, determine if it is hazardous from the SDS sheet. The ONCORE Automated Slide Stainer is

programmed to separate waste streams for hazardous and non-hazardous waste. The carboy used for the hazardous waste stream is

marked “Hazardous Waste.” This carboy must only be used for hazardous waste in order to avoid increasing the volume of any hazardous

waste unnecessarily. If a reagent is known to be hazardous, it will be designated as such within the ‘Reagent Editor’. All hazardous waste

should be disposed of according to local, state, and federal regulations.

Instrument Disposal

If the ONCORE is to be removed from service and disposed of, the instrument must be disinfected using a 10% bleach solution through

the fluid delivery and waste systems and all exposed surfaces disinfected using Lysol® brand industrial cleaner before it is disposed of

in accordance with local, state and federal regulations.

7

Installation Site RequirementsCalibration and performance verifications are conducted prior to shipping. Biocare Medical field service personnel will unpack or

supervise the unpacking of the ONCORE. Biocare field service personnel will verify the system performance. Biocare personnel will also

provide basic operating instructions.

Note: The ONCORE Automated Slide Staining Instrument must be handled using the bottom of the side chassis by at least two people

capable of lifting 75 pounds each. Do not lift the ONCORE Instrument from the front access cover.

The ONCORE Automated Slide Stainer must be placed on a solid, vibration-free laboratory bench with a flat area capable of safely

supporting the weight of the instrument. Additional consideration must be made for the desktop computer, monitor, printers, a minimum

clearance of 5.0 cm (2 in.) on all sides for ventilation and 40.64 cm (16 in.) above the top surface of the instrument to accommodate

the door in the “up” or “open” position.

The label and report printers for the ONCORE Automated Slide Stainer may be located anywhere that allows them to be connected to

the ONCORE Automated Slide Stainer’s dedicated PC. Surge protection is required. The backup uninterruptible power supply (UPS)

should be placed on a surface capable of safely supporting its weight, away from liquids and within 1 meter of the instrument power

cord and within 1 meter of a properly grounded power outlet. The use of a dedicated circuit is recommended for the instrument. Avoid

connecting the instrument on the same circuit as refrigeration equipment.

Environmental Conditions

Placement Indoors

Operating temperature range 15-30°C (59-86°F). Recommended temperature for optimal staining 68-75°F

Maximum programmable heater temperature 110°C (230°F). See Protocol Editor Section for recommendations.

Maximum relative humidity 80%, non-condensing.

Ventilation

Do not block the vent openings on the instrument. Leave a minimum of 5 cm (2 in.) of space between the ONCORE Automated Slide

Stainer and the wall, cabinets or other obstructions.

Venting (exhaust)

The instrument does not need special exhaust ventilation unless required by safety regulations when using certain reagents.

Humidity

Avoid humidity extremes. Low humidity can cause electrostatic problems that may affect the computer. High humidity may create

condensation.

Temperature

The ONCORE Automated Slide Stainer must be placed in a location away from direct sunlight and extreme heat or cold.

8

Support To contact Biocare Medical Technical Support by telephone, please call 1-800-799-9499, Option 3.

You may also email Technical Support at [email protected] or submit a message online at www.biocare.net.

Safety Precautions

The ONCORE is designed for use with FFPE. Use only tissue sections that have been fixed in a biocidal/virocidal/fungicidal fixative.

Infectious sample use is limited to tissues/specimens that are specified on Biocare’s product data sheets. Handle control slides and test

FFPE slides as if capable of transmitting infectious agents and dispose with proper precautions. It is recommended that the specimens

are handled using established good laboratory practices.

Observe the following precautions to ensure your personal safety and to prevent damage to either the instrument or to the equipment

connected to it. Failure to observe these precautions may result in improper operation of the instrument and/or personal injury.

Internal Access and Unauthorized Adjustments

There are no user serviceable parts within the instrument. Avoid a shocking hazard or mechanical trauma by not attempting to gain

access (by means of any tool) to any internal parts of the instrument. Use of controls, adjustments, or performing procedures other

than those described in this document may result in hazardous electrical shock, mechanical trauma, or damage to the instrument.

Power Source

The instrument operates from an AC power source as specified in the Instrument Specifications (100 - 240 VAC; 50/60 Hz; 875 W).

Main supply fluctuations must not exceed ± 10% or contain undue amounts of noise. A protective ground connection (through the

grounding conductor of the power cord) is essential for safe operation of the system.

Operate the power switch located on the rear of the instrument to power off the ONCORE Automated Staining System if there is ever

any question as to whether the instrument is operating safely.

Grounding the Instrument

The instrument is grounded through the power cord. To avoid electric shock, plug the power cord into a properly wired receptacle with

an earth-ground connection. Do this before making other connections to the ONCORE Automated Staining System rear panel.

Operating the Instrument

This device is designed to be operated on a level bench top in a laboratory environment and should not be moved during operation.

If moving the instrument is required, all carboys and peripheral device should be detached. Do not move the instrument without the

expressed consent of Biocare Medical or without the assistance of a Biocare Representative.

Reagents and Chemicals

Some of the reagents and chemicals recommended by Biocare for use on the ONCORE are hazardous. They must always be used

according to the manufacturer’s instructions and good laboratory practices. Always wear gloves, eye protection and a protective lab coat

when handling any chemical solution used on the ONCORE Automated Slide Stainer and when cleaning the equipment or emptying

waste carboys. Obtain a Safety Data Sheet (SDS) from the manufacturer for each chemical constituent. Do not use any flammable

chemicals on the ONCORE Automated Slide Stainer. Danger from hazardous fumes, fire or explosion may result with the possibility

of injury to the operator or damage to the instrument. Maintenance and cleaning procedures may recommend the use of flammable

chemicals.

9

Instrument

Use only the authorized software program that is supplied with the instrument or authorized updates.

Do not install any other software applications onto the ONCORE dedicated computer system. This may cause unexpected operation of

the ONCORE Automated Slide Stainer or corruption of the operating software and will void the warranty.

Do not switch off the power to the computer unless necessary until the ONCORE System Software is properly closed. It is recommended

to shut down the software and the computer once a week for optimal use.

Do not switch off the power to the ONCORE Automated Slide Stainer until all motion has stopped, the robotic arm is in the home

position and the software has been exited.

During a staining run, the front door of the instrument must be closed before staining operation will begin.

Keep Buffer Carboy level with the instrument. Keep Waste Carboys below the level of the instrument. Make sure that Waste Tubing

does not contain kinks or other obstructions. Proper cleaning is important for the reliable operation of the instrument. Follow the

recommended cleaning procedures in the ONCORE Maintenance Section. Make sure that the robotic arm is stopped before opening

the instrument door.

Programming Cautions

Errors in programming staining protocols will likely cause false positive or false negative results. If such errors occur, check the

programming first.

10

Warning SymbolsThe following symbols may appear on the instrument and instrument labeling:

Power

Distributed By

Consult Instructions for Use (consult operating instruction)

Consult Accompanying Documents

In-Vitro Diagnostic Medical Device

Serial Number

Authorized Representative European Community

CE Marking

Manufacturer

11

System Installation Packing List

Ensure that the ONCORE Automated Staining System was received in good condition and includes all of its component parts. The

ONCORE Automated Staining System includes the following components:

� ONCORE Automated Slide Stainer

� 1 USB cable & 1 power cord

� Reagent Rack

� 3 2-liter carboys with caps (1 with quick-disconnect)

� 2 separate tubings (black for hazardous, blue for non-hazardous)

� Desktop computer and monitor with ONCORE System Software

� Label printer

� Report printer

� Uninterruptible power supply

Use after Installation

ONCORE Slide Stainer must be level.The USB-AB cable must be connected to the back of the instrument:

The power cable must be connected to the back of the instrument:

12

The power cable must be connected to the back of the computer. The USB-AB cables from the instrument, the label printer and the

report printer must be connected to the back of the computer. The USB cables from the keyboard and the mouse must be connected

to the back of the computer. The VGA cable from the monitor must be plugged into the back of the computer.

The power cables from the instrument, the computer and the monitor must be connected to the UPS. The UPS must be plugged into

the wall. The power cables from the label printer and the report printer must be plugged into the power strip. The power strip must

be plugged into the wall.

Quick-disconnect

Tubing connection

2-Liter buffer carboy

Hazardous waste

(color-coded black)

Non-hazardous waste

(color-coded blue)

The 2-liter buffer carboy is positioned on the left side of the instrument and is connected using the quick disconnect tubing connec-

tion included with the system.

The two 2-liter waste carboys are positioned below the instrument in a secondary waste container. Tubing is color-coded: black for

hazardous waste and blue for non-hazardous waste.

13

ONCORE System SoftwareSoftware Features & Functions

This chapter is intended to familiarize you with key software features and provide details of the software utilities available to both

Supervisor and Technician level users.

Using the ONCORE Automated Slide Staining System Software

The ONCORE System Software is used to prepare labels, load and unload slides, start a run and access System Utilities and Reports.

Logging in to the ONCORE System Software

Double click the ONCORE System Software Icon from the desktop and the software will display the Login Screen. Type in the User

ID and Password (which are case sensitive). Click the ‘Enter’ button.

ONCORE System Software Home Screen

The Home Screen will appear after successful login. There are eight function buttons located across the top of the Home Screen. The

three buttons to the left of the Date and Time feature are used in order from left to right to start a run. The five buttons to the right of

the Date and Time feature are optional functions and are not needed to start a run. There is also an exit button found at the extreme

right that closes the Home Screen and, when selected, returns the user to the Login Screen.

14

Prepare Labels

The Prepare Labels Module allows the user to enter the pertinent slide information prior to printing the slide labels.

To use this feature select the ‘Prepare Labels’ button found along the top menu of the Home Screen. The ‘Slide Label Editor’ window

will open.

In the ‘Slide Label Editor’, from the drop down menu the user may choose to prepare labels for new slides or to recall information

previously entered from printed, scanned, or processed slides.

The menu provides the following options: ‘New Slides’, ‘Printed Slides’, ‘Scanned Slides’, and ‘Processed Slides’.

� ‘New Slides’ is utilized to create new slide labels.

� ‘Printed Slides’ will recall slide label information for labels that have been previously printed but not scanned or processed.

� ‘Scanned Slides’ will recall slide label information for slides that have been printed and scanned but not previously processed.

� ‘Processed Slides’ will recall slide label information for slides that have previously completed the staining process.

Recalled information may be sorted by selecting the column headings within the ‘Slide Label Editor’. Select the labels that you would

like to print by checking the box located between the No. and Patient ID columns. Then select the ‘Print’ button.

To enter information for new slides select the ‘New Slide’ option in the drop down menu within the ‘Slide Label Editor’. Then click the

‘Add’ button. This will open the ‘Barcode Editor - Add’ window.

Within the ‘Barcode Editor - Add’ screen, enter the appropriate case information. NOTE: Protocol (Antibody), Patient ID, Case Number,

Date, Hospital and Description fields will print on the Slide Label. Block ID, Specimen Type and Doctor fields do not print on the

label. Include both Case Number and Block ID in the Case Number field in order to print the Block ID on the label. Label Example:

LCAPatientCase01/14/2014HospitalDescription 1/2

15

Choose from the ‘Custom Group’ drop down to order an Antibody Protocol from a Custom Group of Available Protocols.*

Select the desired Protocol from the list of Available Protocols. If a Positive Control or a Negative Control for that Protocol is desired,

check the box to the left of ‘Positive’ or ‘Negative’ in the ‘Add With:’ box. Then click the ‘Add’ button. The desired Protocol along with

any desired Positive or Negative Controls will be added to the Selected Protocols field. Note: Do not click the ‘Return’ button prior to

clicking the ‘Add’ button or all currently entered information will be lost.

Select the desired Panel from the list of Available Panels and click the ‘Add’ button. A Panel is a list of previously selected Protocols

and Positive and Negative Controls. Since Panels include Positive and Negative Controls, this feature is inactive.*

If a Protocol or Control is no longer desired, then simply select from the Selected Protocols field and click the ‘Remove’ button.

Once all Protocols have been selected for the current Case, click the ‘Save’ button. Repeat the process of entering case information,

adding protocols and clicking ‘Save’ until all desired slide labels have been created. When finished, click the ‘Return’ button to return

to the ‘Slide Label Editor’.

To delete a Slide Label, select the label that you would like to delete by checking the box located between the No. and Patient ID

columns. Then select the ‘Delete’ button.

To print Slide Labels, select the labels that you would like to print by checking the box located between the No. and Patient ID columns.

Then select the ‘Print’ button. If all Slide Labels listed are desired, check the ‘Select All’ box and click the ‘Print’ button.

Slide Labels will print on the Slide Label Printer. Adhere labels to appropriate slides.

Load and Unload Slides

The ‘Load and Unload Slides’ button raises or lowers all 36 Slide Chambers simultaneously. Following instrument initialization, all

36 slide chambers will be in the “down” or “closed” position. When the slide chambers are in the up position, the ‘Load and Unload

Slides’ button will change to ‘Slide Lids Down’.

Load slides in the desired slide chambers with the label oriented towards the front of the instrument. Make sure that the slide is fully

seated with the label end locked in place by the clips. Align the slide with the slide chamber. The slide should not hang off the side

of the slide chamber. Once all of the slides have been loaded, click the ‘Slide Lids Down’ button. The user should be able to see the

slide label if slides have been loaded correctly.

Note: Preferred slides should not have print/markings under the Slide Chamber edges or port to facilitate sealing of the Slide Chamber to the slide and to prevent generation of paint debris, which may appear as black debris on the stained slide. Slide Compatibility: Thickness: 1mm ± 0.127 mm | Length: 75 mm maximum | Width: 25 mm ± 0.38 mm

Auto Start

The ‘Auto Start’ feature instructs the instrument to automatically scan the loaded slides, verify the loaded reagents, and begin the run.

Note: Be sure to check the boxes for buffer and waste volume.

After loading the bar-coded slides on the instrument, left click on each chamber containing a loaded slide and click the ‘Auto Start’

button. The mouse function of left-clicking and dragging is also available for use here. The user will then be prompted by the software

to designate the number of slides to be scanned for the immediate run. After entering the number of slides, click the ‘OK’ button.

Remain at instrument until the run begins, or check back after 10 minutes to ensure the run has started.

Note: The following function buttons are optional and are not necessary to perform a staining run.

*Custom Groups and Panels must be previously set up for the 'Custom Group' Function and Panels to be available for use.

16

Scan Slides

The ‘Scan Slides’ button can be used to activate the ‘Scan Slides’ feature of the ‘Auto Start’ function independently. Note: If this option

is chosen, the ‘Scan Reagents’ feature will not start automatically once slides are scanned. See ‘Scan Reagents’ section of the manual.

Assign Protocols

‘Assign Protocols’ allows the user to manually assign protocols to loaded slide chambers instead of utilizing the ‘Scan Slides’ feature.

To use this feature, first select the position on the software slide map, and if the user would like to run the same protocol in several

positions they may select positions individually or click and drag the mouse over the desired slide positions.

With the desired slide position(s) highlighted, a user must then click on the ‘Assign Protocols’ button. The ‘Select Protocol’ window

will appear. The top of the window gives the user three options to select Protocols: Normal, Negative or All.

Choosing ‘Normal’ displays all existing Protocols in the system but does not display Negative Controls. There is no distinction between

a Protocol and a Positive Control.

Choosing ‘Negative’ displays only Negative Controls for all Protocols in the system.

Choosing ‘All’ displays all existing Protocols in the system as well as all Negative Controls.

A user would then select which Protocol they would like to assign to the position(s) from the available options offered within the ‘Assign

Protocols’ window and repeat this process until all slides are programmed. If the same Protocol is desired in multiple positions, a user

would first select all of the slide positions and then select the Protocol to be assigned to all of the positions.

17

To unload or clear an assigned Protocol within an assigned position, first click once on the position to remove the Protocol, and then

click a second time to unselect the position. A user can select multiple positions or clear multiple positions by clicking the left mouse

button and dragging across the desired positions of the slides to be loaded/unloaded. Alternatively, a user may also click the ‘Clean

Screen’ button located on the ‘Home Screen’ to clear all positions.

Scan Reagents

Warning! Remove caps from all reagent vials and properly seat the reagent rack in the ONCORE stainer to avoid the RFID antenna crashing into the vials and damaging the ONCORE system.

The ‘Scan Reagents’ button can be used to activate the ‘Scan Reagents’ feature of the ‘Auto Start’ function independently.

A list of required reagents may be printed by clicking "Print Required Reagents." Selecting the ‘Scan Reagents’ button will automatically

open the ‘Reagent Check’ screen. Click the ‘Scan Reagents’ button within the ‘Reagent Check’ screen and the instrument will scan all

40 positions. If all reagents required for completing the staining run are found before all positions are scanned, scanning will cease

as no additional scanning is necessary.

Check the boxes for buffer and waste volume after visually confirming that enough buffer is present and that enough room is available

in the waste bottle. It is recommended to completely fill the buffer and completely empty the waste before each run.

Click ‘Start Staining Process’ to begin the staining run.

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Alternatively, click the ‘Delay Start Staining Process’ button to delay the run. The ‘Delay Start Slide Staining’ window will open. Enter

the date and time corresponding to the desired run completion date and time. Click the ‘OK’ button.

A ‘Slide Staining Process Start Time’ window will then display indicating when the run will begin as well as the ‘Time Left To Start’

countdown. Once the countdown completes, the staining run will begin.

If desired, the ‘Return to Main Screen’ button can be utilized to return to the Main Screen and abort the starting of the run.

Note: The ‘Load Reagent Map File’ is not available for use.

Clean Screen

Upon completion of a staining run, click the ‘Clean Screen’ button to clear all slide positions and start a new run.

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System Utilities - ToolsThe ‘System Utilities’ Module contains several features that allow the user to bake slides, clean the tubing, access reports and

test the heaters. Upon clicking the ‘System Utilities’ button, the user may select from the following tabs: Tools, Editors, Security,

Settings, Network and LIM.

Note: A user logged in under a “Technician” security level will be blocked from accessing certain settings within ‘System Utilities’ as

noted below.

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Baking Slides

� Users may use the ONCORE automated staining platform to perform the necessary baking of slides prior to initiating an IHC or

ISH protocol. When a user selects this option within the ‘Tools’ menu a ‘Baking Slides’ window will appear.

� The slide chambers will automatically move to the “open” position when selecting this option. After loading all slides to be baked,

select the positions where the slides are located and click the ‘Start’ button. Slide lids should be open during this function.

� The timer will count down the pre-selected time to completion.

� A user may cancel the baking process at any time during the countdown by selecting the ‘Stop’ button.

� The completion of the baking process will be indicated by a separate pop-up information window.

� To change the settings for the ‘Baking Slides’ feature, refer to the ‘Settings’ tab within the ‘System Utilities’ Module. The

recommended temperature and time setting is 60°C for 30 minutes.

� It is also possible for the system to automatically bake the slides at the beginning of a staining run. See ‘Baking Slides Before

Staining’ section for more information.

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Load Slide Map File

� Note: Only accessible under ‘Supervisor’ level security log-in.

� This function allows the user to recall slides from a previous run without having to re-enter the case/slide information.

� To utilize this feature click the ‘Load Slide Map File’ button within the ‘Tools’ tab.

� The “Windows Explorer” window will appear displaying all previously completed runs.

� The format of the run files will be displayed as follows:

� RunSet-2013-05-01-03-15-End

� The user will then find the run they wish to recall by date and time.

� They must then select the “Start” version of that RunSet and click the ‘Open’ button located at the bottom of the “Windows

Explorer” window.

� This will automatically import the slide information to the positions on the home screen that was originally loaded in the

previous run.

� Note: When using this feature the software will not allow the user to generate labels or rescan the slides for verification. It is

the user’s responsibility to ensure the slides are loaded in the appropriate positions.

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SP1-Z1 Calibration

� The proper probe position should be centered on the X-axis and close to the posterior of the Y-axis of the port as illustrated below:

� Do not use this feature. Reserved for Biocare field Service Engineer.

SP1-Z2 Calibration

� Do not use this feature. Reserved for Biocare field Service Engineer.

Barcode Calibration

� Do not use this feature. Reserved for Biocare field service engineer.

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Tubing Cleaning

� This function performs a cleaning of the tubing to clear any possible residual build up that may accumulate during the staining process.

� It is required to perform the Tubing Clean after every 150 staining runs or no less than every six months. It is recommended

that Tubing Cleaning be performed every 3 months for optimal performance.

� Upon clicking the ‘Tubing Clean’ button within the ‘Tools’ menu the ‘Tubing Clean’ window will appear.

� Follow the instructions as prompted by the ‘Tubing Clean’ window and click ‘OK’.

� Alternatively, if you wish to exit the Tubing Clean function, you may select ‘Cancel’.

� Please refer to the ‘Maintenance’ Section for complete details on the procedure.

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Generate Reports

� This function allows access to the ONCORE Report Generator.

� Click the ‘Generate Reports’ button to open the Report Generator.

� Choose a report from the menu on the left, select the desired report from the drop down menu on the right and click the ‘Generate

Report’ button.

� Note: Do not open reports program from desktop during a run.

Report Type Description

Protocol ValidationProvides a report for a protocol indicating all of the steps performed, a sign-off section, and a comment section.

Slide Layout MapProvides a graphical description of the slide positions for a previously processed run. Each slide position includes Case, Block, Protocol Name and Antibody Name (fields are configurable).

Reagent Layout MapProvides a graphical description of reagent vials in the reagent rack for a previously processed run. Each reagent includes Catalog #, Reagent Name, Lot, and Starting Volume (fields are configurable).

IHC Summary Provides the following for a specified run: reagent details including Position, Name, Catalog #, Lot, Exp, Tests Used and Tests Remaining; slide details including Position, Case, Block, Protocol Name; a Comments/Sign-Off section for the Pathologist.

IHC Report (by Run)Provides the following for a specified run: slide details including Position, Case, Block, Protocol Name and each step of the protocol; reagent details including Step Name, Reagent Name, Incubation, Lot, Exp.

ISH Report (by Run)Use IHC Report Template

Provides the following for a specified run: slide details including Position, Case, Block, ProtocolName and each step of the protocol; reagent details including Step Name, Reagent Name, Incubation, Lot, Exp.Probe

Slide Report

Provides the following for a previously stained slide: Date of Run, Instrument Serial #, Operator, Position, Case, Block, Protocol (and all steps including Reagent Name, Incubation, Lot, Exp) as well as a Comment section. Requires scanning of the slide barcode to recall information. (Requires handheld scanner.)

Reagent Usage (by Run)Provides the following reagent information for a specified run: Position, Reagent Name, Catalog #, Lot, Exp, Tests Used and Tests Remaining.

Reagent Usage (by Name)Provides the usage information of a specified reagent for all runs performed on the instrument and includes: Date of Run, Run#, Lot, Exp, Tests Remaining and Tests Used.

Reagent Usage (by Date)Provides a list of all reagents used during a specified date range and includes the following: Reagent Name, Catalog #, Lot, Exp, Tests Used and Tests Remaining.

Slide Count by Protocol Provides a slide count for each protocol

Slide Count for a Date Range Provides a slide count for a desired date range.

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� All reports can be exported or printed by utilizing that option while a report is displayed.

� Click the Tools Menu to ‘Import Data Files’, ‘Set Default Report’ or ‘Configure Report Fields’.

� Clicking ‘Import Data Files’ will import all data files for all runs performed on the system. This action occurs automatically

upon Report Generator launch and should not be necessary.

� Clicking ‘Set Default Report’ will open the ‘Set Default Report’ window. Choose desired default report. The Default Report

will be displayed when the Report Generator is invoked from the ‘Run Completion’ window.

� Clicking ‘Configure Report Fields’ will open the ‘Setup Report Fields’ window.

� If 'Slide Layout Map' is selected, four fields may be configured and saved. These fields will print on the Slide Layout Map

Report. Each field can be printed in either Bold or Regular font.

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� If 'Reagent Layout Map' is selected, four fields may be configured and saved. These fields will print on the Reagent Layout

Map Report. Each field can be printed in either Bold or Regular font.

� If 'IHC Summary' is selected, user may choose to either show reagents on the IHC Summary by selecting ‘True’ or not show

reagents (and only show slides) by selecting ‘False’.

Move Arm Aside

� Selecting this button moves the z-head to slide position 6/7 and out of the way of the reagent rack.

Initialize System

� Selecting this button will run the instrument through a series of calibration checks and priming as well as moving the

Z-head to its home position.

Check Modules

� This function allows the user to verify the operation of the heating pads within the slide chamber modules and that the

motion of the chambers is working.

� Make sure to load blank slides in all slide chambers before performing this function.

� Select the ‘Check Modules’ button. Slide Lids will close.

� The user will then be prompted via an information window to close the door to the instrument.

� After closing the instrument door, click the ‘OK’ button.

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� The software will then display a ‘Heater Check’ window with a countdown timer of 20 minutes.

� Upon completion of the check, the software will display an indication if all heaters are functioning properly or alert the

user to a possible faulty module.

Prime Z1 and Z2

� This feature allows the user to manually prime the Z1 (dispense) prove and Z2 (extract) probe in one click. Upon

clicking this button, the system will prime the Z1 pump and Z2 pump five times each. This feature is designed to be used

when the system is set up for the first time or when checking the system before a run.

Prime Pump Z1

� This feature allows the user to manually prime the Z1 (dispense) probe.

Prime Pump Z2

� This feature allows the user to manually prime the Z2 (extract) probe.

Lock Door / Unlock Door

� This button allows the user to manually actuate the door lock to either the “locked” or “unlocked” position. The button is

not available during a run

Backup Report Data

� Do not use this feature. Reserved for future use.

Replace Pump1 Syringe


Replace Pump2 Syringe

� Do not use this feature. Researved for future use.

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System Utilities – Editors

Protocol Editor


� The ‘Protocol Editor’ window displays all protocols currently programmed into the software. The protocols are separated

into groups by detection system. A user may toggle between the different protocol templates by selecting their respective

tabs found at the top of the ‘Protocol Editor’ window.

� The ‘Protocol Editor’ allows the user logged-in under the “Supervisor” setting only to alter 5 parameters within programmed

protocols.

� Note: Some features in the Protocol Editor are reserved for future use.

DS2 (Dewax Solution 2) OptionTo allow for the substitution of the DS2 component of the deparaffinization kit with Buffer, an Enzyme or a Block.

� Some antibodies are sensitive to a component of DS2. In this instance, DS Buffer may be desired instead.

� If an antibody requires enzyme digestion before antigen retrieval, then DS Enzyme would be desired.

� If an antibody requires a block before antigen retrieval, then DS Block would be desired.

� It is recommended to consult a Biocare representative if making changes to the DS2 setting.

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AR (Antigen Retrieval) OptionTo allow for selection of different antigen retrieval solutions (AR1, AR2, AR3 or for the substitution of antigen retrieval with Buffer,

an Enzyme or a Block.

� AR1 is a high pH solution.

� AR2 is a low pH solution.

� AR3 is specific to ISH.

� Some antibodies do not require antigen retrieval. In this instance, AR Buffer would be desired.

� Some antibodies require enzyme digestion instead of antigen retrieval. In this instance, AR Enzyme would be desired.

� If an antibody requires a block and does not require enzyme digestion or antigen retrieval, then AR Block would be desired.

� Be sure to adjust the corresponding Temperature adjacent to the AR Option column to the desired temperature. See Antigen

Retrieval Temperature section below.

� It is recommended to consult a Biocare representative if making changes to the AR setting.

Antigen Retrieval Temperature

� Be sure to adjust the corresponding Temperature adjacent to the 'AR Option' column to the desired temperature.

� The standard temperature for Antigen Retrieval is 101°C.

� The low temperature for Antigen Retrieval is 95°C.

� A temperature above 103°C is not possible.

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Antibody / Probe Incubation Time

a. The default antibody incubation time is 30 minutes.

b. ISH probe incubation times range from one to four hours, depending on the Template chosen.

Antibody / Probe Incubation Temperature

a. The standard antibody incubation temperature is 25°C (ambient).

b. The maximum antibody incubation temperature is 37°C to avoid reagent evaporation.

c. Probe hybridization temperatures vary, depending on the template chosen.

d. CISH RNA do not require a denaturation step, and typically hybridize at 55°C.

e. CISH DNA protocols include a 95°C denaturation step, typically followed by a 40°C hybridization step.

� After making changes to protocols, the user must then click the ‘Save’ button located at the bottom of the ‘Protocol Editor’

window to save the changes.

� To delete a protocol a user must first select the protocol by clicking the column to the far left and then select the ‘Delete’ button.

Upon clicking ‘Delete’, the software will ask for confirmation before permanently deleting the protocol.

� Click on 'Go Back to Manufacturer Default' to revert to Manufacturer Default Protocols. The sofware will ask for confimation.

� To revert a protocol back to the last instance where the ‘Save All Customizations’ button in the ‘Settings’ tab was utilized, select

the protocol to be modified by clicking in the column to the far left and then click the ‘Refresh Protocols with customizations’ button.

� Click 'Display current protocol version' to display current version of protocol.

� Changes that have not been “saved” may be cancelled by clicking the ‘Cancel’ button.

� To close Protocol Editor, click the ‘Return’ button.

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Negative Control Editor


� The system automatically creates a duplicate protocol for each Protocol in the database and assigns the “Universal Negative

Control Serum” in place of the antibody to create a Negative Control protocol. When a Negative Control is ordered for a Protocol,

the system runs an identical protocol except it substitutes the negative control serum assigned in the Negative Control Editor.

� The ‘Negative Control Editor’ allows users to assign specific negative control serums to existing Protocols in the database.

� To utilize this feature, click the ‘Negative Control Editor’ button in the ‘Editors’ tab within ‘System Utilities’. This will cause the

‘Negative Control Editor” window to appear.

� The ‘Negative Control Window’ is divided into two main fields:

� Protocols: List of all of the active protocols programmed within the database.

� Negative Control: List of all of the possible negative control serum options.

� To clear selections that are currently highlighted:

� Click ‘Clear Selected Protocols’ and/or click ‘Clear Selected Negative’.

� No permanent changes occur with this function.

� To confirm the current negative control for a protocol:

� Click on a protocol from the ‘Protocols’ field.

� With the selected protocol highlighted, click the ‘Show Links to Negative’ button.

� This will highlight the negative control serum assigned to that protocol.

� To confirm which protocols are assigned to a particular negative control:

� Click on a negative serum within the ‘Negative Control’ field.

� With the negative control serum highlighted, click the ‘Show Links to Protocols’ button.

� This will highlight all of the protocols that are linked to that negative control serum.

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� To reset all Negative Control protocols to the manufacturer default of ‘Universal Negative’:

� Click the “Reset” button found at the bottom of the ‘Negative Control Editor’ button.

� A confirmation window will appear. To accept, click the ‘Yes’ button. To return to the ‘Negative Control Editor’ without

making any changes, click the ‘No’ button.

� To change the assigned Negative Control for a protocol:

� Select both the protocol and negative control serum you would like to use in creating a negative control protocol.

� With both the protocol and negative control serum highlighted, click the ‘Save’ button.

� To close ‘Negative Control Editor’, click the ‘Return’ button.

Reagent Editor


� The ‘Reagent Editor’ allows the user to add or delete primary antibodies and probes (and their associated protocol within the

protocol database).

� Within the ‘Reagent Editor’ Window the user will see two fields: ‘Reagent Types’ and ‘Reagents’.

� The ‘Reagent Types’ field lists all of the preprogrammed protocol templates and designates them by detection system. After

selecting a designated protocol template in the ‘Reagent Types’ field, the primary antibodies or probes programmed under that

particular template will be displayed in the ‘Reagents’ field.

� To add a new primary antibody or probe:

� A user must first select/highlight the appropriate protocol template they would like to assign to that primary antibody or

prober within the ‘Reagent Types’ field.

� Then click the ‘Add New’ button at the bottom of the window. This will activate the ‘Name’, ‘Viscosity Level’, ‘Protocol

Name’, and ‘Hazardous’ fields.

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� The user will then populate the ‘Name’ field with the name of the primary antibody or probe. This will simultaneously

transfer the same text into the ‘Protocol Name’ field.

� If user would like to change the text within the ‘Protocol Name’ field to something other than the name entered

for the primary antibody or probe. They may do so by clicking in that window and modifying the text.

� All antibodies are classified as Viscosity Level 1. All CISH probes are classified as Viscosity Level 2. For FISH probes, use

Viscosity Level 4.

� If the reagent is classified as hazardous, the user can designate it as such by selecting the “Yes” check box. This should

not be necessary for antibodies.

� All probes should be loaded as ‘ready to use’.

� Once satisfied with the information entered, the user may then click the ‘Save’ button to save the addition.

� To delete a primary antibody or Probe:

� A user must first select/highlight the appropriate protocol template under which the protocol resides within the ‘Reagent

Types’ field.

� Then select/highlight the actual protocol itself (usually designated by primary antibody or probe name) within the

‘Reagents’ field.

� With the protocol highlighted the user will then click the ‘Delete’ button located at the bottom of the ‘Reagent

Editor’ window.

� A confirmation window will open. Click ‘Yes’ to permanently delete. Click ‘No’ to cancel.

� Click the ‘Return’ button to close ‘Reagent Editor’.

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RFID Editor


� The RFID Editor allows a user to verify information in the RFID Tag of a reagent vial or encode the RFID tag of an Improv (user

fillable) vial with the pertinent user-provided information.

� To encode (or write) information to an Improv vial:

� Follow the vial preparation instructions on the Improv vial data sheet to prepare for use.

� Load the Improv vial to be encoded in the RFID Reagent Vial Registration Position (in between Reagent Vial #40 and

Slide Chamber #25).

Reagent Vial Slide Chamber #25

� Select ‘RFID Editor’ within the ‘Editors’ tab in the ‘System Utilities’ window.

� This will open the ‘RFID Tag Editor’ window.

� The ‘ONCORE Tag Editor’ window has two columns of information fields on either side with the field titles located in the middle.

RFID Reagent Vial

Registration Position

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� The column on the left side will display the information currently coded into a particular reagent vial RFID tag when read by the RFID

Reader and the column on the right side contains the fields utilized by a user to enter information to be coded to the RFID tag.

� The user will enter information either manually or using the provided drop down menus within the column on the right.

� After entering all of the information, the user will then click the ‘Write Tag’ button to encode the information into the loaded

Improv vial.

� To confirm that the Tag was written to correctly, click the ‘Read Tag’ button.

� The RFID tagged Improv Reagent Vial is now ready for use.

� Notes:

� Only user created reagents are available for writing to the Improv Reagent Vial RFID Tag

� Only 7mL Improv Reagent Vials are available for use

� Recommended ‘Storage Temperature’ is 2-8°C

� Do not use the ‘Configure RFID’ button. Contact a Biocare Representative.

� To add a new Manufacturer to the Manufacturer Name drop down menu:

� Click the Manufacturer Name drop down menu and choose ‘---Add or Remove---’

� The ‘Add Manufacturer Information’ window will open

� Enter the new Reagent Manufacturer in the ‘Company Name’ field

� Click the ‘Add’ button

� The window will close and the new Manufacturer will be ready for use

� To Delete a Manufacturer:

� Follow the same procedure

� Choose the Manufacturer that you wish to delete from the drop down menu in the ‘Add Manufacturer Information’

window and click the ‘Delete’ button. Click the ‘Return’ button to close the window.

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Custom Group Editor

In the ONCORE System Software, users may create Custom Groups of protocols that are commonly used. The creation of a Custom

Group will expedite the process of finding frequently used protocols from the complete list of antibodies/protocols. Panels may then

be used as a shortcut to add multiple protocols to a case at one time. This feature can then be utilized when creating Slide Labels

in Slide Label Editor.


� To utilize the Custom Group Editor, click the ‘Customer Group Editor’ button within the ‘Editors’ tab in ‘System Utilities’.

� The ‘Edit Custom Groups’ window will open.

� At the top of the window is a drop down menu listing all of the created Custom Groups.

� The field on the left lists all of the ‘Available Protocols’ contained within the protocol database.

� The field on the right displays the ‘Selected Protocols’ that have been chosen and added to a Custom Group and are visible

when that Custom Group is chosen in the drop down menu for ‘Custom Group Name’.

� To Create a Custom Group:

� Within the ‘Edit Custom Groups’ window, click the ‘Add New Custom Group’ button.

� The ‘Add New Custom Group Name’ window will open.

� The user will then enter the name they wish to assign to the Custom Group and then click the ‘Add’ button. (The name

of the facility is commonly used.)

� A confirmation window will open. Click the ‘OK’ button.

� Click the ‘Return’ button to close the ‘Add New Custom Group’ window.

� With the name of the newly created Custom Group displayed in the ‘Custom Group Name’ field, the user will then select

the protocols they wish to add to the Custom Group by selecting the protocols of interest from the ‘Available Protocols’

field and clicking the ‘Add Protocol’ button.

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� Alternatively, if a protocol was added to a Custom Group in error, the user may highlight the protocol to be removed from

the ‘Selected Protocols’ field and click the ‘Remove Protocol’ button.

� Once satisfied with all of the information entered, click ‘Save’ to save changes and then click ‘Return’ to close the ‘Edit

Custom Groups’ window.

� To Modify a Previously Created Custom Group:

� If a user wishes to modify a previously created custom group they must first open the ‘Edit Customs Group’ window and

select the Custom Group to be modified from the ‘Custom Group Name’ drop down menu.

� They may then add or delete individual protocols as needed using the ‘Add Protocol’ or ‘Delete Protocol’ buttons.

� After all changes have been made the user must then click the ‘Save’ and ‘Return’ buttons to return to the ‘Editors’ window.

� To Delete a Custom Group:

� To delete a previously created Custom Group, click the ‘Custom Group Editor’ button to open the ‘Edit Customs Groups’

window and select the Custom Group to be modified from the ‘Custom Group Name’ drop down menu.

� With the custom group name displayed in the drop down menu field, click the ‘Delete This Custom Group’ button.

� NOTE: The software will not ask for confirmation of deletion when performing this step. It is not necessary to

click ‘Save’ after performing this action.

� After all deletions have been made the user must then click the ‘Return’ button to return to the ‘Editors’ window.

Panel Editor


� Panels may be used as a shortcut to add multiple protocols to a case at one time. This feature allows the user to create a

Panel of frequently used antibody protocols instead of scrolling through the list of protocols when preparing Slide Labels

in Slide Label Editor. Examples: Breast, Lung.

� Click the ‘Panel Editor’ button within the ‘Editors’ tab in System Utilities.

� The ‘Edit Panels’ window will open.

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� At the top of the window is a drop-down menu listing all of the created panels.

� The field on the left lists all of the Available Protocols contained within the protocol database.

� The field on the right displays the ‘Selected Protocols’ that have been chosen and added to a Panel and are visible

when that Panel is chosen in the drop down menu for ‘Panel Name’.

� To Create a New Panel:

� Within the ‘Edit Panels’ window, click the ‘Add New Panel’ button.

� The ‘Add New Panel’ window will open.

� Enter the name of the Panel in the ‘New Panel Name’ field and click the ‘Add’ button.

� A confirmation window will open. Click the ‘OK’ button.

� Click the ‘Return’ button to close the ‘Add New Panel’ window.

� With the name of the newly created Panel displayed in the ‘Edit Panels’ field, the user will then select the protocols they

wish to add to the Panel by selecting the protocols of interest from the ‘Available Protocols’ column and clicking the ‘Add’ button.

� If a Positive Control and/or Negative Control is also desired to be added to a Panel along with an Available Protocol,

check the box next to Positive and/or Negative prior to clicking the ‘Add’ button.

� Alternatively, if a protocol was added to a Panel in error, the user may highlight the protocol to be removed from the

‘Selected Protocols’ field and click the ‘Remove’ button.

� Once satisfied with all of the information entered, click ‘Save’ to save changes and then click ‘Return’ to close the ‘Edit Panels’ window.

� To Modify a Previously Created Panel:

� If a user wishes to modify a previously created panel they must first open the ‘Edit Panels’ window and select the Panel

to be modified from the ‘Panel Name’ drop down menu.

� The user may then add or delete individual protocols as needed using the ‘Add’ or ‘Remove’ buttons.

� After all changes have been made the user must then click the ‘Save’ and ‘Return’ buttons to return to the ‘Editors’ window.

� To Delete a Panel:

� To delete a previously Panel, click the ‘Panel Editor’ button to open the ‘Edit Panels’ window and select the Panel to be

modified from the ‘Panel Name’ drop down menu.

� With the Panel name displayed in the drop down menu field, click the ‘Delete This Panel’ button.

� NOTE: The software will not ask for confirmation of deletion when performing this step. It is not necessary to

click ‘Save’ after performing this action.

� After all deletions have been made the user must then click the ‘Return’ button to return to the ‘Editors’ window.

Change Protocol Template

� Note: These settings will be configured by a qualified Biocare Representative and should not be altered unless specified to do so by Biocare Medical Technical Support.

39

System Utilities - Security TabThe ‘Security’ Tab within the ‘System Utilities’ menu allows “Supervisor Level” users to change their password, to add new users and

to modify user security level settings. The latter two are under User Administration.

� Note: “Technician Level” users will only be able to utilize the ‘Change Password’ option detailed below.

� To Change Password:

� The ’Change Password’ button in the ‘Security’ tab allows only the currently logged-in user to change their password for log-in.

� To change password, click on the ‘Change Password’ button.

� The ‘Change Password’ window will open.

� Complete the fields as prompted. Then click the ‘Change’ button followed by the ‘Return’ button to return to the ‘Security’

menu. The password is now changed.

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� User Administration

� This feature of the software allows a “Supervisor Level” user to add, delete, and/or modify the security settings of users.

� Note: “Technician Level” users are blocked from accessing the ‘User Administration’ feature.

� To Add or Delete a User:

� Click the ‘User Administration’ button within the ‘Security’ menu of ‘System Utilities’.

� Re-enter User ID and Password for confirmation.

� Following successful log-in, the ‘User Administration’ window will appear.

� To add a user, click the ‘Add User’ button. The ‘Add User’ window will open.

� Enter the fields as prompted. When finished, click the ‘Add User’ button.

� A confirmation window will appear. Click the ‘OK’ button to close the window. The ‘Add User’ window will close as well.

� Alternatively, click the ‘Return’ button to close the ‘Add User’ window without adding a new user.

� To delete a user, click the column to the far left to highlight the line of the user to be deleted.

� Click the ‘Delete User’ button.

� A confirmation window will appear. Click ‘Yes’ to confirm or ‘No’ to cancel the action.

� Click ‘Return’ to close the ‘User Administration’ window and return to the ‘Security’ tab.

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System Utilities - Settings Tab

Baking Slide Settings

� Note: Only assessable using the “Supervisor” level log-in.

� The ‘Baking Slide Settings’ button allows the user to modify the default temperature and time of the ‘Baking Slides’ feature

located within the ‘Tools’ menu.

� To change the settings, click the ‘Baking Slide Settings’ button within the ‘Settings’ menu.

� The ‘Configure Baking’ window will open.

� Users may change the values of the ‘Temperature’ and ‘Baking Time’ fields by clicking into those fields and changing the

number values and then clicking the ‘Save’ button.

� 60°C for 30 minutes is the recommended temperature and time setting.

� The maximum temperature allowed is 85°C.

� The maximum time allowed is two hours.

� Click the ‘Return’ button to exit the ‘Configure Baking’ window and return to the ‘Settings’ menu.

42

2D Barcode Format

� Note: Only assessable using the “Supervisor” level log-in.

� The 2D Barcode Format allows users to change the configuration of the information printed on the slide labels. The following

is an explanation of the information that may be altered on the slide labels using the ‘Barcode Label Options’ window.

� Date Format - There are three possible options for the display of the date on the slide labels:

1. MM/dd/yyyy

2. MM/dd/yy

3. yyMMdd

� To change the Date Format display, click on the corresponding button.

� The active Date Format will be displayed in the ‘Date Format’ window.

� Check or uncheck the box next to ‘Copy Patient Information to New Record’ to either or activate or deactivate this feature.

When activated, after a slide label is generated by clicking ‘Save’ in ‘Barcode Editor – Add’, the Patient ID will be retained and

the last Protocol ordered will remain highlighted.

� Label Format – This option allows the user to alter the information displayed on the slide labels.

43

� After clicking the ‘Label Format’ button within the ‘Barcode Label Options’ window, the ‘Label Formater’ window will open.

� Users may select which text they would like displayed on the printed slide labels by choosing from the options provided

within the drop down menus for each field.

� After making the selections, the user must ensure to click the ‘Save’ button to save changes prior to selecting ‘Return’ to

exit back to the ‘Barcode Label Options’ window.

� Edit Doctor Name List – This option allows the user to add or remove a Doctor’s name from the Doctor Name database for

reporting purposes.

� To use this feature – click the ‘Edit Doctor Name List’ button within the ‘Barcode Label Options’ window.

� The ‘Edit Doctor Name List’ window will open.

� To add a Doctor’s Name:

� Type the name of the doctor in the field provided and click the ‘Add’ button.

� To delete a Doctor’s Name:

� Choose the Doctor’s Name to be deleted from the drop down menu in the ‘Edit Doctor Name List’ window and

click the ‘Remove’ button.

� Click the ‘Return’ button to return to the ‘Barcode Label Options’ window.

� Line1 & Line2

� The ‘Barcode Label Options’ window also allows a user to modify the Line1 and Line2 text that is displayed within the

‘Barcode Editor - Add’ window when making slide labels.

� Line1 and Line2 input fields are divided into two columns: Label and Entry.

� The Label field displays the title for the text field within the ‘Barcode Editor’ window.

� The Entry field displays the input information within the ‘Barcode Editor’ window should a user decide to have

default information automatically populated in this field.

� Users may write text within these fields in the ‘Barcode Label Options’ window to display the text as a default in the

“Barcode Editor - Add’ window. Alternatively, users may leave these fields blank.

� Manufacturer defaults:

� Line1:

� Label: Hospital Name

� Entry: blank

� Line2:

� Label: Description

� Entry: blank

44

� Printer Settings and Configuration

� These settings allow the user to configure printer type, margins, label width, and font darkness.

� These settings will be configured by a qualified Biocare Representative and should not be altered unless specified to do

so by Biocare Medical Technical Support.

Check Heater Settings

Not available for use.

Save All Customizations

� Note: Only assessable using the “Supervisor” level log-in. � The ‘Save All Customizations’ button locks all Protocols as the new “manufacturer default”

� The ‘Save All Customizations’ button sets the current Protocol settings in ‘Protocol Editor’ as the default for each individual

protocol so that when the ‘Refresh Protocol’ button is used, the Protocols will roll back to these settings

� Once a Supervisor level user has made changes in ‘Protocol Editor’ in the ‘Editors’ tab, clicking ‘Save All Customizations’ in

the ‘Settings’ tab will activate this feature

Get Device Version

� Selecting this option within the ‘Settings’ tab of ‘System Utilities’ will provide the user with information pertaining to the current

version of the ONCORE software.

Baking Slides Before Staining

� The ONCORE Automated Slide Stainer also offers an option of having the slides undergo the baking protocol prior to the start

of a run.

� To activate or deactivate this feature a user must select the ‘Settings’ tab within ‘System Utilities’ and check (or uncheck) the

box labeled “Baking Slides Before Staining”. Checking the box activates the feature. Unchecking the box deactivates the feature.

� After making the selection, the user must click the ‘Save’ button before exiting the ‘Settings’ tab to save the changes.

� To change baking temperature and duration, use the ‘Baking Slide Settings’ button.

Changing Software Text Language


System Utilities - Network Tab


System utilities - LIM Tab


45

ONCORE MaintenanceRecommended Tissue Placement Guidelines

RMONCP034 REV C

IHC

TIS

SU

E P

LA

CE

ME

NT G

UID

E

Place Tissue A

nywhere in the G

reen Zone

No P

ainted or Etched P

rint in Red Zone

75

mm

Max S

lide Length

RMONCP104 REV A

ISH

TIS

SU

E P

LA

CE

ME

NT G

UID

E

Place Tissue A

nywhere in the G

reen Zone

No P

ainted or Etched P

rint in Red Zone

75

mm

Max S

lide Length

For IHCDue to the configuration of the slide chamber, the active

staining area of the slide is limited to three fourths of the

available sample area of the slide for IHC applications. Tissues

placed outside of the active staining area may result in limited

or no staining. The following illustration demonstrates the active

staining area recommended for performing IHC on the ONCORE

Automated Stainer.

For ISHDue to the configuration of the slide chamber and the

evaporation due to the requisite high temperatures sustained

for ISH applications, the active staining area is limited to the

lower two-thirds of the sample area on the slide. Tissues placed

outside of the active staining area may result in sub-standard

or no staining. The illustration below highlights the active

staining area for ISH on the ONCORE Automated Stainer.

46

Daily Maintenance

Slide Chamber CleaningPerform this Slide Chamber Cleaning procedure after every run.

Immediately after removing slides from Slide Chambers, use a folded alcohol wipe to clean thoroughly all surfaces that were in contact

with the slides, the black Slide Heater Plate, Slide Chamber Housing and Slide Chamber hinge area. Ensure each surface is clean and

free of remaining reagents and chromogen, using fresh alcohol wipes as needed.

Note: Ensure there is no lint left behind on the Slide Chamber surfaces as this may compromise staining results. If glass shards are observed in the hinge area, use the ONCORE Chamber Cleaning Brush to remove the glass from the hinge area and then wipe away with an alcohol wipe or vacuum (not provided). Be sure to use appropriate personal protective equipment when clearing glass shards from the ONCORE.

Slide Module Cleaning Immediately after removing slides from Slide Chamber Housing, visually inspect for leftover fluid on the Slide Chamber Modules and

the surrounding area, including the black Slide Heater Plate. Use alcohol wipes to clean Slide Chamber Modules and black Slide

Heater Plate and absorb residual fluid. Remove the Slide Chambers. While viewing the underside of the Slide Chamber, gently press

on each Slide Chamber Port to check for cracks in the blue gasket material. If cracks are observed, replace the Slide Chamber. To

clean away any buffer salts or remaining reagents, wrap an alcohol wipe around your index finger and wipe around the inside edges of

the Slide Module lids from which the Slide Chambers were removed.

47

Weekly MaintenancePerform the following cleaning procedures weekly, or every 5 runs, whichever comes sooner.

Slide Chamber CleaningRun ‘Clean Chamber’ protocol to remove residual DAB stains from slide chambers.

1. Use ONCORE Chamber Cleaning Kit.

2. Fill the empty vial provided with DI Water.

3. Highlight all 36 slide positions by left clicking on position 1 and dragging mouse to position 36. Click ‘Assign Protocols’ button,

choose ‘Clean Chamber’ protocol. Click ‘Select’.

4. Click ‘Load Unload Slides’ button and place blank slides in all positions. Click ‘Slide Lids Down’ when finished.

5. Click ‘Scan Reagents’ button.

6. Load all vials from ONCORE Chamber Cleaning Kit. Make sure to fill the empty vial provided with DI Water. Fill the Buffer container

and empty the Waste container.

7. Click ‘Scan Reagents’ button.

8. Once all reagents have scanned, close lid and click ‘Start Staining Run’. Run will take approximately 2.5 hours to complete.

9. Once Clean Chamber run is complete, remove the following vials from the Reagent Rack: Clean 1, Clean 2, Clean 3, DI Water.

10. Pop the Slide Chambers out and clean with alcohol wipes on all sides. Also clean the interior edges of the Slide Chamber Housing

with alcohol wipes.

Dispense and Extraction Probe Tip and Wash Station CleaningSalt may build up at the tip of the probes and on the wash station surfaces over time. Use an alcohol wipe to clean the tips of the

probes and wash station weekly or as often as needed to remove salt build-up. To clean the probe tips and wash station, click on the

Systems Utilities button, go to the ‘Tool’ tab, and click on ‘Move Arm Aside’ to move the z-head to slide position 6/7 and out of the

way of the reagent rack. Click on ‘Slide Lids Down’. Wipe the outside of the Wash Station housing and the Probe Tips with alcohol

wipes. Using a small beaker of alcohol and cotton tipped applicators, clean the inside of the probe cleaning slot in the Wash Station

where the Probe Tips are normally washed.

Disinfect Buffer and Waste Carboys 1. Follow the Bottle Cleaning Procedure on the buffer and waste carboys.

2. Empty the buffer carboy and both waste carboys. Fill all carboys with 500mL of a 10% Lysol solution. Professional LYSOL®

Brand Antibacterial All Purpose Cleaner (Concentrate)* is recommended.

3. Shake the carboys so that the walls of the carboys are well washed.

4. Add an additional 500mL of 10% Lysol solution and let carboys sit for 20 minutes.

5. Pour solution out. Flush all carboys with multiple changes of tap water.

6. Flush all carboys with DI Water.

48

Monthly MaintenancePerform the following cleaning procedures monthly, or every 10 runs, whichever comes sooner.

Deep clean slide chambers with bleach. 1. Remove the chambers from the modules:

a. Click ‘Load Unload Slides’ button to open the lids.

b. Gently press down on the upper near portion of the blue and beige chamber until it releases.

c. Gently press down on the upper far portion until it falls to the black heater pad.

d. Check for any cuts or rubber separating from the plastic in the blue silicone rubber, all around the chamber

and in the port area. Replace if damaged.

2. Take all 36 chambers and soak in 20% bleach for 15 to 20 minutes.

3. Shake chambers in bleach, wipe and repeat until the chamber surface is free of DAB residue.

4. Rinse in at least eight changes of running tap water until all bleach has been removed.

5. Air dry chambers.

6. Wipe chambers with alcohol swab.

After cleaning the Slide Chambers with bleach, inspect each Slide Chamber for any cracks in the plastic or blue gaskets, or for shrinkage

of the gaskets indicated by the gasket pulling away from the plastic. If cracks or shrinkage are evident, replace the affected Slide Chamber.

*Lysol is a registered trademark of the Reckitt Benckiser Group.

Inspect Slide ModulesOn a monthly basis, immediately after performing the Slide Module Cleaning procedure, press down on black Slide Heater Plates to

check for fluid oozing from underneath. If fluid is observed, perform a heater test. If the heater test results in a bad heater, note the

Slide Module position and contact Biocare Technical Support.

Quarterly MaintenancePerform the following cleaning procedure quarterly.

Disinfect Buffer and Waste Carboys

1. Follow the Bottle Cleaning Procedure on the buffer and waste carboys.

2. Empty the buffer carboy and both waste carboys. Fill all carboys with 500mL of a 10% Bleach solution.

3. Shake the carboys so that the walls of the carboys are well washed.

4. Add an additional 500mL of 20% bleach solution and let carboys sit for 20 minutes.

5. Pour solution out. Flush all carboys with multiple changes of tap water.

6. Flush all carboys with DI Water.

Semi-annual MaintenanceRequired: perform the following procedure every six months, or 150 runs, whichever comes sooner.

Recommended: perform every 2 months for optimal performance.

Tubing cleaning

Run ‘Tubing Clean’ function to clear any possible residual buildup from the lines that may accumulate during the staining process.

1. Use ONCORE Tubing Clean Kit.

2. Click ‘System Utilities’.

3. Select ‘Tubing Clean’.

4. Follow on-screen instructions. Load the following vials from the Tubing Clean Kit: Tubing Cleaning 1 and Tubing Cleaning 2.

5. Note: the first Attention point can be ignored as no units have the RFID antenna attached to Z2. So no special Reagent Rack is required.

6. Procedure will take approximately 20 minutes.

49

Troubleshooting

Problem Possible Causes Solution

After system initialization, the XYZ motor

and the slide module lids are not moving

Invalid robotic and slide module

addresses were assigned

Contact Technical Support to configure

correct addresses for the robotic and

slide modules

No staining, light staining, uneven

staining, inconsistent staining Insufficient buffer in carboy

Fill the buffer carboy and initialize system

by priming Z1 and Z2 (5-10 times) until

no air remains in the buffer line

Dirty slide chamber Bleach clean (see monthly maintenance)

Broken Slide Chamber / cracked gasket Replace Slide Chamber

Empty Improv reagent vial Add reagent to vial

Wrongly assigned location of reagent vial Correct reagent vial location

Clogged probe Run the Tubing Clean protocol

Possible heater malfunctionContact Technical Support to replace the

slide module

Possible slide module motor malfunctionContact Technical Support to replace the

slide module

Possible syringe pump malfunctionContact Technical Support to replace the

syringe pump

Unable to print a Slide Barcode Label USB cable connection between computer

and printer

Secure the USB connection from

computer to printer

Printer selection in softwareSelect the correct printer from the

Barcode Label Options screen

Printer selection on computerSet Zebra Printer as Default Printer

under Devices and Printers

Unable to insert a slide into the slide

module Hinge block spring plunger is stuck Clean the hinge block spring plunger

“Could Not Open Barcode Port” error

message Invalid COM Port was assigned

Contact Technical Support to configure

the correct barcode COM port

Poor or no USB cable connection

between instrument and computer Secure the USB connections

Unable to scan the barcode label Missing or unreadable label on slide Replace label

Slide label not in red zone (slide loaded

backwards) Ensure label is within the red zone

Barcode Read Position out of calibration Contact Technical Support to calibrate

Barcode Read Position

Scanner not initialized (COM port

assignment)

Contact Technical Support to correct

COM port assignment

Defective scanner Contact Technical Support to replace

scanner

50

“Could not Open RFID Port” error

message

Poor or no USB cable connection

between instrument and computer Secure the USB connections

Invalid COM Port was assignedContact Technical Support to configure

the correct RFID COM port

Unable to read an RFID tag Missing or defective RFID tag Replace Improv vial

Defective RFID reader/antenna Contact Technical Support to replace

reader or antenna

RFID position calibration Contact Technical Support to calibrate

RFID Position

RFID system not initialized (COM port

assignment)

Contact Technical Support to correct

COM port assignment

ISO15693 box is checked Contact Technical Support to uncheck

ISO box in RFID Tab of System Server

Low temp error message Run cancelled Start a new run

Possible sensor malfunctionContact Technical Support to replace the

slide module

Possible heater malfunctionContact Technical Support to replace the

slide module

High temp error message Sensor connection Check if sensor is properly connected to

the correct terminal

Controller Board shorted Contact Technical Support to replace the

slide module

Sensor failed Contact Technical Support to replace the

slide module

Heater failed Contact Technical Support to replace the

slide module

51

Ordering Information

Materials and Reagents Needed But Not Provided:Reagents and materials such as primary antibodies, probes, detection kits, chromogens and ancillary reagents are not provided.

Description Catalog No*

Microscope slides, positively charged, 75 mm length (max.) N/A

Positive and negative tissue controls N/A

Wash Buffer ORI6012

Dewax Solution Kit ORI6004K

ISH Dewax Solution Kit ORI6020K

Pretreatment Reagent (Antigen Retrieval 1 (AR1), high pH) ORI6006

Pretreatment Reagent (Antigen Retrieval 2 (AR2), low pH) ORI6005

Pretreatment Reagent (ISH Retrieval 3 (AR3), ISH) ORI6021

ISHzyme ORI6039K (ORI6022 & ORI6023)

Primary antibody multiple

Probes multiple

Probe enhancer (RNA) ORI6024

Mouse HRP Detection ORI6007

Rabbit HRP Detection ORI6008

Mouse Amp HRP Detection ORI6050

Mouse AP Detection ORI6044

Rabbit AP Detection ORI6043

Multiplex Detection 2 ORI6045

ISH HRP Detection ORI6047K (ORI6025 & ORI6026)

Universal Negative Control Serum ORI6013

RNA Positive Control Probe ORA6057

RNA negative control probe ORA4029

DAB Chromogen Kit ORI6056K

Fast Red Chromogen Kit ORI6042K

Hematoxylin CATHE

Bluing Reagent HTBLU

EcoMount (Mounting Media) EM897

Xylene (could be replaced with xylene substitute, such as Slide Brite) SBT-G1

Ethanol or reagent alcohol N/A

Deionized or distilled water N/A

DS Enzyme ORI6049

Chamber Cleaning Kit ORI6031K

Tubing Cleaning Kit ORI6036K

* Biocare Medical Products: Refer to a Biocare Medical catalog or www.biocare.net for further information.

52

Additional products available for purchase:

Description Catalog No

Desert Chamber Pro™ (Drying Oven) DRY2008

Chamber Cleaning Kit ORI6031K

Tubing Cleaning Kit ORI6036K

Improv Reagent Vials ONC101

2-Liter Non-Hazardous Waste Bottle with Cap ONC030-NHW

2-Liter Hazardous Waste Bottle with Cap ONC030-HW

2-Liter Buffer Bottle with Modified Cap, Fittings ONC004

Slide Chamber ONC005

70% Isopropyl Alcohol wipes, 100 count ONC099

ONCORE Chamber Cleaning Brush ONC103

ONCORE Reagent Rack ONC007

Terminology and Abbreviations

AP Alkaline Phosphatase

AR Antigen Retrieval

DNA Deoxyribonucleic acid

DS Dewax Solution

HRP Horseradish Peroxidase

IHC Immunohistochemistry

ISH in situ Hybridization

Multiplex or Dual Double staining

Rb Rabbit

RFID Radio-frequency identification

RNA Ribonucleic acid

CISH Chromogen in situ Hybridization

FISH Fluorescent in situ Hybridization

800.799.9499

60 Berry Drive

Pacheco, CA 94553 www.biocare.net

904-017-032618