realizing effective digital-enabled anatomic pathology ... · • allows us to record the location...

Realizing Effective Digital-Enabled Anatomic Pathology Workflow

The Henry Ford ExperienceJ. Mark Tuthill, MD

Division of Pathology InformaticsHenry Ford Hospital

Detroit, MI [email protected]

Digital Pathology and AI WorkshopColumbus, OH

December 7-8, 2018

Objectives1. Understand digital integration prerequisites2. Present examples of operational systems used and

digitally integrated at HFHS3. Highlight common strategies the lead to success4. Describe the integration of WSI including bar code

harmonization

Philosophical Hypothesis• “We can integrate AP workflow so that it models

efficiency of the clinical laboratory”– What are the pre-requisites?– What is the low hanging fruit?

• Sequence– What are the technology gaps?

• Advanced robotics and pipeline development– Automation of manual processes

Operational Systems

Digital Integration

Lab Information

System

TECHNICAL & SUPPORT STAFF

PATHOLOGISTS

Information Technology

Sunquest :Lab and CoPath Histotrak HLA

MAS POCAqueduct Hematology

Lane Faxing

LAB PORTAL Atlas

APOLLO Pathpacs

Scantron

LAB USER’S GUIDE

pathology.hfhs.org/lug

Digital PathologyRoche

MikroScanDigital Cameras− Store AP Req Scans

− Store Clin Path Req Scans− Integrate External AP Results− Telepath Integration− Associate Imaging to Reports− Interface to acquisition devices

Cameras (1-2 M records/yr)- Gels-Microbiology

− Surg Path Reqs− Cytopath Reqs− Clin Path Reqs− Outreach Documents

SCANNING

TISSUE BIOREPOSITORY

DOCUMENT CONTROL

Master Control

HEALTHSTREAMTraining (HFHS U)

Competency

Wired

Molecular Pathology and NGS

EpicSyapse

Clinical Pathology SystemsFunctional Areas Applications• Chemistry• Hematology• Coagulation• Urinalysis• Blood Bank• Microbiology• Serology• Virology• HLA• Molecular• Genomic Pathology• Point of Care

– Glucometers >650– Coagulation clinics

• SunquestLab• SMART – barcoded specimen tracking,

management. and archiving

• >140 Instrument Interfaces via Sunquest Instrument Manager (SIM)

• Autovalidation• Macroscheduler automated jobs• Histotrac: HLA laboratory system• MSQL Report Writer w/ Crystal• Results transmitted to EPIC• Beckman Automation Line; Conexus;

Remisol

Anatomic Pathology SystemsFunctional Areas Applications• Histology• Molecular Pathology

– Illumina NGS

• Cytology• Frozen Room• Autopsy• CP Integration

– Special Hematology– Flow Cytometry– Immunohistochemistry– Microbiology

• Sunquest CoPath• Biomaterial tracking system (BTM)• Scantron: requisition scanning• mTuitive: synoptic checklists• JFCC reporting via ePath• Barcoded LEAN production• Apollo Digital photography• Telepathology: Mikroscan• WSI: Ventana Virtuoso, Mikroscan

– Ventana Connect

• Dako Connect• Tens of molecular pathology applications

Other LIS Applications and Operations Functions• Atlas Portal: Outreach EMR; order entry and result reporting• Scantron: Document scanning for regulatory retention• LUG: Laboratory Users Guide• Lane Faxing: supports all Health system laboratory faxing• BTM: Tissue Biorepository• IT Service Now: Helpdesk; PI Change Control database for compliance• Apollo PathPACS: image storage integrated with both

Sunquest systems (Lab & CoPath)

Road Map for Digital WorkflowThe Big Picture

• Pre analytic– Prior to receiving or analyzing the sample– Preparing samples for analysis

• Analytic– The process of analyzing the tissue

• Post analytic– The reporting of diagnostic information– Preparing for additional analytic studies

Prerequisites for Anatomic Pathology Digital Workflow

• Sophisticated electronic medical records system– Electronic orders interface for Anatomic Pathology

• Bar code labeled assets with the laboratory– Assets with unique identifiers

• Development of robotic technologies– *Grossing*– Embedding, Sectioning– Tissue transport– Sampling– Storage systems: cassettes and slides


• Sophisticated electronic medical records systems– Such systems will enable clinical orders to be sent to the

anatomic pathology information system as well as supporting:

• Decision support• Gathering of accurate and required information• Positive patient identification• Generation of laboratory ready labels to the point of

service• Tracking of samples to the laboratory including

monitoring of conditions


• Electronic orders interface to the Anatomic Pathology Laboratory Information System (AP-LIS)– Similar to the clinical laboratory, a flow of orders to the LIS

will enable:• Sample receipt• Tracking• Routing• Analytic Processing• Automation of several elements of case accessioning

– Decrease errors– Increased throughput


• Bar code labeled assets within the laboratory– This is most essential early prerequisite to achieve

automation within the laboratory– Bar coding of assets allows for:

• Bar code driven workflow• Identification error reduction due to mislabeling• Improved efficiency by reducing manual labeling• Automation of subsequent activities

– Integration whole slide imaging, interface devices– This is the key requirement for all automation


• Bar code labeled assets within the laboratory– Critical for each asset to have an unique ID embedded in the bar

code– This will allow each block and slide to be managed uniquely

supporting (Assets)• Sophisticated routing• Tracking of assets • Digital Pathology (unique ID on slides will be essential!)• Systems interfaces

• Without uniquely identified assets the clinical laboratory could not have achieved the level of automation currently experienced

Examples of Anatomic Pathology Digital Workflow

Real World Examples and Status Updates

Examples of AP Digital Workflow• Automation of histology orders (stain protocols)• Interfaced immunostain orders to automated immunostain

platform• Bar code labeling automation

– Automated production of cassettes at accessioning– Cassette driven generation of labeled slides

• Tracking, routing and storage• Automated tissue embedding• Automated microtome's

Examples of AP Digital Workflow• Automated block sampling• Automated slide sampling

– Laser capture micro dissection• Conveyor belt systems, tubes, roving robots: routing• Slide collation robotics• Automatic diagnostics

– Whole slide imaging algorithms for immunostains quantification

– Automated pap smear readers

Examples of AP Digital WorkflowHistology Protocols

• Automated ordering histology protocols for different sample types at case accession– When a particular part is accession the appropriate blocks and

initial stain orders are generated– Initial billing fee codes are applied– Histology logs are electronically sent and printed providing early

notification of work• This has increases efficiency and allows for LEAN processes

– Work is standardized– Revenues were enhanced through better charge capture

• This is not easy and required iterative re-work and constant attention to defects to get the most satisfactory end result

Examples of AP Digital WorkflowReal Time Labeling

• Essential first step to widespread AP automation• As previously stated the implications of bar code labeled

assets drives all other processes• By themselves, the impact of automation of cassette

labeling following by slide label generation are profound

21

This case is submitted in 3 specimen containers consisting of:part A - sigmoid colon biopsy, part B - transverse colon biopsy and part C - stomach biopsy with standing preorder

for Helicobacter pylori immunostain.

Protocol driven information is reflected in the slide labels dictating 2 levels cut for each part.

The stomach biopsy protocol, part C, calls for an additional 2 blanks slides to be cut, one for the immunostain & a 4th left unstained.

1

4

3

2

Barcode SpecifiedWork Processes

Outcome• With 'real-time labeling' the batch slide label printing

process has now been entirely eliminated

• Specimen misidentification rates have been reduced

• Workflow efficacy in the histology lab has increased as cassette reading defects have been eliminated– Barcode reading defects required the histotechnologist to

manually type in cases numbers, leading to increased risk of patient misidentification

Results: Misidentification Rates

Baseline Linear BarCodes(Jan.2007)

2D BarCodes(June2012)

45

18

10

5

10

15

20

25

30

35

40

45

Number Mis-IDDefectsPercent of Cases

1.67%

0.62%

0.02%

Chart1

BaselineBaseline

Linear Bar Codes (Jan. 2007)Linear Bar Codes (Jan. 2007)

2D Bar Codes (June 2012)2D Bar Codes (June 2012)

Number Mis-ID Defects

Percent of Cases

45

1.67

18

0.62

1

0.02

Sheet1

Number Mis-ID DefectsPercent of Cases

Baseline451.67

Linear Bar Codes (Jan. 2007)180.62

2D Bar Codes (June 2012)10.02

To resize chart data range, drag lower right corner of range.

• Allows us to record the location and status of specimen assets (parts, blocks, slides, etc.) as they are processed and move through the pathology laboratory

• All components of a case can be tracked from when they are accessioned on through to storage or eventual disposal

• Tracking allows for us to locate case assets and identify who has handled them and where assets have been (i.e. history)

• I will not address routing and processing protocols as it applies to conveyance systems which we are not yet using

Examples of AP Digital WorkflowSpecimen Tracking and Routing

AP-LIS: CoPath Plus v6.0 (6.1)(Sunquest Information Systems, Tuscon, AZ)

CoPath Specimen Management Routing and Tracking (SMART) module

InfoMaker reports were created using PowerBuilder software

(Sybase, Dublin, CA).

Specimen TrackingTechnology

• We defined specimen points of tracking (SPOTs) in the AP-LIS dictionary Each SPOT is linked to a specific workstation as defined on the

health system’s internal network

• As each asset is scanned and processed – location, scan time, status, and associated user data are

automatically recorded

• Standard tracking tools allowed us to monitor assets in real-time

DesignSpecimen Tracking

AP Workflow Design*

*

** *

*

*

* * *

*

*

*

*

Design: SPOT Implementation

• Currently 145 SPOTs have been defined

Histology Lab

Pathologists

Tracking Activities Tracking Reports

Asset Manager Asset Location Report

Specimen Discard Parts/Blocks/Slides at a SPOT

Specimen Tracking Update Parts/Blocks/Slides Aging Report

Slide Status Update Scan History Log

View/Update Specimen Tracking Specimen Tracking Scan Errors

Asset Reconciliation SPOT Turnaround Time Report

Unique ID Report

• Some functions are workflow specific while others can be utilized at multiple points in the process

Parts/Blocks/Slides Aging Report• Lists the time elapsed since

the most recent tracking event Can be used to show

which specimen assets have been at a workstation the longest

Useful for when:o Blocks unaccounted for

in histologyo Slides unaccounted for

by the pathologist

Parts/Blocks/Slides Aging Report• Lists the time elapsed since

the most recent tracking event Can be used to show

which specimen assets have been at a workstation the longest

Useful for for when:o Blocks unaccounted for

in histologyo Slides unaccounted for

by the pathologist

Scan History Log• Lists all tracking events for

for an asset and shows where each event occurred

• This report can be a useful QA tool – can tell if users are

compliant with scanning specimen assets

– Can identify scanning errors due to inappropriate case editing

SPOT Turnaround Time Report

• Displays the time between when assets were tracked at one SPOT (i.e. Accessioning) to when they were tracked at the next SPOT (i.e. Grossing)

• This can be used to find out how long it takes assets to be processed from one workstation to another

Workload Reports• Scan events can be

tracked at individual SPOTS and users

• Allows us to provide workload and productivity data for lab managers Example: Slide

counts by microtomyperson

Asset Reconciliation• Allows the user to reconcile the assets in hand with the

assets assigned to a case• Can be use iteratively

– Gross– Accession– Embedding– Foldering

• Perhaps the most commonly automated process in the current AP lab– Including automated cover slipping

• This saves hundreds of man hours per year• Has more consistent results versus manual staining and

cover slipping• Digital interfaces with AP LIS will further enhance

productivity and decrease errors

Examples of AP Digital WorkflowAutomated Staining Platforms

Automated ImmunostainingInterface Design

• An HL7 interface was created between CoPath and the Dako autostainer Link 48 platforms– Allowed IHC orders placed in CoPath to be directly transmitted

and received by the DakoLink instrument control software; used Dako labels

• Our CoPath LIS was upgraded to version 6.0 which provided the capability to uniquely identify and track each case assets – Assign unique identifiers to each and every case asset (i.e.

parts, blocks, and slides)– With this in place, unique slide IDs (linked to IHC orders in the

AP-LIS) were transmitted to Dako autostainer control software– Dako autostainer instruments could then read and utilize

native CoPath labels

New workflow after deployment of the automated stainer interface

Stains Ordered

Slide are cut & labeled

Creates HL7 message

Slides placed onto instruments

Slide labels scanned

Slides processed

CoPath Interface

IHC

Special stains

CoPath – Dako New Workflow1. Stains are ordered in CoPathPlus.2. Stain orders are released to the interface on demand or

scheduled.3. Interface creates an HL7 message and delivers to Dako 4. Message is routed to instrument. Slide labels print from CoPath. 5. Slides are cut in the laboratory and Slide labels print from

CoPath and labels are applied to slides.6. Slides are placed into the instrument. Label is scanned by

instrument which indicates the reagent stain workup.7. Slides are processed.

From CoPath Printer to Slides to DakoBypassing Dako Relabeling

Results• With elimination of relabeling the slides and dual order

entry through automation markedly decreases assay run time – This saves upward of ~700 hours of manual effort per

year while eliminating errors, improving patient safety and improving laboratory throughput

• Increases order accuracy by reducing keystroke errors.• Enhances operational efficiency by automating processes.• Enforces safe, consistent, efficient handling of specimen.

Examples of AP Digital WorkflowAP EMR Orders Interface

• Project initiated to transmit AP orders from our EMR to CoPath• This will solve several problems:

– Elimination of unsolicited results as orders will be fulfilled in the EMR

– Proper encounter selection– Routing to provider inboxes– Better tracking or AP tissue– More efficient accessioning

• ADT, MD, Part Type, ICD, Clinical History and ask at order entry questions will be transmitted from EMR to CoPath

AP Orders Interface• Project initiated to transmit AP orders from our EMR direcdtly to

CoPath• Impact based on time studies

– 1.5 minute average decrease in case accession– 100,000 cases as a baseline for our math

• Savings of 2500 hours• Minimum of $50,000, direct cost savings!

• Time savings doesn’t include elimination of the complexities of mis-accessioned cases and required resolution– Elimination of defect in encounter selection alone will have huge

impact

Examples of AP Digital WorkflowDigital Pathology

• Not just whole slide imaging! (WSI)• Distributed microscopic images• Distributed EM• Gross images• Scanned documents• Image analysis• Clinical lab images: gels, plates, hematology analyzers• Cytogenetics analysis• Digital Pathology is:

– digitally capturing, storing, moving, analyzing, interpreting tissues (and other assets) submitted to the laboratory for the purpose of diagnosis, clinical communication, documentation and quality assurance

Apollo EPMM Implementation• Apollo EPMM Image management provides:

– Expandable EMC SAN based storage– Access and management for all existing image-generating

devices – Security management for users

• Permission-based logon, very nuanced• Thick-client and Thin-client access

– LIS integration • Interfaces for ADT and images• Images to be send to the EMR via AP-LIS (CoPath)

– Sophisticated device integration including interfaces and file mover services

TECHNOLOGYFile mover services leveraged

Autopsy suite

Apollo EPMM

Specimen X-rays

Grossing stations

DocumentScanners

Autopsy suite

Robotic Telepathology

LIS Integration

Final Workflow• Cases accessioned into CoPath

– ADT sent to Apollo• Images acquired for case automatically stored in Apollo• Images “links” are sent back to CoPath (or not) as

“results”– Those returned are configurable:

• Associated with the case• Embedd into the report

• Images viewable in Apollo or CoPath• Report send to EMR with or without images as desired

Examples of AP Digital WorkflowWSI: Drivers for HFHS

• Maturity of the WSI technology platforms – Improved performance– Decreasing costs

• The need for a distributed digital pathology workflow to support diagnostic studies– Move images not glass!

• Loss of support for our robotic telepathology platforms• The desire to adopt cISH and image analysis for diagnostic

panels

Decisions and Goals• Stand up technology to replace robotic telepathology

– Selected Mikroscan as a vendor• Stood up four D2 systems in each hospital to allow for

telepathology support of intraoperative consultation• Select WSI partner for cISH analysis and distributed diagnostic

imaging– Selected Ventana Roche as a partner

• Implement iScan Coreo and Coreo HT platforms• Interface these platforms with Sunquest CoPath• Validate the Ventana Ultra cISH platform• Harmonize bar code labeling symbologies so that CoPath

generate bar codes labels would be used• Integrate this technology into CoPath and Apollo workflow

TECHNOLOGYFile mover services leveraged

Autopsy suite

Apollo EPMM

Specimen X-rays

Grossing stations

DocumentScanners

Autopsy suite

Whole Slide Imaging

LIS Integration

Prerequisites for Interfacing WSI• Requisite hardware and software for WSI capable of

using HL7 messaging– Network attached storage solution– Network bandwidth

• We had WSI in place since January 2016• An LIS capable of communicating with WSI systems via

HL7• Electronic histology orders used for all histology

processes• Bar code labeled assets with unique ID’s

Value of Interfacing WSI• Immediate case access by pathologist

– No annotation• Significantly more data is populated

– Part, Block, stain– Patients details: age, sex, DOB; – Assigned pathologist

• Leveraging bar code technology• Case available to pathologist immediately upon

successful scan– No need to annotate and release

CoPath

Dako

Apollo Imager

SAM

Stain orders

Stain status updates

Image ordersImage orders

Image results Image results

Past Setup

Sunquest Application Manager (SAM)

CoPath

Dako

Apollo Imager

Dako stain orders

Stain status updates

Image ordersImage orders

Image results Image results

Ventana Connect

Dako stain orders

Dako Stain status updates

Dako & Ventana stain ordersVentana Stain status updatesVentana Image Results

Ventana stain orders

Roche Setup

SAM

Sunquest Application Manager (SAM)

Benchmark Ultra

Virtuoso

Ventana Stain status updatesVentana Connect

Dako & Ventanastain orders Ventana images

Ventana stain orders from CoPath

Roche Setup

Coreo PC

Ventana imagesHT PC

Ventana image results

Dako & Ventana stain orders

iScan HT Digital Workflow• Cases are created in CoPath at accession• HL7 message is sent to Ventana Connect and onto

Virtuoso• Slides cut, stained and placed on HT for scanning• Scanned images automatically associated with patient,

CoPath accession and pathologist• Scanned images ARE NOW available to be viewed

through CoPath interface• Select fields can be exported and integrated into the

CoPath report using Apollo EPMM

Summary

Realizing Effective Digital-Enabled Anatomic Pathology Workflow

SummaryRealizing Effective Digital-Enabled Anatomic Pathology Workflow

• Many aspects of AP can be digitally integrated– More integration is available than meets the eye– We don’t count some of these that have a big impact

• Digital integration saves time, money and improves patient safety

• Very few gaps in robotic solutions remain– Gaps will close– Pricing will come down

• Build upon your foundations: sequence carefully!

Conclusion

Philosophical Hypothesis tenable: We can integrate AP workflow so that it models the

efficiency of the clinical laboratory!

Questions?J. Mark Tuthill, MD

Division of Pathology InformaticsHenry Ford Hospital

Detroit, MI [email protected]

Digital Pathology and AI WorkshopColumbus, OH

December 7-8, 2018

Realizing Effective Digital-Enabled Anatomic Pathology Workflow�The Henry Ford ExperienceObjectivesPhilosophical HypothesisOperational SystemsSlide Number 5Slide Number 6Clinical Pathology Systems��Functional AreasApplicationsAnatomic Pathology Systems��Functional AreasApplicationsOther LIS Applications and Operations FunctionsRoad Map for Digital Workflow�The Big PicturePrerequisites for Anatomic Pathology Digital WorkflowPrerequisites for Anatomic Pathology Digital WorkflowPrerequisites for Anatomic Pathology Digital WorkflowPrerequisites for Anatomic Pathology Digital WorkflowPrerequisites for Anatomic Pathology Digital WorkflowExamples of Anatomic Pathology Digital WorkflowExamples of AP Digital WorkflowExamples of AP Digital WorkflowExamples of AP Digital Workflow�Histology ProtocolsExamples of AP Digital Workflow�Real Time LabelingSlide Number 21OutcomeResults: Misidentification RatesExamples of AP Digital Workflow� Specimen Tracking and RoutingSpecimen Tracking�TechnologyDesignAP Workflow DesignDesign: SPOT ImplementationSlide Number 29Parts/Blocks/Slides Aging ReportParts/Blocks/Slides Aging ReportScan History LogSPOT Turnaround Time ReportWorkload ReportsAsset ReconciliationSlide Number 36Slide Number 37Slide Number 38Examples of AP Digital Workflow�Automated Staining PlatformsAutomated Immunostaining�Interface DesignNew workflow after deployment of the automated stainer interface CoPath – Dako New WorkflowFrom CoPath Printer to Slides to Dako�Bypassing Dako RelabelingResultsExamples of AP Digital Workflow� AP EMR Orders InterfaceAP Orders InterfaceExamples of AP Digital Workflow� Digital PathologyApollo EPMM ImplementationSlide Number 49TECHNOLOGYFinal WorkflowExamples of AP Digital Workflow� WSI: Drivers for HFHSDecisions and GoalsTECHNOLOGYPrerequisites for Interfacing WSIValue of Interfacing WSISlide Number 57Slide Number 58Slide Number 59iScan HT Digital WorkflowSlide Number 61Slide Number 62SummarySummary �Realizing Effective Digital-Enabled Anatomic Pathology WorkflowConclusionQuestions?