clinical digital workflow - 3dhistech ltd. · clinical digital workflow begins. specimen pathology...
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A.C.F. Makkus. MD
PAL Dordrecht, Dordrecht, The Netherlands
www.paldordrecht.nl
Clinical digital workflow
A.C.F. Makkus. MD
PAL Dordrecht, Dordrecht, The Netherlands
www.paldordrecht.nl
Clinical digital workflow
What is clinical workflow?
Receiving a sample and send out a report with findings what happens in our
laboratory in between is the workflow
We are a paperless laboratory
• everything is tracked using barcodes
• no paper, not even a request form
• Normally we use the slide as a reference to track
• Digital pathology means you do not have a slide, only images
• Tracking your cases becomes crucial
What I’m trying to convey to you?
• Take you on a tour of what happens to a tissue sample in our laboratory
• What impact digital pathology has on the workflow: The good, the bad and the
ugly
• I will skip the creation of the reports
• I will skip the reasoning for a diagnosis
• I will skip the intricacies of safe reporting
• No gory pictures
Why?
• Try to do a varying workload with the same people
• Time saving ($) for the pathologists and technicians• Measurements, cases immediately available when clinicians call
• Running around assigning cases and retrieving them
• Consultation/review/panels through digital slides
Opportunities forTime Saving
Laboratory chores
• Less Time Matching• Matching paperwork to case
• Matching new stains upon arrival
• Tracking receipt of ordered slides
• less Correcting: • Transporting case to correct pathologist
• Reducing duplicate slides ordered
• Picking up wrong slides / missing slides
• Retrieving prior cases
Administration chores
• Saving Time Transporting Cases: • Packing cases for consult
• Organizing Cases:
• Tracking cases ready for review
• Tracking cases for conferences
• Saving Time checking for Cases: • Checking if STAT cases have arrived
• Visibility of overdue cases
• Searching cases when receiving a call
Foundation
9 pathologists
1 trainee
2 hospitals
STZ hospital (full service)
GP’S in the area
Private practices
Output
~ 140,000 slides
~ 50,000 requested slides
~ 250 outside consultations
~ 400 outside revisions
~ 36,000 cases Histology
~ 105,000 blocks
500 Double Width slides
Scanning
600 GB/day – 155 TB/year
50 TB / year
230 GB / day
Storage
225 DAYS
85 DAYS
~ 200 SLIDES / DAY
ISO 15189 certified for histology, cytology, autopsy pathology and molecular pathology
Requests vs all Cases
Budget
Additional stains (30%)
Would need 3x scanners
3x the storage
3x the network load
We want Double width slides
Pathologists
The microscope is faster on routine cases
Poor initial acceptance
“let me look at it with my own microscope”
“Low hanging fruit”
Workflow
Would need Case Assignment by Laboratory management system
Need a system to distribute the cases, fairly according to (workload, tumor boards and
interest)
Visible needs• Scanner
• Viewer
• Invisible requirements
• Workflow• Assign cases to pathologists
• Keeping track of the cases…
• Interests, who’s in, equal workload
• Assign the requested slides to pathologist
• Trackable
• Integration with other systems• Seamless
• Case-mixup proof
• Acces anywhere
• Stable, uptime 99,99%
• Scalable
ORDERS
Pathology orders are electronically requested
o Patient ID and clinicians ID are automatically added
o The physician fills out relevant clinical history
o Markings are noted
o Mayor tumor types have a mandatory clinical data set to
be entered Eg Breast: tumor’s location, sentinel node, previuos
therapy
o Subsequently a barcode label is printed and affixed to the container
o Transportation to the laboratory
o Which is scanned in the lab en the specimen enters:
Clinical Digital Workflow begins
Specimen
Pathology specimens are electronically entered
o The barcode is scanned and all the associated
clinical information is retrieved from the hospital
and electronically transferred into the laboratory
information system (LIS)
o The LIS queries the national as well as local
database for the pathology history
o In pathology not the patient is the identifying
object but the specimen
STAGE 1 in the LIS
Grossing-cassettes
Cassettes with tissue ready to be processed
o Cassettes are printed and a barcode is printed on fortracking
o Cassettes are filled with patient material
o A report of the grossing is dictated into a speechrecognition system and (after recognition andredaction) added as a grossing report to the case
o Protocols are used for cut-up, making sure specimensare adequately sampled
o The LIS now knows how many cassettes constitute a case, the last printjob lets the LIS know it has entered
STAGE 2 in the LIS
Embedding
Cassettes ready to be blocks
o Based on the barcode on the cassette the grossing is retrieved
o The content of the cassette is compared to the grossingdescription
o The number of biopsies is checked
o Biopsies are ordered and orientated
o etc
o When the data is retrieved from the LIS, it’s at embedding
STAGE 3 in the LIS
Sectioning
The blocks are cut
o Based on the barcode on the cassette the grossing is retrieved
o Based on the barcode of the cassette the appropiate slides are printed
o With appropiate label and barcode also for the special stainers
o Slices of tissue are put on the slides
o The printing of the slides with unique numbers lets the LIS know how many slides and with what staining there should beand the stage
STAGE 4 in the LIS
Staining
The slides are stained
o Based on the barcode on the slide the stain is selected
o H&E
o Special stains like Fe, PAS, Grocott
o Immunohistochemistry
o Entry in the staining machine signals to the LIS that they
have entered
STAGE 5 in the LIS
Coverslipping
The slides are coverslipped
o When the slide leaves the coverslipper it’s barcode is
scanned
o Exiting the coverslipper signals to the LIS that they have
entered
STAGE 6 in the LIS
Scanning
The slides are scanned
o When the slide leaves the coverslipper they enter the
scanner
STAGE 7 in the LIS
PAPERLESS & GLASS SLIDES
= GREEN !
PAPERLESS & DIGITAL SLIDES
= CLUELESS
XML-COMMUNICATION
The slides barcode is scanned by the scanner
o When the slides barcode number (5943239) is scanned bythe scanner, this number is used to set-up communicationwith the LIS
o LIS responds: case, block, number, stain, profile among others
o Resulting in a slidename: T18-16301 C 03 Vimentin
o The scanners applies profile: Scanprofile_default
o This signals the LIS that the slide is at
But is the case complete?
STAGE 8 in the LIS
QUESTION BY CASECENTER
<?xml version="1.0" encoding="UTF-8"?>
<lmsinfo nummer="5943239"/>
REPLY BY LIS
<?xml version="1.0" encoding="utf-8"?>
<antwoord type="ack">T18-16301
<rubriek naam="scancode">5943239</rubriek><rubriek naam="staining">Vimentin</rubriek><rubriek naam="materialname">paraffine cassette</rubriek><rubriek naam="block">3</rubriek>
<rubriek naam="techniquename">Histochemisch</rubriek><rubriek naam="number">1</rubriek><rubriek naam="name">Scanprofiel_default</rubriek>…..</antwoord>
Full integration: LIS - Casecenter
Bi-Directional update of status change
o Achieved through XML
Creating LIS <<=
>>
CaseCenter
Opening LIS <<=
>>
CaseCenter
Closing LIS <<=
>>
CaseCenter
Deleting LIS <<=
>>
CaseCenter
Viewing LIS <<=
>>
CaseCenter
Lessons from P1000
Obsessed with getting the diagnosis out fast
o It’s fast… Images are beautiful
o The network and servers can easily support fully digital
o But…
if a case is being scanned when will it arrive???
Lessons from P1000
o Assign cases prior to scanning or after scanning.
o Which leads to cases without images they come later or substantial delay
if assigned after scanning.
o It is made worse by the capacity of the P1000
It must be done while they are still in the scanner
By the LIS!
What do you need from the LIS as a pathologist
Accurate information regarding:
o Case complete -> assign to pathologist
o Incomplete, for primary diagnosis -> wait...
o Additional requests case complete -> report
complete
o Additional requests case INcomplete -> report
with different colour
Lab
Pathologist
•Pathologists present
•Part-Time Factor•MDT Times•etc
Local Specialties
• Gynecolgy• Urology• Traning• etc
Distribution Software
Re-Assign
Day Listoverzicht
WorkOverview
Primary diagnosis
• Analogue
• Collect the slides after they leave the cover slipper
• Make sure the case is complete, if not wait for the remainder of the slides
• Assign the case to available pathologist, with regard to expertise
• Deliver the slide tray to the pathologist
• Digital
• The scanner scans the slides after they leave the cover slipper
• The XML signals that a slide is available
• The LIS checks whether the case is complete
If complete assign the case
If Incomplete wait…
• Have to have a means to find the cases that are not completely scanned after a certain time
• NB Done while the slide itself might be in the scanner
Requested additional slides
• Analogue
• Collect the slides after they leave the cover slipper
• Make sure the case is complete, if not wait for the remainder of the slides
• Assign the slides to the requesting pathologist, or his/her substitute
• Deliver the slide on a tray to the pathologist
• Digital
• The scanner scans the slides after they leave the cover slipper
• The XML signals that a slide is available
• The LIS checks whether the case is complete
• If complete assign the case, if Incomplete assign it with a different colour
Failover cluster Palga
National database
workstations
Servers:
• Storage
• Speechrecognition
• ImageServer
• Lab. Management System
• PALGA (authorized content, reports)
• Test Servers
• LMS, ImageServer, Palga, speech
Web based communication, xml:
<?xml version="1.0" encoding="utf-8"?>
<antwoord type="ack">T13-04000
<rubriek naam="scancode">746880</rubriek>
<rubriek naam="staining">PAS+</rubriek>
<rubriek naam="stainingnameextension"/>
<rubriek naam="materialname">cassette</rubriek>
<rubriek naam="techniquename">Histochemisch</rubriek>
<rubriek naam="sampledate_out">20130409143750</rubriek>
<rubriek naam=”specimen">1</rubriek>
<rubriek naam="block">1</rubriek>
<rubriek naam=”scanprofiel">scanprofiel_PAS+</rubriek>
<rubriek naam="paraffinenumber">1</rubriek>
</antwoord>
WORKFLOW
List of scanned images:
• Newly scanned cases (completed slidesets)
• Red when they are incomplete
• Signed out cases with new scanned images (eg Her2Neu)
• Cases disappear when digitally authorized or manually removed
Drop down list:
• All digitized slides
• Separate entries for each pathologist
Drop down list of images to be evaluated:
• Requested images
• Last week images
• Yesterdays image(sets)
Grossing
Tissue
Processing
Slide storage
Stainers, immuno
Scanner
Slide
storage
Scanner
Grossing
Tissue
Processing
Slide storage
Stainers, immuno
Scanner
time saved:
5 hours each day
@ 130.000 slides
Time saving:in line with other laboratories
Scan_profiles
• Continous loading possible no user/technician interaction
• Scan profiles are automatically selected based on stain or protocol
• 20x - 40x
• Lighter / darker presentation
• Scan entire slide if it is very fatty tissue
• For cytology: scan everything within the circle
Web based communication, xml:
<?xml version="1.0" encoding="utf-8"?>
<antwoord type="ack">T13-04000
<rubriek naam="scancode">746880</rubriek>
<rubriek naam="staining">PAS+</rubriek>
<rubriek naam="stainingnameextension"/>
<rubriek naam="materialname">cassette</rubriek>
<rubriek naam="techniquename">Histochemisch</rubriek>
<rubriek naam="sampledate_out">20130409143750</rubriek>
<rubriek naam=”specimen">1</rubriek>
<rubriek naam="block">1</rubriek>
<rubriek naam=”scanprofiel">Scanprofiel_PAS+</rubriek>
<rubriek naam="paraffinenumber">1</rubriek>
</antwoord>
Easy acces viewing
WORKFLOW
PATHOLOGYIMAGEEXCHANGE
PROJECT OF THE DUTCH PATHOLIGIST AND THE AUTOMATED PATHOLOGY
DATABASE TO WHICH ALL DUTCH LABS ARE CONNECTED SINCE 1980
Slide kindly provided by Dr. André Huisman, Medical PHIT
• Facilitate workflow of the exchange of Whole Slide Images (WSI), between pathology laboratories
• By Connecting current information systems like PALGA the solution is easily used/accepted
• Patient care is improved by easy and timely consultation / panelreview
• Future proof
• The solution has to be in compliance with dutch law
• Dicom is used for exchange of images, provided by 3DHistech
Goals project PIE
Slide kindly provided by Dr. André Huisman, Medical PHIT
• Process takes up to14 days (50% > 4 days)
• Patient has to wait for definitive result and treatment
• Stress, loss of productivity and quality of life
• Optimal mail logistics: process 2 days
• Low volume (250/400 cases) but high impact
Digitally: same day?
Logistics revisions and consultations
• Scan slides
• Upload to server
• Send message
• Log into server
• Assess
• Make report
• Send report to requesting pathologist
Done on the same day
Logistics revisions and consultations
Pathology Lab A
Pathology Lab
B
Players
suppliers• Sectra
• DTHS
• RAM Infotechnology
vendors• Sysmex (3DHistech)
• Hamamatsu
• 3DHistech (dicom converter)
• Philips
• Pilot Labs:• Manual upload: Pal (Dordrecht) &
ErasmusMC
• Automatic upload: Radboudumc & UMCU
• Pilot Panels: • Soft tissue Panel Noord NL (UMCG)
• ThymomA Panel (Maasstad/ErasmusMC)
• Heamatology Panel (Radboudumc)
• LANS oesophagus Panel (AMC)
Revisions consultations / panels
Pathology Lab A Pathology Lab B
Panel members
Answer
Panel diagnosisRequest
LoginUpload Images
Easy synoptic reporting
Easy creation of snapshots for long time storage with
the report
THANK YOU
QUESTIONS ?