digital diagnostic and research pathology...2019/10/03 · digital diagnostic and research...
TRANSCRIPT
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Bela MolnarM.D, PhD, ScD,.
CEO 3DHISTECH Ltd.
Digital diagnosticand research pathology
3DHISTECH’ andPartners’ meeting
2018
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Pathological images , slidesin the pathological lab
Digital Image
Center
Report
Pathologist
Autopsy
HE
IHC
FISH
Grossing
Scanning
The digital case
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Diagnostic workflow and 3DHISTECH digital solutions
Track and sign
Case Center Case ManagerCase ViewerQuantcenter
CaseViewer
FishQuantBestCyte
Pathonet
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Laboratory and diagnostic pathology workflowsolution : the LIS and PIS
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Track and sign : Barcode-based pathological sample tracking
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Case related informations(when, what, who, where)
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TnS and Casecenter linkopening of digital slides with CaseViewer
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• Voice recording tothe selected case In case of the new
voice recording, automaticmessages to the
administrator
• Annotated and live macro image
Digital case Attachments in the TnS
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3DHISTECH’ diagnostic solution in the pathology workflow:CaseManager
Track and sign
Case Center Case ManagerCase ViewerQuantcenter
CaseViewer
FishQuantBestCyte
Pathonet
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Digital Routine workflow of Pathologist
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PIS accept
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Case overview
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Digital slide overview
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Case forward or consultation
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Image analysis
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Reporting
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Digital microscope for the diagnostics of a pathology case :CaseViewer
Track and sign
Case Center Case ManagerCase ViewerQuantcenter
CaseViewer
FishQuantBestCyte
Pathonet
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CaseViewer digital slide tray
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CaeViewer: slide synchronization and ROI overlay
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CaseViewer: integrated IHC Quantification
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CaseViewer: H/E Morphology and multi colour
FISH slides with overlay
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CaseViwer : morphology and genetic analysis
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Plugins of CaseViewer
1. 2. 3. 4. 5. 6.
1. QuantCenter
2. Virtual tray
3. DDIC
4. Gradient map
5. MarkerCounter
6. TMA spot detection
QuantCenter
• Image Anaslysis module
• Embedded to the CaseViewer (from 2.2)
• Annotation features are available
• Fast result mask rendering
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CaseViewer 2.2 The new release
1. „Case-view: present all slide thumbnail in a list”
2. „Paralell slide view for more than 2 samples”
3. „Open digital slides from other vendor”
4. „ Increased interface for large screen view”
5. „Open different image formats like jpeg and tiff”
6. „Fastest file conversion”
7. „Macintosh support”
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Case-view
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Slide multi-view function
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The slide stack mode
1. Slide alignment 2. Investigation of the same ROI
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2. The slide stack mode
Haematoxylin-eosinEstrogen Her2Ki-67Her2/Cep17 FISH
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Fresh frozen surgery diagnostics with digital slidesor live imaging
Track and sign
Case Center Case ManagerCase ViewerQuantcenter
CaseViewer
FishQuantBestCyte
Pathonet
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Fresh Frozen Section telediagnostics
with the digital slide
Surgerygetting samples
Fresh frozen SpecimenNo sample
No pathologist movement
Immediate access diagnostic
Pathologyfresh frozen diagnostic
Case Center
Digital report
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New live : image based telediagnostics
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Digital pathology based molecular diagnosticsFISH analysis
Track and sign
Case Center Case ManagerCase ViewerQuantcenter
CaseViewer
FishQuantBestCyte
Pathonet
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A B Z-stacking
„Extended focus”
3
2
1
C
D
E
F
Single focus Extended focus
Digital microscopy – FISH scanning and evaluation
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Digital cervical cytology screening solutionin cooperation Cell solutions inc.
Track and sign
Case Center Case ManagerCase ViewerQuantcenter
CaseViewer
FishQuantBestCyte
Pathonet
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Specimen collection &
submit to lab CellSolutions Slide
processing Papanicolaou Staining
(manual or automated)
Coverslipping
(manual or automated)
CellSolutions Slide Product
Traditional screening
3D Histech Whole Slide ImagingCellSolutions BestCyte Digital Review
The CellSolultions Process
• Diagnostic Accuracy
• Optimum Quality
• Efficient
• Automation
• Scalable
• Low Cost
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Cell Sorter
• Fully automated slidescanner
capable of 24/7 operationprocessing BestPrep slides.
• Networked storage for virtual
slides.• Whole slide image analysis
using a new generation ofalgorithms that are highly
accurate.
• Detection of abnormal cells of all types, grouping those accordingto appearance and specific characteristics - presented in high
resolution.• Distributed networked system design allows system to scale to
match demand.
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Digital pathology solutionfor the sharing,teaching, training, QC: Pathonet
Track and sign
Case Center Case ManagerCase ViewerQuantcenter
CaseViewer
FishQuantBestCyte
Pathonet
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Slide seminar support
Slide seminar collection in PathoNet
• Case description
• Grosing images
• Slide samples
• Public acess
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Pathonet
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Integrated solutions for digital medical work
Track and sign
Case CenterCase ManagerCase ViewerQuantcenter
CaseViewer
FishQuantBestCyte
Pathonet
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LIS – PIS – Slide server Integration
PMS
HL7 3rd party LIS
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Contact person: Mr. Gábor Garányi
1. Requirements Project definition
2. Cooperation agreement with the
3rd party LIS/HIS vendor
3. System test definition:
Description of test enviroment and test process
4. Handover: closing - the end of the project
Integrations How to define integration request?
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Integration experiences and partners
Hospital/Lab City HIS/LIS Vendor Company HIS/LIS Application name Integration Type
Kantonsspital St.Gallen St. Gallen Basysdata PathoWin web
Atrium Medical Center Heerlen Palga Foundation Palga xml
Memorial Sloan Kettering Cancer Center NY-USA Cerner CoPathPlus HL7
Jan Yperman Hospital Ieper (Ypres) Pegasus Pegasus documentation
Bács-Kiskun Megyei Kórház Kecskemét Skyline Computer Custom Application xml
Synlab/Technipath Limonest LogSystem Cyan HL7
University Hospitals of Paris-Sud Bicêtre Paris Infologic Diamic xml
Laboratorium voor Pathologie Dordrecht Finalist Noord Nederland B.V. LMS/FinaLims web
SOTE I. Pathology Budapest ISH KFT. / T-Systems MedSol xml
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3DHISTECH macro and micro imaging systems
• Autopsy:
- Single images- Videos- Voice
• Grossing:- Single images
- Measurements- Annotations
• HE Morphology Labs:- Continuous scanning- In 2-3 hours available- Without measurements
• IHC Labs:- Batch scanning
- In 1 hours available- Without measurements
• FISH Labs:- Batch scanning- In 1-2 day hours available
- Special multichanel focus measurements
Pannoramic 250
iSaCS
Panoramic Midi Confocal
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New scanning workflow, New User experience
Live teleconsultation: Remote access for multiple users (one active and several passive) to
enable live teleconsultation
Planner/Scheduler mode: Tiered profile handling
New, more sensitive auto threshold algorithm for more accurate detection of adipose tissue
„Take all preview” function
Flexible fluorescence prescan profiles with user-selected filter types (including color preview)
Emergency/Urgent slide eligibility
Fluorescence filter table for easy overview and management
Focus quality measurement
New Features for Routine Pathology Labs
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New scanning workflow, New User experience
User Interface for Clinicians/Assistant
Overview of the whole scanning processDetailed view , Scan status of the slide
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New features
„Take all preview” function
Fully automatic process
Preview type:
- Brightfield
- Darkfield
- Low resolution prescan
- High resolution prescan
- High resolution prescan +
Use the slide sensor
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New Preview Window
Redesigned functions
Fat tissue detection
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New features
Direct access to Case Viewer from the software
Microscope mode:- After scan finished
Planner mode:- Profile card shows the URL of scanned slide
Scanning History:- Links to scanned digital slides
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New features
Live teleconsultation
- Real-time live teleconsultation
- Multiple users can connect
- Chat window
- The available functions for the client users:
- Full-screen live image
- Preview window
- Profile content
- Microscope Control
- Stage Control
- Start scan
Host side
Client side
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New features
Live teleconsultation
Chat window
Profile content
Preview window
Brightfield live image on the client side
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Image slide export and converter function
• Export images as JPEG and TIFF• Cus
• 16-bit uncompressed• Dicom
• Formats Aperio, Hamamatsu, etc.
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Z-stacking
„Extended focus”
2008: DeskSingle slide
BF
•Pannoramic – own brand
2006: 150Racks 6x50
BF+Fluor300 slides/day
2009: MidiTray of 12
BF+Fluor50 slides/day
Pannoramic slide scanner series
PANNORAMIC digital slide scanner series
2016: 250 Flash IIIRacks 6x50
BF+Fluor600 slides/day
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Plan- Apochromat 20x Plan - Apochromat 40xC-Apochromat w40x Plan-Apochromat
oil 63x
3DHISTECH new optical units for high quality slides
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The P1000 System in 2018
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• 100 slides / hour scanning at 40x
• Double width slide compatible
• Slide loading directly from stainer
and cover slipper magazine
• 3 objectives
20x dry, 40x dry, 40x immersion
• Brightfield only
• Completely new hardware
design
• New control software
Pannoramic 1000: Overview
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• Proprietary stage design
• Measurement instrument granite basis
• High speed, low vibration
• Optical encoder
Pannoramic 1000 FLASH IV Stage
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• Different slide racks are supported
Pannoramic 1000 FLASH IV Slide loading and racks
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Histology Research and Education products
• FL multiplex molecular imagingScanning
Visualisation: autofluorescence compensation
• Image analysisAI and rule based IA research tools
multiplex labeled fluorescent slide analysis
• Tissue Microarrays
Scanning enhancementsTMA preparation SW enhancements
• ImmunoHistochemistry staining and quantificationHigh throughput automations
• Educationparallel teaching rooms
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New functions of scanner software 2.0
• Take pre-view from all slides
• Pseudo colored, and zoomed preview
• Quick focusing with mouse in LIVE microscope
mode
• New filter table
• More profiles to one slide
• Profile history/Settings milestones
• Scanning history
• Separate scanning for TMA
• Live image Tools
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New functions of scanner software 2.0
Take all preview
- From all loaded slide
- With predefined preview type
- Fully automatic way
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Pannoramic Scanner Software 1.23 Pannoramic Scanner Software 2.0
Manual mode:- Routine Work- Preview- Focus- Service
Automatic mode:- Routine Work- Barcodes- Preview- Focus- Service
Microscope mode:- Profile settings panel- Individual preview window- Microscope Control panel- Take all preview
Planning mode:- Planner menu- Rack menu- Slide menu- Preview for each slide- Urgent slide
Profile settings panel
Microscope control panel
Microscope mode /(Manual scan )
Planning mode (Automatic scan modes)
Planner mode/(Automatic scan )
Redesigned functions
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Main Toolbar
Redesigned functions
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Main Toolbar
Illumination mode
Slide loader
Objective changer
Live on/off
Scan Properties
Start Scan
Stop progress
Take All Preview
Attach profile
Open profile
Save profile
Magnification
Redesigned functions
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Profile settings panel
Redesigned functions
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Microscope control panel
Redesigned functions
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Microscope mode
Redesigned functions
Microscope control panel
Preview window
Live focus contorol
Exposure time control on Live image
Stage control
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New Preview Window
Scanmap Source
Preview Source
Remove Coverslip
Fill holes inside scanmap
Remove Specks
Threshold
Calculate Threshold
User Marker with Threshold
Everything within marker
Delate mask
Redesigned functions
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New functions of scanner software 2.0 Color inversion
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Molecular multiplex pathology:
The MIDI Confocal system
No AutofluorescenceNo FL Crosstalk0.17 um /pixel resolution
FISHIn situ mRNAIn situ miRNA
Protein – ProteinDistance, interaction FRET
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Intensity statistic flat field correction
40.0x - Mouse Kidney Section
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Maxima extended focus mode
40x, Brain tissue section
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Autofluorescence filtering
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Midi - Standard FLZeiss Plan-Apochromat 20x
Midi Confocal - True ConfocalZeiss Plan-Apochromat 20x
Sample Images Fl vs. Confocal20 µm Cryostat Section of Mouse Kidney
DAPI, WGA-Alexa Fluor 488, Phalloidin-Alexa Fluor
568
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Pannoramic Confocal
Confocal – Standard FL comparison20x magnification
FL MIDI
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Confocal – Standard FL comparison 60x magnification
Pannoramic Confocal FL MIDI
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Confocal – Standard FL comparison 60x magnification
Pannoramic Confocal FL MIDI
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Confocal – 3D reconstructed slide
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DAPI + Opal 520
Visualization of 7 channels
DAPI + Opal 540
DAPI + Opal 550 DAPI + Opal 620
DAPI + Opal 650 DAPI + Opal 690
7 Fluorescent channels in one image
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Image analysis in the QuantCenter SW
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IHC Quantification modules
• PatternQuant: Pattern-based tissue segmentation andclassification
• HistoQuant: General purpose image analysis tool
• NuclearQuant: Automated IHC nuclear stain measurement
• MembraneQuant: Automated IHC membrane stainmeasurement
• CellQuant: Flexible IHC
measurement for cell nucleus / cytoplasm / membrane
• DensitoQuant: Easy and fast results for immunostainintensity
• FISHQuant: Powerful FISH evaluation on whole digitalslides
• CISHQuant: CISH evaluation on whole digital slides
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Image analysis enhancements
Localisation into languages : English, Hungarian
Whole slide image analysis Batch of slides analysis
Multistep decision tree
AI based image analysis
Faster and more simple measurement definition Gallery images
High resolution diagrams Exportable diagrams
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AI based PatternQuant training
EPITHEL
CONNECTIVE
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AI PatternQuant result
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ER-stained Breast Tissue
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Histological stains – identification of tissue elements
Different histochemical character – different color
HistoQuant for research purposes
HistoQuant segmentation
Color information
Intensity informations
Fluorescent and brightfield support
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Investigation of signal colocalization
Double stain:
CD8/Cd45red/green
Colocalization: yellow
Colocalisation:
• Two protein expression in one sample
• Parallel visualization of two signal
• Signal overlapping = colocalization
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SC ANNING THE H&E SLIDES
TMA Workflow and Tools
C A SESELECTION
Histopathological,
Clinical Data
Donor Blocks
H & E sections
A NALYSIS OF SLIDES DNA isolation
DNA amplification
DNA
sequencing
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Redesigned functions
TMA score detection
with new threshold
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New features
Separate scanning
- One profile to all separated scan areas
- Each separated scan area has different profile
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• Support for closed freehand annotations
• Language localization, ability to receive translations from our partners
• Possibility to repunch or override problematic tissue cores
• The number of PCR cores allowed in a single tube was increased
• Label pictures can be enhanced by changing contrast, brightness and gamma saturation
• Donor block image names are recognizable for the human eye
• Faster Slide Overlay function
• Stability and usability improvements in the Calibration menu
• New information sheet in the Excel export file for TMA GM users
• Tutorial videos for TMA Master users as well
• TMA Register: The ultimate tool for TMA slide planning
New features in TMA Control 2.7 & TMA Control 2.8
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The TMA Register
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TMA Control
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• Better TMA block quality
• Faster operaion
• Better donor block image quality
• Tool size measurement
• Block height measurement
• Easier sampling for molecular analysis
The TMA Master II SW quality
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iSaCS:
immunohistochemical Staining-automatic Coverslipping Scanning
Digital CaseIHCQuantification
In OncoTeam: Digital Case
visualisation
IHC stainingCoverslippingScanning
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iSaCS - Modular construction
4 rendszer folyamatos működésben
Modules:
- digital slide scanner
- slide preview module
- slide moving arm
- pipetting module
- reagent changer
- incubation module
- wash & rinse pumps
- air wiper module
- coverslipping module
- supporting frame
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Changes in the software of iSaCS
New failure management :
- Covering unit: we check the vacuum after the coverslip is taken
up
- Scan : Continous communication between the staining and
scanning parts
Improuved reagent recognation:
Virtual reagent card shows the needed reagent type for the
staining
Emergency STOP
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Changes on the hardware
Covering unit:
- Opto sensor for X axis
- Keyence Sensor for tip detection
- Mounting medium level engraving
- Mounting medium level clamp
- Accessories gate
Moving arm:
» Belt guide
» Fixed vane
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Changes on the hardware
Pipetting unit:
- Opto sensor for X axis
Accessories:
- Teflon coated reagent chamber
- Complete new tanks
- Black painted incubator
- Slide deflector for the incubator chamber
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Education
AnatomyPathologyPhysiologyCytologyVeterinery MedicineAuditorium
ProjectionsSingle roomMultiroomInteractive
Examinations
Semmelweis Uni.Anatomy Dept.
Budapest
Temesvar Uni.Dept. Of Pathology
Romania