Digital diagnostic and research pathology...2019/10/03 · Digital diagnostic and research...

Bela MolnarM.D, PhD, ScD,.

CEO 3DHISTECH Ltd.

Digital diagnosticand research pathology

3DHISTECH’ andPartners’ meeting

2018

Pathological images , slidesin the pathological lab

Digital Image

Center

Report

Pathologist

Autopsy

HE

IHC

FISH

Grossing

Scanning

The digital case

Diagnostic workflow and 3DHISTECH digital solutions

Track and sign

Case Center Case ManagerCase ViewerQuantcenter

CaseViewer

FishQuantBestCyte

Pathonet

Laboratory and diagnostic pathology workflowsolution : the LIS and PIS

Track and sign : Barcode-based pathological sample tracking

Case related informations(when, what, who, where)

TnS and Casecenter linkopening of digital slides with CaseViewer

• 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

3DHISTECH’ diagnostic solution in the pathology workflow:CaseManager

Track and sign


CaseViewer

FishQuantBestCyte

Pathonet

Digital Routine workflow of Pathologist

PIS accept

Case overview

Digital slide overview

Case forward or consultation

Image analysis

Reporting

Digital microscope for the diagnostics of a pathology case :CaseViewer

Track and sign


CaseViewer

FishQuantBestCyte

Pathonet

CaseViewer digital slide tray

CaeViewer: slide synchronization and ROI overlay

CaseViewer: integrated IHC Quantification

CaseViewer: H/E Morphology and multi colour

FISH slides with overlay

CaseViwer : morphology and genetic analysis

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

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”

Case-view

Slide multi-view function

The slide stack mode

1. Slide alignment 2. Investigation of the same ROI

2. The slide stack mode

Haematoxylin-eosinEstrogen Her2Ki-67Her2/Cep17 FISH

Fresh frozen surgery diagnostics with digital slidesor live imaging

Track and sign


CaseViewer

FishQuantBestCyte

Pathonet

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

New live : image based telediagnostics

Digital pathology based molecular diagnosticsFISH analysis

Track and sign


CaseViewer

FishQuantBestCyte

Pathonet

A B Z-stacking

„Extended focus”

3

2

1

C

D

E

F

Single focus Extended focus

Digital microscopy – FISH scanning and evaluation

Digital cervical cytology screening solutionin cooperation Cell solutions inc.

Track and sign


CaseViewer

FishQuantBestCyte

Pathonet

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

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.

Digital pathology solutionfor the sharing,teaching, training, QC: Pathonet

Track and sign


CaseViewer

FishQuantBestCyte

Pathonet

Slide seminar support

Slide seminar collection in PathoNet

• Case description

• Grosing images

• Slide samples

• Public acess

Pathonet

Integrated solutions for digital medical work

Track and sign

Case CenterCase ManagerCase ViewerQuantcenter

CaseViewer

FishQuantBestCyte

Pathonet

LIS – PIS – Slide server Integration

PMS

HL7 3rd party LIS

Contact person: Mr. Gábor Garányi

[email protected]

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?

mailto:[email protected]

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

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

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

New scanning workflow, New User experience

User Interface for Clinicians/Assistant

Overview of the whole scanning processDetailed view , Scan status of the slide

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

New Preview Window

Redesigned functions

Fat tissue detection

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

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

New features

Live teleconsultation

Chat window

Profile content

Preview window

Brightfield live image on the client side

Image slide export and converter function

• Export images as JPEG and TIFF• Cus

• 16-bit uncompressed• Dicom

• Formats Aperio, Hamamatsu, etc.

Z-stacking

„Extended focus”

2008: DeskSingle slide

BF

•Pannoramic – own brand

2006: 150Racks 6x50

BF+Fluor300 slides/day

2009: MidiTray of 12


Pannoramic slide scanner series

PANNORAMIC digital slide scanner series

2016: 250 Flash IIIRacks 6x50


Plan- Apochromat 20x Plan - Apochromat 40xC-Apochromat w40x Plan-Apochromat

oil 63x

3DHISTECH new optical units for high quality slides

The P1000 System in 2018

• 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

• Proprietary stage design

• Measurement instrument granite basis

• High speed, low vibration

• Optical encoder

Pannoramic 1000 FLASH IV Stage

• Different slide racks are supported

Pannoramic 1000 FLASH IV Slide loading and racks

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

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

New functions of scanner software 2.0

Take all preview

- From all loaded slide

- With predefined preview type

- Fully automatic way

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 )


Main Toolbar


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


Profile settings panel


Microscope mode



Preview window

Live focus contorol

Exposure time control on Live image

Stage control

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


New functions of scanner software 2.0 Color inversion

Molecular multiplex pathology:

The MIDI Confocal system

No AutofluorescenceNo FL Crosstalk0.17 um /pixel resolution

FISHIn situ mRNAIn situ miRNA

Protein – ProteinDistance, interaction FRET

Intensity statistic flat field correction

40.0x - Mouse Kidney Section

Maxima extended focus mode

40x, Brain tissue section

Autofluorescence filtering

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

Pannoramic Confocal

Confocal – Standard FL comparison20x magnification

FL MIDI

Confocal – Standard FL comparison 60x magnification

Pannoramic Confocal FL MIDI

Confocal – 3D reconstructed slide

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

Image analysis in the QuantCenter SW

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

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

AI based PatternQuant training

EPITHEL

CONNECTIVE

AI PatternQuant result

ER-stained Breast Tissue

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

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

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


TMA score detection

with new threshold

New features

Separate scanning

- One profile to all separated scan areas

- Each separated scan area has different profile

• 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

The TMA Register

TMA Control

• 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

iSaCS:

immunohistochemical Staining-automatic Coverslipping Scanning

Digital CaseIHCQuantification

In OncoTeam: Digital Case

visualisation

IHC stainingCoverslippingScanning

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

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

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

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

Education

AnatomyPathologyPhysiologyCytologyVeterinery MedicineAuditorium

ProjectionsSingle roomMultiroomInteractive

Examinations

Semmelweis Uni.Anatomy Dept.

Budapest

Temesvar Uni.Dept. Of Pathology

Romania

Digital diagnostic and research pathology...2019/10/03 · Digital diagnostic and research...

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