configuring your digital pathology system based on ...€¦ · scanning platforms – an overview...

Configuring Your Digital Pathology System Based on Strategic Departmental Goals

Ulysses G. J. Balis, M.D., FCAP, FASCP, Fellow AIMBEProfessor of PathologyDirector, Division of Pathology InformaticsDirector, Computational Pathology Lab SectionDepartment of PathologyMichigan [email protected]

Faculty Disclosure

Advisory Board: Inspirata, Inc.

Plateau of ProductivitySlope of Enlightenment

Trough of Disillusionment

Peak

of I

nfla

ted

Expe

ctat

ions

Innovation Trigger

Phase

The Hype Cycle as Witnessed within Digital Pathology

Time

Expe

ctat

ions

Deep Learning All-digital Whole Slide Imaging Workflow

Specific DP Reimbursement Models

High ThroughputScanners

Digital Consultation Outreach

Mul

tiple

x as

says

FDA Clearance for Primary Diagnosis

QuantitativeImmunoscoring

Info

rmed

Det

ectio

nConventional MachineLearning

NLP

DICOM

Liqu

id B

x

Effective Federated Integration with AP-LIS systems

Digital Pathology System Configuration

Strategic Considerations Selection of a portfolio of scanning appliances, matching device capabilities to intended

use cases

Determination of storage needs and storage strategy

Computational requirements, both onsite and offsite

Tactical Considerations (also important but covered elsewhere in this workshop) Funding model

Physical Space and device colocation

Workflow

Equipment recharge/refresh model

Inter

Scanning Platforms – An overview

Scanning instruments have evolved through at least four major generations since commercial availability in 2001 (Aperio T1), with improvement seen in: Scanning speed

Image quality

Batch scanning capacity

WSI scanning appliances are now largely commoditized, with a growing number of models now slated for near-term FDA approval

Contemporary scanners, while far-superior to original offerings, still have opportunities for improvement in: Speed

Point spread function

Scan to view timing latency

Capture of additional optical modes besides brightfield (Z-stack, fluorescence, phase contrast, polarization, hyperspectral, just to name a few)

Workflow (pre-, analytical, and post-analytical)

Ease of integration with host AP-LIS systems and image interoperability

3DHistech

Hungarian company based in Budapest; founded in 1996 First European manufacturer of full turn-key solutions for WSI scanning Added expertise in tissue microarray management Significant Software portfolio Added offerings in Pathology Workflow

Digital Pathology

Frozen Section

Gross Examination

Remote Consultation Portal

Tumor Board Module

Numerous Educational solutions Scanner exhibit superb mechanical and optical design

3DHistech - Pannoramic DESK II (DW)

Entry-level low volume, single slide scanner

Default single-objective magnification of 41x ( 26x and 90x options)

1x3 inch and 2x3 inch slide (DW) capability

90 second scan time at 26x (15mm*15mm)

No fluorescence capability

No Z-stacking

Requires external PC to drive instrument

3DHistech - Pannoramic MIDI

Intermediate level, low volume, 12 slide scanner Two-objective design with default magnifications of 26x and 41x

Optional 90x brightfield Optional 20x, 32x, and 64x for fluorescence

1x3 inch only slide capability 90 second scan time at 26x (15mm*15mm) Fluorescence capability No Z-stacking Requires external PC to drive instrument

3DHistech - Pannoramic SCAN II

Intermediate level, moderate volume, 150 slide scanner Two-objective design with default magnifications of 26x and 41x


1x3 inch only slide capability 90 second scan time at 26x (15mm*15mm) Fluorescence capability No Z-stacking Requires external PC to drive instrument

3DHistech - Pannoramic 250 Flash II

High-volume, intermediate speed, 250 slide scanner

Two-objective design with default magnifications of 26x and 41x Optional 52x brightfield

Optional 20x, 32x, and 64x for fluorescence

1x3 inch only slide capability



Fluorescence capability

No Z-stacking


3DHistech - Pannoramic 250 Flash III

High-volume, high speed, 250 slide scanner Two-objective design with default magnifications of 26x and 41x


1x3 inch only slide capability 20 second scan time at 26x (15mm*15mm) 60 second scan time at 40x (15mm*15mm) Fluorescence capability No Z-stacking Requires external PC to drive instrument

3DHistech – Other Systems

Pannoramic 1000 – 100 slides / hour, water and oil immersion

Pannoramic Confocal

Pannoramic Midi II

Hamamatsu NanoZoomer SQ

Low-volume, low-speed, single slide scanner One-objective design with default magnification of 20x

0.23 micron pixels at 40x 0.46 micron pixels at 20x

1x3 inch slide capability 150 second scan time at 20x (15mm*15mm) 275 second scan time at 40x (15mm*15mm) No Fluorescence capability True Z-stacking capability Requires external PC to drive instrument Exceptionally precise slide scanning mechanism

Hamamatsu NanoZoomer S60

Intermediate-volume, intermediate-speed, 60 slide scanner 30 slide capacity with 2x3inch option

One-objective design with default magnification of 20x 0.23 micron pixels at 40x 0.46 micron pixels at 20x

1x3 inch and 2x3 inch slide capability 60 second scan time at 20x (15mm*15mm) 150 second scan time at 40x (15mm*15mm) Fluorescence capability as an option True Z-stacking capability Requires external PC to drive instrument Exceptionally precise slide scanning mechanism

Hamamatsu NanoZoomer S210

High-volume, intermediate-speed, 210 slide scanner One-objective design with default magnification of 20x

0.23 micron pixels at 40x


1x3 inch slide capability only 60 second scan time at 20x (15mm*15mm) 150 second scan time at 40x (15mm*15mm) No Fluorescence capability True Z-stacking capability Requires external PC to drive instrument Exceptionally precise slide scanning mechanism

Hamamatsu NanoZoomer XR

High-volume, high-speed, 320 slide scanner One-objective design with default magnification of 20x



1x3 inch slide capability only 35 second scan time at 20x (15mm*15mm) 45 second scan time at 40x (15mm*15mm) Fluorescence capability as an option True Z-stacking capability Requires external PC to drive instrument Exceptionally precise slide scanning mechanism

Huron TissueScope PE

Low-volume, low-speed, Two or 1-slide scanner 1 slide capacity when loading 2x3 slides

Two-objective design with magnifications of 20x and 40x 0.25 micron pixels at 40x


1x3 inch and 2x3 inch slide capability 300+ second scan time at 20x (15mm*15mm) 300+ second scan time at 40x (15mm*15mm) No Fluorescence capability No Z-stacking capability Requires external PC to drive instrument Exceptionally well-designed optical pathway with very uniform lighting

Huron TissueScope LE

Low-volume, low-speed, 12 slide scanner 6 slide capacity for 2 x 3 inch slides

4 slide capacity for 3x4 inch slides




Two-objective design with magnifications of 20x and 40x 0.25 micron pixels at 40x 0.50 micron pixels at 20x

300+ second scan time at 20x (15mm*15mm) 300+ second scan time at 40x (15mm*15mm) No Fluorescence capability No Z-stacking capability Requires external PC to drive instrument Exceptionally well-designed optical pathway with very uniform lighting

Huron TissueScope CF

Low-volume, low-speed, 12 slide fluorescence scanner 6 slide capacity for 2 x 3 inch slides






300+ second scan time at 20x (15mm*15mm) 300+ second scan time at 40x (15mm*15mm) Advanced Fluorescence capability No Z-stacking capability Requires external PC to drive instrument Exceptionally well-designed optical pathway with very uniform lighting

Huron TissueScope LE120

Intermediate-volume, low-speed, 120 slide scanner 60 slide capacity for 2 x 3 inch slides






300+ second scan time at 20x (15mm*15mm) 300+ second scan time at 40x (15mm*15mm) No Fluorescence capability No Z-stacking capability Does not requires external PC to drive instrument – has integrated touchscreen controller Exceptionally well-designed optical pathway with very uniform lighting

Leica Aperio CS2

Low-volume, low-speed, 5-slide scanner 1 slide capacity when loading 2x3 slides

One-objective design with magnifications of 20x (plus a 2x optical changer to yield 40x) 0.25 micron pixels at 40x 0.50 micron pixels at 20x

1x3 inch and 2x3 inch slide capability 100 second scan time at 20x (15mm*15mm) 300 second scan time at 40x (15mm*15mm) No Fluorescence capability Local Z-stacking capability Requires external PC to drive instrument Numerical aperture of light condenser pathway is suboptimal Extensive companion FDA-cleared diagnostic software available

Leica Aperio FL

Low-volume, low-speed, 5-slide fluorescence scanner 1 slide capacity when loading 2x3 slides


1x3 inch and 2x3 inch slide capability 100 second scan time at 20x (15mm*15mm) 300 second scan time at 40x (15mm*15mm) Integrated Fluorescence capability Local Z-stacking capability Requires external PC to drive instrument Numerical aperture of light condenser pathway is suboptimal Extensive companion FDA-cleared diagnostic software available

Leica Aperio AT2

High-volume, intermediate-speed, 400 slide scanner 1 slide capacity when loading 2x3 slides


1x3 inch and 2x3 inch slide capability 60 second scan time at 20x (15mm*15mm) 155 second scan time at 40x (15mm*15mm) No Fluorescence capability Local Z-stacking capability Requires external PC to drive instrument Numerical aperture of light condenser pathway is suboptimal Extensive companion FDA-cleared diagnostic software available

MicroScan SL5

Low-volume, intermediate-speed, 1 or 2 slide scanner One-objective design with user-selectable magnifications

2x: 4.54 micron pixels 4x: 2.27 micron pixels 10x: 0.908 micron pixels 20x: 0.454 micron pixels 40x: 0.227 micron pixels

45 second scan time at 20x (15mm*15mm) 169 second scan time at 40x (15mm*15mm) No Fluorescence capability No Z-stacking capability Requires external PC to drive instrument Early versions exhibited optical scan artifacts in the digital images

Now corrected

Motic EasyScan

Low-volume, low-speed, 1 or 6 slide scanner

One-objective design, making use of a high numerical aperture 20x lens 20x: 0.52 micron pixels

40x: 0.26 micron pixels



No Fluorescence capability

True Z-stacking capability


Motic EasyScanPro

Low-volume, intermediate-speed, 1 or 6 slide scanner

One-objective design, making use of an ultra-high numerical aperture 20x lens 20x: <0.52 micron pixels

40x: <0.26 micron pixels






Objective Imaging Glissando

Low-volume, intermediate-speed, 1 or 2 slide scanner 1 slide capacity when loading 2x3 slides

One-objective design, making use of a magnification doubler 20x: 0.50 micron pixels 40x: 0.275 micron pixels

35 second scan time at 20x (15mm*15mm) 140 second scan time at 40x (15mm*15mm) No Fluorescence capability True Z-stacking capability Requires external PC to drive instrument

Philips UFS

High-volume, high-speed, 300 slide scanner One-objective design with magnifications of 40x


Random access system for each slide basket 1x3 inch slide capability only 35 second scan time at 20x (15mm*15mm) 60 second scan time at 40x (15mm*15mm) No Fluorescence capability No Z-stacking capability in current model(planned for next model) Does not requires external PC to drive instrument– has integrated touchscreen

and controller Part of overall FDA-cleared “pixel pipeline” for primary histopathological

diagnosis

Roche Ventana iScan Coreo

High-volume, low-speed, 160 slide scanner Multi-objective design with magnifications of:

4x: 2.27 micron pixels 10x: 0.908 micron pixels 20x: 0.454 micron pixels 40x: 0.227 micron pixels

1x3 inch slide capability only 120 second scan time at 20x (15mm*15mm) 450 second scan time at 40x (15mm*15mm) No Fluorescence capability Local Z-stacking capability Does not require external PC to drive instrument – has integrated touchscreen and

controller Extensive companion FDA-cleared diagnostic software available

Roche Ventana iScan HT

High-volume, high-speed, 360 slide scanner Multi-objective design with magnifications of:

4x: 2.27 micron pixels 10x: 0.908 micron pixels 20x: 0.454 micron pixels 40x: 0.227 micron pixels

1x3 inch slide capability only 45 second scan time at 20x (15mm*15mm) 72 second scan time at 40x (15mm*15mm) No Fluorescence capability Local Z-stacking capability Does not require external PC to drive instrument – has integrated touchscreen and

controller Extensive companion FDA-cleared diagnostic software available

Sakura VisionTek

Low-volume, low-speed, 4 slide scanner Three-objective design with magnifications of:

2.5x: 2.2 micron pixels

10x: 0.55 micron pixels 20x: 0.275 micron pixels

1x3 inch slide capability only 175 second scan time at 20x (15mm*15mm) >400 second scan time at 40x (15mm*15mm) No Fluorescence capability True Z-stacking capability Requires external PC to drive instrument

Sakura VisionTek M6

Low-volume, intermediate-speed, 4 slide scanner Three-objective design (Carl Zeiss) with magnifications of:

2.5x: 2.2 micron pixels

20x: 0.275 micron pixels 40x: 0.138 micron pixels

1x3 inch slide capability only 90 second scan time at 20x (15mm*15mm) 360 second scan time at 40x (15mm*15mm) No Fluorescence capability True Z-stacking capability Requires external PC to drive instrument

Grundium Ocus

Low-volume, single scanner

Single-objective design (proprietary), based on a ground-up redesign of optics obtained from experience in the design of smart phone high-performance cameras

with magnifications of:

20x: 0.48 micron pixels or

40x: 0.24 micron pixels

1x3 inch slide capability only




No external PC required to drive instrument – Smart phone interface-capable

Grundium Ocus

Extremely compact, owing to miniaturization technologies developed in the smart phone industry

Potential for portable stand-alone operation with WiFi connectivity, owing to battery operation

Fully roboticized stage and focus Auto-focus Integrated Web Server technology yielding

capability for stand-alone operation without the use of an image-server

Potential for effective utilization in low resource settings

Given a single slide’s typical 1 x 1 cm2 scanning area(or 3.7 cm2 if we’re being honest)

05

• (1k - 2k) *300 MB = 300-600 Gb per day

• 9 - 18 Tb per month

• 108 - 144 TB per year (for 1 x 1 cm slides)

• 1.479-1.971 PB per year (for actual 3.7 cm2 slide areas)

Actual Production Storage Required

041000 - 2000 slides/day from a typical practice causes upwards scaling of storage requirements

Scaling Up

03Reduced to ~300 MB

LosslessCompression

0240k x 40k = 1.6 GB (single channel) or4.8 GB (RGB), prior to lossless compression

1 cm2 patch

1 cm x 10 mm/1 cm x 1000 microns/1 mm x 4 pixels/micron =

40,000 pixels/cm

01Slide Linear Density

Typical Cloud Storage Pricing Calculation

Service (1 x 1 cm) Monthly Fee

30 TB of Multi-Regional Storage 399.36

6 TB Network Traffic (6,050GB) at $0.11/per GB 675.77

Network Ingress 0.00

$0.05/per 10,000 PUT/POST/GET bucket/GET service requests: $1.00 1.00

$0.004/per 10,000 GET object and HEAD requests: $10.00 10.00

Total per month 1,086.13

Total per year 13,033.56

Service (3.7 x 3.7 cm) Monthly Fee

60 TB of Multi-Regional Storage 1,597.44

9TB Network Traffic (9,216GB) at $0.11/per GB 1,013.76

Network Ingress 0.00

$0.05/per 10,000 PUT/POST/GET bucket/GET service requests: $1.00 1.00

$0.004/per 10,000 GET object and HEAD requests: $10.00 10.00

Total per month 2,622.20

Total per year 31,466.40

Assuming 80,000 cases per year (@ 10 slides/case)….$0.016 per slide for storage and networking

$0.039 per slide for storage and networking

Closing Thoughts

Generate a comprehensive set of use-cases and requirements for each workflow, prior to acquiring any hardware

Attempt, whenever possible, to engineer “device refresh” terms into purchase or lease contracts

Be cautious of single-vendor solutions, as a diverse ecosystem can confer “hybrid vigor” to the overall continuity of service

Be vigilant of the emergence of practice guidelines that will inform rational data retention strategies, given the large associated storage requirements for WSI workflow

configuring your digital pathology system based on ...€¦ · scanning platforms – an overview...

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