Configuring Your Digital Pathology System Based on Strategic Departmental Goals

Transcription

1 Configuring Your Digital Pathology System Based on Strategic Departmental Goals Ulysses G. J. Balis, M.D., FCAP, FASCP, Fellow AIMBE Professor of Pathology Director, Division of Pathology Informatics Director, Computational Pathology Lab Section Department of Pathology Michigan Medicine

2 Faculty Disclosure Advisory Board: Inspirata, Inc.

3

4 Time The Hype Cycle as Witnessed within Digital Pathology Expectations Multiplex assays Informed Detection Liquid Bx Peak of Inflated Expectations Deep Learning Digital Consultation Outreach Conventional Machine Learning NLP DICOM Quantitative Immunoscoring High Throughput Scanners Specific DP Reimbursement Models FDA Clearance for Primary Diagnosis Effective Federated Integration with AP-LIS systems All-digital Whole Slide Imaging Workflow Innovatio n Trigger Phase Trough of Disillusionment Slope of Enlightenment Plateau of Productivity

5 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

6 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

7 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

8 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

9 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

10 3DHistech - Pannoramic SCAN II Intermediate level, moderate volume, 150 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

11 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 36 second scan time at 26x (15mm*15mm) 90 second scan time at 40x (15mm*15mm) Fluorescence capability No Z-stacking

12 3DHistech - Pannoramic 250 Flash III High-volume, high 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 20 second scan time at 26x (15mm*15mm) 60 second scan time at 40x (15mm*15mm) Fluorescence capability No Z-stacking

13 3DHistech Other Systems Pannoramic slides / hour, water and oil immersion Pannoramic Confocal Pannoramic Midi II

14 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 Exceptionally precise slide scanning mechanism

15 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 Exceptionally precise slide scanning mechanism

16 Hamamatsu NanoZoomer S210 High-volume, intermediate-speed, 210 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 only 60 second scan time at 20x (15mm*15mm) 150 second scan time at 40x (15mm*15mm) No Fluorescence capability True Z-stacking capability Exceptionally precise slide scanning mechanism

17 Hamamatsu NanoZoomer XR High-volume, high-speed, 320 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 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 Exceptionally precise slide scanning mechanism

18 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 0.50 micron pixels at 20x 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 Exceptionally well-designed optical pathway with very uniform lighting

19 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 2 slide capacity for 4x5 inch slides 1 slide capacity for 5x7 inch slides 1 slide capacity for 6x8 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 Exceptionally well-designed optical pathway with very uniform lighting

20 Huron TissueScope CF Low-volume, low-speed, 12 slide fluorescence scanner 6 slide capacity for 2 x 3 inch slides 4 slide capacity for 3x4 inch slides 2 slide capacity for 4x5 inch slides 1 slide capacity for 5x7 inch slides 1 slide capacity for 6x8 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) Advanced Fluorescence capability No Z-stacking capability Exceptionally well-designed optical pathway with very uniform lighting

21 Huron TissueScope LE120 Intermediate-volume, low-speed, 120 slide scanner 60 slide capacity for 2 x 3 inch slides 40 slide capacity for 3x4 inch slides 20 slide capacity for 4x5 inch slides 10 slide capacity for 5x7 inch slides 10 slide capacity for 6x8 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 Does not requires external PC to drive instrument has integrated touchscreen controller Exceptionally well-designed optical pathway with very uniform lighting

22 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 Numerical aperture of light condenser pathway is suboptimal Extensive companion FDA-cleared diagnostic software available

23 Leica Aperio FL Low-volume, low-speed, 5-slide fluorescence 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) Integrated Fluorescence capability Local Z-stacking capability Numerical aperture of light condenser pathway is suboptimal Extensive companion FDA-cleared diagnostic software available

24 Leica Aperio AT2 High-volume, intermediate-speed, 400 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 60 second scan time at 20x (15mm*15mm) 155 second scan time at 40x (15mm*15mm) No Fluorescence capability Local Z-stacking capability Numerical aperture of light condenser pathway is suboptimal Extensive companion FDA-cleared diagnostic software available

25 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: micron pixels 20x: micron pixels 40x: 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 Early versions exhibited optical scan artifacts in the digital images Now corrected

26 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 180 second scan time at 20x (15mm*15mm) 360 second scan time at 40x (15mm*15mm) No Fluorescence capability True Z-stacking capability

27 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 90 second scan time at 20x (15mm*15mm) 180 second scan time at 40x (15mm*15mm) No Fluorescence capability True Z-stacking capability

28 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: 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

29 Philips UFS High-volume, high-speed, 300 slide scanner One-objective design with magnifications of 40x 0.25 micron pixels at 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

30 Roche Ventana iscan Coreo High-volume, low-speed, 160 slide scanner Multi-objective design with magnifications of: 4x: 2.27 micron pixels 10x: micron pixels 20x: micron pixels 40x: 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

31 Roche Ventana iscan HT High-volume, high-speed, 360 slide scanner Multi-objective design with magnifications of: 4x: 2.27 micron pixels 10x: micron pixels 20x: micron pixels 40x: 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

32 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: 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

33 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: micron pixels 40x: 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

34 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 120 second scan time at 20x (15mm*15mm) No Fluorescence capability True Z-stacking capability No external PC required to drive instrument Smart phone interface-capable

35 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

36 Given a single slide s typical 1 x 1 cm 2 scanning area (or 3.7 cm 2 if we re being honest) 01Slide Linear Density 1 cm x 10 mm/1 cm x 1000 microns/1 mm x 4 pixels/micron = 40,000 pixels/cm 02 1 cm 2 patch 40k x 40k = 1.6 GB (single channel) or 4.8 GB (RGB), prior to lossless compression slides/day from a typical practice causes upwards scaling of storage requirements 03 Scaling Up Lossless Compression Reduced to ~300 MB (1k - 2k) *300 MB = Gb per day 9-18 Tb per month TB per year (for 1 x 1 cm slides) PB per year (for actual 3.7 cm 2 slide areas) 05 Actual Production Storage Required

37 Typical Cloud Storage Pricing Calculation Service (1 x 1 cm) Monthly Fee Service (3.7 x 3.7 cm) Monthly Fee 30 TB of Multi-Regional Storage TB of Multi-Regional Storage 1, TB Network Traffic (6,050GB) at $0.11/per GB TB Network Traffic (9,216GB) at $0.11/per GB 1, Network Ingress 0.00 Network Ingress 0.00 $0.05/per 10,000 PUT/POST/GET bucket/get service requests: $ $0.05/per 10,000 PUT/POST/GET bucket/get service requests: $ $0.004/per 10,000 GET object and HEAD requests: $ $0.004/per 10,000 GET object and HEAD requests: $ Total per month 1, Total per year 13, Total per month 2, Total per year 31, Assuming 80,000 cases per year (@ 10 slides/case). $0.016 per slide for storage $0.039 per slide for storage and networking and networking

38 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