System to automatically image multiple tissue microarray slides stained by immunohistochemistry and in situ hybridization followed by image analysis

1. BioGenexBioGenex
VISIONVISION
Automated Imaging SystemAutomated Imaging System
20032003

2. Capturing the ResultsCapturing the Results
Tissue based assays generate
large amounts of image data.
Converting images into
STANDARDIZED numerical
values is critical.
Automation of “image capture
and analysis” of primary
importance.

3. What Are Our ProductsWhat Are Our Products
Tissues/Tissues/
Tissue arraysTissue arrays
PretreatmentPretreatment
ReagentsReagents
Antibodies/Antibodies/
ProbesProbes
DetectionDetection
ReagentsReagents
Manual ReagentsManual Reagents
Automation & Auto- ReagentsAutomation & Auto- Reagents
Slide labelSlide label
printerprinter
(500)(500)
AnAn
RetrievalRetrieval
(1000)(1000)
SlideSlide
StainerStainer
(6000)(6000)
SlideSlide
imagerimager
(Vision)(Vision)

4. Automated Image Capture and AnalysisAutomated Image Capture and Analysis
A walk-away “microscope”
Reads and analyzes 50
slides
Can automatically find
tissue on the slide and then
take images
Can convert images into
numbers
For analyses of single
tissue sections (I and G)
For rare cell detection (I)
For imaging of TMAs (G)
Vision

5. FeaturesFeatures
 Digital capture
 Live-view observation
 Magnification (2 to 40x)
 Autoloading (50 slide capacity)
 Batch scan mode
 Single tissue scans
 Scoring and reporting flexibility (images, %I, %P,
area, length, hot spots, histograms)
 Rare cell analysis
 Tab delimited data exportability
 Random Access: Any slide, any protocol.

6. Vision Hardware SpecificationsVision Hardware Specifications
Slide handling
 50 slide random access autoloader with integrated barcode reader with >100
linkable protocol barcodes
Imaging platform
 Brightfield microscopy. Automated BX-series microscope with motorized X-Y-Z
stage (scanning speed - 0.3 seconds/field with sub-micron resolution) and
joystick control. Plan achromatic 2x, 4x, 10x, 20x (40x optional) lenses
Camera
 DVC 1.4 megapixel (1330 x 1030 pixels) CCD digital camera; 10 bits/color
channel (30 bits 3-color)
Imaging parameters
Pixel size field of view scanning time
2x lens 3.33 µm/pixel 4.2 mm x 3.4 mm ~ 10 sec. (2cm x 2cm)
4x lens 1.66 µm/pixel 2.1 mm x 1.7 mm ~ 40 sec. (2cm x 2cm)
10x lens 0.66 µm/pixel 0.85 mm x 0.67 mm ~ 4 min. (2cm x 2cm)
20x lens 0.33 µm/pixel 0.42 mm x 0.34 mm ~ 16 min. (2cm x 2cm)
40x lens 0.16 µm/pixel 0.21 mm x 0.17 mm ~ 64 min. (2cm x 2cm)
File sizes
 JPEG image: ~150 kb; TIFF image: ~8 mb; complete ivision result file: ~300mb

7. iVision Software: Single Tissue ScansiVision Software: Single Tissue Scans
Steps:
1. Enter Slide and batch info
2. Scan
3. Open Results
4. Analyze Results
5. Export Results to Report

8. iVISION: Start ScreeniVISION: Start Screen

9. iVISION:iVISION:
Enter slide informationEnter slide information
Select
slides
Data
Entry
Unique
ID No.

10. iVISION:iVISION:
Load SlidesLoad Slides

11. iVISION: Set up a batch scaniVISION: Set up a batch scan
Click on
batch
Setting
Select
Protocol
Select
Slide
Set-up

12. iVISION:iVISION:
Review Batch scan resultsReview Batch scan results
Click
on
Result
Click
on
Thumbnail
Click
on
Transfer

13. iVISION: MeasurementsiVISION: Measurements
Complete
Slide
Image
Magnified
Image
Measurement
Tools
Magnified
Image

14. iVISION: Measure AreaiVISION: Measure Area
Values
(um2)

15. iVISION: Quantitate (free-hand)iVISION: Quantitate (free-hand)
Histogram
(pixel
intensity)
Selection
Area
Selection
Number
1
Staining
intensity

16. iVISION: Annotate an imageiVISION: Annotate an image
Breast CarcinomaBreast Carcinoma
ER-, PR-, HER-2 +ER-, PR-, HER-2 +
HER-2 FISH inconclusiveHER-2 FISH inconclusive

17. iVISION: False coloriVISION: False color
Image (hot spot)Image (hot spot)
BlackBlack = maxm.
RedRed = medm.
YellowYellow = low
staining

18. iVISION:iVISION:
Estrogen ReceptorEstrogen Receptor
in Breast Cancerin Breast Cancer
Staining
and
Population
values
Selection
number
Selected
regions
4
3
2
Export
to Excel

19. iVISION: Rare cell detectioniVISION: Rare cell detection
Location of
Selected cell
Selected
cell
Found
cells
Selected
cell

20. iVISION: Set up quantitationiVISION: Set up quantitation
HSI
settings
Tissue/
Non-Tissue
HSI
values
Values from
the settings

21. iVISION: Generate ReportsiVISION: Generate Reports
Patient/Sample
Information
Image
Thumbnail
Bargraph for
Significance

22. Tissue Array ImagingTissue Array Imaging

23. Imaging Tissue ArraysImaging Tissue Arrays
Biggest bottleneck is Imaging
The GenoMx Vision
•can automatically find tissue elements
on a slide
•can semi-automatically map the tissue
elements
•can capture each element as a
separate image
•can convert images into hard
numbers
A1
A2A3 A4
B1B1
B1 B1
•Intensity of stained
and unstained
•Proportion of cells
with staining

24. GenoMx VISION: Tissue array scansGenoMx VISION: Tissue array scans
The most rapid high-resolution imager for
Tissue arrays (0.3sec/field)
Will identify tissue array elements of any
size at any density <1200 elements/slide.
Will map the tissue array elements
automatically!
Will quantitate all the tissue array
elements and generate a report
automatically
Will produce image files (JPEG or TIFF)
for all the elements on a TMA

25. GenoMx VISION: SetupGenoMx VISION: Setup
TMA
region
Focus
points
(1 of 3)

26. GenoMx VISION:GenoMx VISION:
Mapping windowMapping window
Defining
number of
partitions

27. GenoMx VISION:GenoMx VISION:
MappingMapping
Virtual
Cores
Partition
label
(user-defined)

28. GenoMx VISION: Core locationsGenoMx VISION: Core locations
Automated
Mapping

29. GenoMx VISION:GenoMx VISION:
False color imagesFalse color images
Analysis
Options

30. GenoMx VISION: Core listGenoMx VISION: Core list
Simultaneous
quantitation
Saves all
images in
the
core list

31. GenoMx VISION: Core analysisGenoMx VISION: Core analysis

32. GenoMx VISION: Core analysisGenoMx VISION: Core analysis

33. GenoMx VISION: AnalysisGenoMx VISION: Analysis

34. GenoMx VISION:GenoMx VISION:
Detection ParametersDetection Parameters
Intensity
Color depth
Tissue
v/s
white space
Color

35. GenoMx ReportGenoMx Report
Thumbnail
images
Map location of
each TMA core
Quantitative
Graphical
interpretation

36. Vision: Future DirectionsVision: Future Directions
Fluorescence
imaging (multiple
analytes)
Flexible data
management via
Filemaker
Remote/Satellite
stations for analysis
of archived results

37. Analyzing 1 TMA slideAnalyzing 1 TMA slide
Type Name Here
Type Title Here
Load Slide
(Label to right)
Type Name Here
Type Title Here
Start Genomyx
Run Calibration

38. CompetitionCompetition
Features BioGenex Bacus Lab ChromaVision Applied Imaging Aperio/Dako
Digital/Color Yes/Yes Yes/Yes No/Yes No/No Yes/Yes
Sens/Resol 1.1 B/1.3M 16.8 M/1.3 M 16.8 M/0.3 M 16.8 M/0.3 M 16.8 M/1.3 M
Slide/Access 50/All 1/1 100/4 50/All 1/1
Bar Code Yes No Yes No No
Bright/Fluo Yes/Yes* Yes/No Yes/No Yes/Yes Yes/No
Speed/Size 8 min/1.5 GB ~2 hr/4.5 GB ~ 1/2 hr/1.5 GB .. ..
(200 Core 0.6 TMA)
*In development
Flex Report Yes No No .. ..
TMA Yes Yes Yes .. ..
Auto Map Yes No No .. ..
Core List Yes No No .. ..
Core Scan Yes No No .. ..
Flex Protocols Yes No No .. ..

39. ChromavisionChromavision

40. Applied ImagingApplied Imaging

41. ZeissZeiss