Transcript 10Oct_1700_Solomon

DICOM INTERNATIONAL
CONFERENCE & SEMINAR
Oct 9-11, 2010
Rio de Janeiro, Brazil
Whole Slide Imaging
in DICOM
Harry Solomon
GE Healthcare
WSI Supplements
• Two DICOM Supplements developed by
WG-26 Anatomic Pathology
• Supplement 145: Whole Slide Imaging
– Adopted August 2010
• Supplement 122: Specimen Module
– Adopted June 2008
The Whole Slide Problem
• Need image resolution comparable to optical microscope
• Need image access as rapid as microscope (pan, zoom,
focus)
Yukako Yagi – UPMC
Digital slides are huge
• Sample size ~ 20mm x 15mm
• Resolution of .25 μm/pixel (40X objective)
• 80,000 x 60,000 pixels = 4.8 Gp
• 24-bit color = 14.4 GB / slide
• 40:1 compression = only 360 MB / typical slide
Unless
• Larger specimen
• Higher resolution (100X objective)
• Multiple focal planes
• Multi-spectral imaging (16-bit / band)
And
• A typical study may be 10 slides
Sup 145 Tiling and
Multi-frame encoding
• Whole Slide Image divided into tiles
• Each tile encoded into a frame of multi-frame
image object
• Per-frame header gives
spatial location for each
tile: X, Y, and Z (focal plane)
Multi-frame image object
Fixed Header
Per-frame header
Dimension data
Pixel data
Multiple
focal planes
Z-planes (focal planes)
↑
Z
↑
Z
Cover slip
Specimen
Slide substrate
(glass)
• Z-planes are identified as
nominal physical height of
image focal plane above
reference surface (μm)
• Z-plane information is
used for relative spatial
positioning of image
planes, and nominal interplane distance
• An image plane may track
variable specimen
thickness / surface
contour, but only one Zvalue used
Z planes may track
curved surface
Z plane 1
Z plane 2
Z plane 3
Z plane 4
Tile 1
Tile 2
Tile 3
Tile 4
Tile 5
Tile 6
Tile 7
Tile 8
Viktor Sebestyén Varga – 3DHISTECH Ltd.
Total Pixel Matrix
Total
Pixel
Matrix
Origin
Columns →
Rows
Frame
Pixel
Matrix
Origin
• Total pixel matrix origin at top
left hand corner of imaged
volume
• Frame (tile) rows and columns
align with total pixel matrix
rows and columns
• Frames limited to 216 columns
and rows each
• Total pixel matrix limited to
232 columns and rows
Total pixel matrix coordinates used for frame location
and for annotation
Sparse tiling
• Slides may have substantial area with no specimen
• Empty tiles may be absent from multi-frame image
Access: Navigation and
Zoom
Need to rapidly access:
• High resolution image of small areas
– Facilitated by tilling
• Low resolution image of whole slide
– For overview and navigation
• Intermediate resolutions
– Smooth zooming
Lower resolution images may be
pre-computed
• Hierarchical pyramid
• May add ~ 33% to size of data
Tiling and multi-frame at all
hierarchical levels
Single frame image
Thumbnail
Image
Multi-frame image
(single object)
Intermediate
Image
Baseline
Image
Multi-frame image
(single object)
may include multiple
Z-planes, color planes
All image objects
typically in 1 DICOM Series
Localizer image “flavor”
• Thumbnail image (single frame)
plus navigation links to each frame
at each resolution
– Each tile of other resolution images
has its corresponding area identified
in thumbnail
• Full description of target tiles
– Object Unique ID and frame number
– Resolution
– Z-plane, color
• Multiple target frames can overlap
– Different resolution, Z-plane, color,
etc.
• Presentation and any interactive
behavior is not defined in standard
Optical paths
Illumination
Filters
Lens
Illumination
Method
Lens
Filters
Sensor
• Each combination of light source, lenses, illumination method,
detected wavelengths, etc. used in a scan is an optical path
• Three primary mandatory attributes:
• Illumination color or wavelength
• Illumination method (e.g., transmission, epifluorescence , darkfield,
differential interference contrast)
• Detection color
• Additional optional attributes for lenses, filters, prisms, etc.
• Examples:
• Full spectrum light, transmission, RGB color sensors
• UV excitation, epifluorescence, 535 nm emission filter, monochrome
sensor
Multi-spectral imaging
• Typical color image stored
with RGB or YBR
photometric interpretation
3 x 8-bit RGB
– 3 color values / pixel
• Multi-spectral image stored
with MONOCHROME
photometric interpretation
– 1 color value / pixel / color plane
– Multiple color planes – may be
stored in single image object
– Each frame references its optical
path in per-frame header
n x 16-bit multi-spectral
Standard DICOM mechanisms
for annotation of WSI
• Color Presentation State
– Displayed Area Selection relative to WSI total matrix
– Graphic and text annotation with sub-pixel location resolution, even with 8M
columns or rows
• Segmentation
– Can be created pixel-by-pixel against selected frames of original image
– 1-bit/source-pixel, or 8-bits/source-pixel
– Display of segmentation implicitly invokes blending with source image
• Structured Reporting
– Captures measurements, clinical observations, analyses, and findings
• Real World Value Mapping
– Specifies a mapping of the stored pixel values of images into some real world
value in defined units
– Allows quantitative methods with monochrome images (original or derived)
Anatomic Pathology Imaging
Workflow
Interpretation Worklist
by accession
Pathology order
Slide preparation
Slide preparation
history data
LIS /
APLIS
Specimen
accessioning data
Modality Worklist Query
by slide barcode
Gross
specimen
accessioning
Surgical or
biopsy
procedure
Workstation
Imaging task w/
slide preparation
history data
Imaging task
completion w/
list of images
and specimen IDs
Whole Slide
Scanner
Images
Images w/
slide prep history
Images – X-ray, U/S,
optical, etc.
PACS
Images
Sup 122 Specimen Module
• Support for pathology lab workflow, specimen-based
imaging
– Gross specimens, blocks, vials, slides
– Image-guided biopsy samples
• Specimen Module at image level of hierarchy
– Identification, processing history (especially stains applied)
• Modality Worklist can convey Specimen Module
– Enables automated slide scanning devices to fully populate image
header
– Processing history can be used to set up acquisition (based on stain)
• Modality Performed Procedure Step identifies imaged
specimen
– Allows LIS/APLIS to track images for specimens
Specimen Imaging
Information Model
Patient
1
1
Basic DICOM
Information
Model
Disambiguates specimen and
container
Is
source
of
Has
n
Study
Container is target of image
n
Container may have more
than one specimen
1
Contains
Specimens have a physical
derivation (preparation)
from parent specimens
n
Equipment
1
Modality
n
Creates
Series
1
When more than one
specimen in an imaged
container, each specimen is
distinguished (e.g., by
position or color-coding)
Contains
n
Image
1
Is
acquired
on
1
Component
Base, Coverslip
1
n
Has
Container
Box, Block, Slide, etc.
1
n
Specimen
Contains
Physical object
n
Is child of
1
1
n
Has
Preparation
Step
Collect, Sample,
Stain, Process
Enabling Transformation
to Digital Pathology
• Supplements 145 and 122 establish the foundation for a
true market for digital imaging in anatomic pathology
– Comparable in importance to the introduction of DICOM to radiology
in 1993
• Enables quantitation and collaboration
• In the next 5-10 years, we should expect a profound
transformation of pathology from a highly manual
process to a digital workflow
• The use of the DICOM Standard across radiology,
pathology, surgery, and radiation therapy opens the door
to truly integrated data from screening to biopsy to
diagnosis to treatment