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Mixed-Mode Storage of Whole Slide Pathology Images

Mixed-Mode Storage of Whole Slide Pathology Images. Proposal for DICOM WG-26 & WG-6 Kemp Watson Objective Pathology Services Ltd. Toronto, Canada (905) 770-7802 www.objectivepathology.com. Whole Slide Image scans are HUGE and SLOW !!!. Image Size Comparison (to scale).

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Mixed-Mode Storage of Whole Slide Pathology Images

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  1. Mixed-Mode Storage ofWhole Slide Pathology Images Proposal for DICOM WG-26 & WG-6 Kemp Watson Objective Pathology Services Ltd. Toronto, Canada (905) 770-7802 www.objectivepathology.com

  2. Whole Slide Imagescans areHUGEandSLOW!!!

  3. Image Size Comparison(to scale) • Typical DICOM image is ~3 megapixels • DICOM image maximum is 64K x 64K = 4096 megapixels • WSI scan is 500K x 250K = 125 gigapixels • 30 – 40,000 times larger, with current technology 50mm x 25mm WSI scanned at 100x = 500,000 x 250,000 pixels = 125 Gigapixels Largest DICOM Image

  4. Download Time Comparison(to scale) • Based on a 10 mbps Ethernet connection, 20:1 compression • a 3 megapixel typical DICOM image takes ~0.3 seconds • a 64K x 64K DICOM image would take ~8 minutes • our example WSI scan would take over 4 hours • Bandwidth equivalent of over 40,000 radiology images WSI scan D C M

  5. Multi-resolution Representation • Because these images are so huge, we require: • regional navigation (pan) feature • scalability in size and resolution (zoom and progressive quality) • Many (if not all) vendors using some form of multi-resolutiontiled image pyramid: • mathematically a “Gaussian Pyramid” • spatial + frequency localization • JPEG 2000 actually uses similar conceptsin its codec, but implementationdetails are less visible

  6. Limits of JPEG 2000 in DICOM • JPEG 2000 itself is very capable of representing huge, multidimensional images • But neither Supplement 61 (JPEG 2000 Transfer Syntaxes) nor Supplement 106 (JPEG 2000 Interactive Protocol) extend image size beyond 64K x 64K pixels • Compression times are on the order of ~10x slower than JPEG • Decompression times are ~6x slower than JPEG • The quality:compression ratio is somewhat better, though

  7. Current Image IOD size IEs • Image X & Y dimensions are stored as Rows (0028,0010)& Columns (0028,0011) • VR of US (unsigned short integer) • maximum value 64K pixels in each direction • Image length (file size) is stored within Pixel Data (7FE0,0010) • VR of UL (unsigned long integer) • maximum file size of 4 GB • WSI scans can be hundreds or thousands of times larger • Access to full image only • no panning to subregions • no zooming to subresolutions • except on client – very inefficient for WSI scans

  8. Fixing Image Dimensions • Want to be backward-compatible where possible • Add optional UL VR elements • maximum value 4G pixels in each direction • don’t replace current US VR elements • However, an image must be reconstructable from the original US VR elements for backwards compatibility

  9. Fixing Image Length • Current standard is actually OK re length if you read the details • the Pixel Data Element (7FE0,0010) is stored with either an OB or an OW Value Representation • OB/OW VR’s normally have a Value Length of up to 4 GB of data with and Explicit VR representation • but the Value Length field of OB/OW VRs can be set to FFFFFFFF to indicate arbitrarily long data, which then must be terminated by a Sequence Delimitation Item, which is Data Element (FFFE,E0DD) • So size is OK, but interactive navigation may still be a problem

  10. What About the Image Data? • Store a “base image” exactly as it already is defined • fairly compatible; little work for vendors to implement • existing compressions and transport syntaxes • Add an optional “extended image” • several vendors suggest tiles for performance • most vendors want JPEG (not 2000) for performance andInternet browser compatibility • others want JPEG 2000 since it’s already in the standard • OK! Let’s do both • and who knows what’s next?

  11. Why Two Images? • Doesn’t have to be, but can be two images • Not recommending any new transfer syntax thatwould obstruct base image compatibility • Large image is optional; it may have a new transfer syntax • Can specify the “line” between large and small image resolutions • by choice of X & Y US and UL VR’s (matching the data of course) • Base image may be a thumbnail, or may be as large as desired

  12. Case 1: Extended Image as 2nd Image • Any currently supported format, including JPEG 2000 • but may have problems with interactivity unless it’s JPEG 2000,tiled, or other pan/zoom capable multi-resolution format • note that base image may have this problem too,though technically deliverable through DICOM now

  13. Case 2: Extended Image as Tiles • Pixel Data stored as nested Sequence Items (FFFE,E000) • not Series-level container • Requires an index to map resolutions and locations to images • Each resolution level as a nested Sequence within the main Sequence • Tiles are standard DICOM pixel data

  14. Case 3: Extended Image isActually a Part of the Base Image • For example, one large JPEG 2000 file • But must be accessible to all current DICOM implementations • Both versions of X & Y length must refer to same image • Could be problems with existing implementations of JPEG 2000 • Not addressed here

  15. Base and Extended Image Modules • Create new Extended Image Pixel module • Pathology Image IOD would contain modules: • General Image (mandatory) • Image Pixel (mandatory – exactly as now) • Extended Image Pixel (optional) • and others… • DICOM implementations could easily see base image • and see extended image with more work • Option: extended image could not just be a larger version of the base image, but could be a differential image • saves 25-33% space, but more computation

  16. Extended Image Module • Larger dimensions • Sequence option for tiled images • Data Elements required: • Pixel Data Provider URL 1C • Rows 1 UL (larger than before) • Columns 1 UL (larger than before) • Tile Image Directory 1C SQ (new) • Extended Pixel Data 1 (SQ or single OB/OW Data Element) • and others similar to Image Pixel module… • Tile Image Directory will contain sizes and tile counts of each resolution layer • If present, SQ will contain a sequence of tiled Pixel Data attributes structured as a folder (DICOM terminology – see spec) holding the tiled image pyramid • Needs more detail, hope you see the general structure 

  17. Streaming and Navigation • Image streaming is absolutely crucial for real-time navigation • DICOM has methods for retrieving Sequence Items • JPIP for JPEG 2000 • So we’re probably OK • If not, we need new streaming syntax

  18. Further Issues • Should extended image format be available as a base image in DICOM? • then available to other modalities • impact on existing implementations? • JPEG 2000 accessible as base size as well as extended size • Image container must be flexible for future transfer syntax enhancement to support multi-spectral, high dynamic range(16-bit +), z-axis focusable, and other imaging formats, as well as adoption of other compression codecs • Image annotation • File format for media representation

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