Proposal for Storing Whole Slide Images for Pathology in DICOM DICOM Working Group 26 1/17/07

Agenda Introduction Description of Problem Characteristics of Whole Slide Images DICOM Limitations and Characteristics Description of Proposed Solution

Introduction Pathology is undergoing a transformation Digital imaging is increasingly important Driven by availability of instruments for digitizing microscope slides, resulting in whole-slide images (WSI) WSI are different to other images stored in DICOM Size - larger Access patterns – pan, zoom, focus It is desirable to support WSI for Pathology in DICOM Will facilitate interoperability with other modalities Will foster adoption of Digital Pathology

Description of Problem Characteristics of WSI Image dimensions, data size Typical: 20mm x 15mm @ .25mpp (“40X”) = 80,000 x 60,000 pixels = 4.8Gp = 15GB Extreme: 50mm x 25mm @ .1mpp (“100X”) = 500,000 x 250,000 pixels = 125Gp = 375GB x 10 Z-planes => 3.75TB

Description of Problem Characteristics of WSI Access patterns Pathologists cannot view entire microscope slide at diagnostic resolution Pan around at low res (2.5mpp = “4X”), then zoom in at high res (.25mpp = “40X”) Requires organization to support rapid panning & zooming Multiple Z-planes may be captured Requires organization to support rapid focusing

Description of Problem Characteristics of WSI Simple image organization: Stripped Does not support efficient panning image strips image pixels region to be viewed or processed region (strips) to be loaded

Description of Problem Characteristics of WSI More complex image organization: Tiled Does support efficient panning image pixels region (tiles) to be loaded region to be viewed or processed image tiles

Description of Problem Characteristics of WSI Still have an issue with zooming lower resolution, larger image region highest resolution, small image region

Description of Problem Characteristics of WSI Pyramid addresses zooming Baseline Image Tile Thumbnail Image (low resolution) Intermediate Zoom Image Tile Baseline Image (highest resolution) Intermediate Zoom Image (intermediate resolution) Retrieved image region

Description of Problem DICOM Limitations and Characteristics 16-bit signed integer for pixel dimensions: 32K x 32K 32-bit signed integer for image object size: 2GB No subregion access to images

Description of Problem DICOM Limitations and Characteristics DICOM Characteristics Successful, widely adopted An important reason why is extension process DICOM extensions Conservative – only extend standard when necessary, leverage existing standard Encourage innovation – involve vendors in process, enable vendors to innovate within [extended] standard Better products for market Discourage proprietary solutions Backward compatible – maximize compatibility with existing [non-extended] systems, degrade gracefully

Description of Proposed Solution Store WSI Pyramid as DICOM Series Each “tile” of each level of each plane of WSI corresponds to image in series DICOM Series Thumbnail Image Intermediate Image Tiles Baseline Image Tiles

Description of Proposed Solution Store WSI Pyramid as DICOM Series Tile size can vary (240 … 1K … 4K … 32K) Each resolution level stored separately in the series (typically thumbnail is first) Each Z-plane stored separately in the series Each image in series identified by coordinates X, Y offsets Zoom (resolution) Z offset (plane)

Description of Proposed Solution Characteristics of Proposed Solution Works around DICOM limitations 16-bit pixel dimension: okay, tiles will be less than 32K x 32K 32-bit image size: okay, tiles will be smaller than 2GB No subregion access: okay, each tile is individually addressible as an image Encompasses storage of single image in a series by itself as proper subset

Description of Proposed Solution Characteristics of Proposed Solution Will require little change by PACS vendors They already handle images in series Degrades gracefully for existing DICOM viewers Thumbnails / low-level images display “as is” High-res images display as pieces of entire image (Pathologists will require purpose built viewer) Rapid pan, zoom, etc. Simple to implement for WSI vendors Solution is similar to blocked TIFF, which most WSI vendors use for storing WSI now Simple to export from DICOM to TIFF For compatibility with existing viewers, image analysis tools, and other WSI applications

Description of Proposed Solution Characteristics of Proposed Solution Issues not addressed by proposed solution Compression type Support uncompressed, lossless (e.g. LZW), and lossy (e.g. JPEG, JPEG2000) As per current DICOM specification Transport mechanism Support image retrieval and JPIP Multichannel / multispectral data Solution addresses how to store images and pixels Not composition / format of pixels May need to extend DICOM specification to allow format and content of pixels to be defined for images in series