Tools for Manipulating JPEG-2000 Based Whole Slide Image Formats Toby Cornish, M.D., Ph.D.

1. Tools for Manipulating JPEG-2000 Based Whole Slide Image Formats Toby Cornish, M.D., Ph.D. Department of Pathology Johns Hopkins Medical Institutions Baltimore, MD

2. Overview • JPEG-2000 is a highly-efficient compression standard well-suited to storage of whole slide images • JP2 and Aperio SVS are two WSI file formats that employ JPEG2k compression • Although the file formats are different, the data is essentially stored in the same format • Few tools exist for manipulating these formats • It should be possible to open, manipulate, and interconvert these formats using readily available, free and open libraries

3. JPEG-2000 Compression Codestreams File Formats JP2 Aperio SVS Design Access SVS Data Convert SVS to JP2 Results

4. JPEG-2000 Compression Codestreams File Formats JP2 Aperio SVS Design Access SVS Data Convert SVS to JP2 Results

5. JPEG-2000 • A standard for wavelet-based image compression • Joint Photographic Expert Group as a replacement for JPEG • ISO/IEC 15444-1 and 15444-2 (parts 1 and 2) • Part 1 defines a self-contained codestream (JPC) as well as a file format (JP2) that can wrap the codestream

6. JPEG-2000, cont. • JPIP (ISO/IEC 15444-9) is a related standard for streaming of large JPEG2k codestreams • Several encoders/decoders both free and proprietary for JPEG2k • Vary widely in the implementation of the standard, but most support JPEG2k part 1 • Mostly used for high capacity image storage in videogames, satellite imagery, and, more recently, medical imagery

7. JPEG-2000, cont. • Features: • Highly efficient compression • Native tiling support for large images • Native multiresolution decompression from a single codestream • Support for an arbitrary number of image components (i.e. channels) • JPEG2k codestreams are self-contained and can be embedded in other file formats

8. JPEG-2000 Compression Codestreams File Formats JP2 Aperio SVS Design Access SVS Data Convert SVS to JP2 Results

9. JPEG-2k codestreams • The codestream are capable of indepently being decoded into an image • All codestreams are tiled, but the simplest and most common form is the single tile codestream • Single tile images are good for small images • Multiple tile images better for handling large image data such as WSI

10. 1 JPEG2k codestream, single tile One codestream – One tile

11. JPEG2k codestream, single tile start of codestream SOC image and tile size SIZ coding style defaults COD quantization defaults QCD comments COM JPEG2k codestream Main header start of tile Tile header 1 SOT start of data Tile data 1 SOD Packet 1 EOC Packet n end of codestream EOC

12. 1 9 11 12 13 14 15 16 10 2 3 4 5 6 7 8 JPEG2k codestream, multiple tiles One codestream – Multiple tiles

13. JPEG2k codestream, multiple tiles start of codestream SOC image and tile size SIZ coding style defaults COD quantization defaults QCD Main header comments COM Tile header 1 start of tile JPEG2k codestream SOT Tile data 1 start of data SOD Packet 1 Tile header n Packet n Tile data n start of tile SOT start of data SOD Packet 1 EOC Packet n end of codestream EOC

14. JPEG-2000 Compression Codestreams File Formats JP2 Aperio SVS Design Access SVS Data Convert SVS to JP2 Results

15. JP2 • Wrapped JPEG2k codestream • Composed of mandatory and optional header boxes • Extensible via UUIDs (Universal Unique Identifiers) and/or XML

16. JP2 file format, cont. Main header Tile header 1 JPEG2k signature box Tile data 1 File type box JP2 header box Contiguous codestream box JPEG2k codestream Tile header n XML boxes Tile data n UIUD boxes EOC

17. JPEG-2000 Compression Codestreams File Formats JP2 Aperio SVS Design Access SVS Data Convert SVS to JP2 Results

18. Aperio SVS file format • Developed by Aperio, Inc. (San Diego, CA) • Essentially, a TIFF file with a tiled layout • Tile data are JPEG2k codestreams • Can consist of multiple images (pages) derived from slide scanning with one Image File Directory (IFD) per image • Image metadata is stored in Tags • The highest resolution data is always tiled

19. SVS/TIFF structure Image Pyramid Thumbnail Label Macro

20. SVS/TIFF structure, cont. Byte order Version number IFD 1 IFD offset Tag entry count Tag 1 IFD 2 Tag n IFD 3 Image data IFD 4 Tag entry count IFD 5 Tag 1 Tag n IFD 6 Image data

21. 1 9 11 12 13 14 15 16 10 2 3 4 5 6 7 8 SVS/TIFF Tiling Multiple tiles – one codestream per tile

22. SVS/TIFF tiling, cont. JPEG2k codestream Tiff Tiles Tag entry count Tag 1 Tile 1 Main header Tile 2 Tile header 1 Tile 3 Tile data 1 IFD 1 Tag n Image data Tile n EOC

23. SVS/TIFF v JP2 • Differences: • JP2 contains one JPEG2k codestream, which contains multiple tiles • SVS/TIFF contains multiple tiles, each of which contains one codestream with exactly one tile • Similarities: • The tile data is essentially the exact same, but packaged • Should permit direct copying of tile data between formats

24. JPEG-2000 Compression Codestreams File Formats JP2 Aperio SVS Design Access SVS Data Convert SVS to JP2 Results

25. Design • Open source libraries (LibTiff, ImageMagick/Jasper) • C programming language for portability • First two goals: • Read SVS/TIFF image data using custom software • Convert SVS/TIFF files to JP2 without decompressing

26. Read SVS/TIFF Main header Tile header Decode Tile data 1 EOC TIFF Header Tiff Tiles IFD Main header SVS Image data Tile 1 Tile header Tile data 2 Decode Tile 2 EOC Tile n Main header Tile header Tile data n Decode EOC

27. SVS/TIFF to JP2 conversion Merged codestream Main header Tile header Tile data 1 Main header Tile header EOC Tile data 1 TIFF Header Tiff Tiles JP2 Header IFD Main header Tile 1 Tile header Tile header JPEG2k Codestream SVS Image data Tile data 2 Tile data 2 Tile 2 EOC Tile header Tile n Tile data 2 Main header Tile header EOC Tile data n EOC

28. Issues • SVS format “quirks” • Somewhat unusual component subsampling • Limits the number of decoders that will read the data without complaining • SVS tiles are transformed into YCrCb color space • Requires a transform to RGB color space before use • A compliant JP2 reader should do this, but not all do

29. JPEG-2000 Compression Codestreams File Formats JP2 Aperio SVS Design Access SVS Data Convert SVS to JP2 Results

30. Results • Several tools were created, allowing: • Direct access to SVS tile data • Manipulate, extract, and montage tiles • See LOCI Bioformats project • Direct conversion of SVS files to JP2 • Requires the SVS tile dimensions to be multiples of 64 • Embedded ICC profiles not propogated

31. Future work • Implement software in Java • Create a JP2  SVS/TIFF converter • Investigate limitations: • Why must tile dimensions be multiples of 64? • Why do most decoders (notably the JAI decoders) fail to decode JPEG2k codestreams from SVS? • Include ICC profiles • Develop a generic LibTIFF plugin for encoding/decoding JPEG2k image data

32. Acknowledgements Johns Hopkins Kristen Lecksell University of Wisconsin-Madison, LOCI Melissa Linkert Curtis Rueden References Taubman and Marcellin, JPEG2000 Image Compression Fundamentals, Standards and Practice Aperio Technical Docs (http://www.aperio.com/documents/) Libraries LibTIFF (http://www.remotesensing.org/libtiff/) ImageMagick (http://www.imagemagick.org/script/index.php) Jasper (http://www.ece.uvic.ca/~mdadams/jasper/)