JP2 WSI Converter

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JP2 WSI Converter is a virtual slide (whole-slide image) conversion application, which is designed to convert most existing scanner vendor formats into JPEG2000 in a 64-bit, multi-CPU environment, thereby enabling rapid conversion speed and integration with routine slide processing workflow.

JP2 WSI Converter produces JPEG2000 files with optimal code-stream parameterization for virtual microscopy, which we have described in our earlier study. The software is targeted for Microsoft Windows® operating systems, featuring a command line interface for batch usage and a graphical user interface with the option to process either a single file or a whole directory of files in sequence.




This software is provided 'as-is', without any express or implied warranty. In no event will the authors be held liable for any damages arising from the use of this software. You can use it freely for non-commercial purposes. 

Version 1.0.2, 14.6.2012

For 32-bit Windows: JP2 WSI Converter (x86)
For 64-bit Windows: JP2 WSI Converter (x64)



Supported virtual slide scanner vendor formats for input:

  • Aperio - BigTIFF slides
  • MIRAX - MRXS slides
  • Surveyor - SWS slide workspaces
  • Hamamatsu - NDPi NanoZoomer slides

Supported general file formats for input:

  • BMP - uncompressed, 24-bit
  • JPEG - 24-bit
  • PPM - binary encoded, 24-bit
  • TIFF - 24-bit RGB with PackBits, LZW or no compression (BigTIFF supported)

Supported output file formats:

  • JPEG2000 - lossless or lossy (setting the compression ratio to 1:1 will yield a lossless compression; the actual compression ratio will be ~2:1)

JP2 WSI Converter can also be used from command line by using the following syntax:

JP2WSIConverter ...
  -i <file> -- input file (see help for supported formats)
  -o <file> -- output file (see help for supported formats)
  -c <n>    -- target compression ratio

Optional parameters:
  -t <n>    -- tile size, n*n pixels (default: no tiling)
  -m <n>    -- # of threads to be utilized (default: # of CPU cores)
  -s        -- write the processing statistics to auxiliary CSV file
  -d        -- delete the input file after successful compression
  -help     -- display help