Whole-slide histology slide processing

Converting to OpenSlide compatible format

OpenSlide is a library with a Python interface for reading whole-slide images. Not all slide scanners generate OpenSlide-copmatible files. These notes descibe how to convert images to this format.

• You need to install the package VIPS as described here

• For most files, this command works:

  vips tiffsave input_file.ext output_file.tiff \
       --vips-progress --compression=jpeg --Q=80 \
       --tile --tile-width=256 --tile-height=256 \
       --pyramid --bigtiff