VIPS image processing system now supports OpenSlide

[Benjamin Gilbert]

VIPS is an image processing system that can work with large images 
without loading the entire image into RAM.  It includes a library, 
libvips, and a graphical interface, nip2.  As of libvips 7.28.3 and nip2 
7.28.2, VIPS supports reading whole-slide images with OpenSlide.

VIPS is available here:
     http://www.vips.ecs.soton.ac.uk/


Exporting slide data with vips
------------------------------

libvips includes a command-line program, "vips", that can be used to 
export data from a whole-slide image to another format.

To convert level 0 of a slide to an LZW-compressed tiled TIFF:
     vips openslideload CMU-1.mrxs slide.tiff[tile,compression=lzw]

To convert level 3 instead:
     vips openslideload --level 3 CMU-1.mrxs \
         slide.tiff[tile,compression=lzw]

or, equivalently:
     vips tiffsave CMU-1.mrxs[level=3] slide.tiff --tile \
         --compression=lzw

To save the "label" associated image as a PNG:
     vips openslideload --associated label CMU-1.mrxs label.png


Viewing a slide with nip2
-------------------------

nip2 is the VIPS GUI.  It can only work with one slide level at a time, 
so it does not provide an efficient zoomable interface.  However, unlike 
other conventional image viewers/editors, it can handle very large images.

nip2 has a slightly different syntax for loading slides.

To load level 0:
     nip2 CMU-1.mrxs

To load level 3:
     nip2 CMU-1.mrxs:3

To load the "label" associated image:
     nip2 CMU-1.mrxs:,label


Okay, but don't you mean "layer"?
---------------------------------

OpenSlide 3.3 and above will use the term "level" instead of "layer", 
since the first seems to be more commonly used for pyramidal images. 
The VIPS OpenSlide interface follows the new convention.


--Benjamin Gilbert