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Dockerfile for libvips
Installs libvips on Ubuntu 14.04 as base image.
This modified version builds openslide from github source and then builds libvips from source mostly following this procedure.
This dockerfile can then be used to run libvips with OpenSlide directly from the command-line (see cookbook below for examples):
Supported tags
How to use
Download the image using:
$ docker pull marcbachmann/libvips
# .... pulling down imageUseful resources
- OpenSlide and VIPS
- OpenSlide on Aperio format
- libvips issue about checking if OpenSlide is working
- building libvips + openslide
Cookbook for important commands
Tests to confirm that OpenSlide is installed correctly using VIPS
NOTE: we have to map the volume into the container and prepend the path with '/home' or vips can't find the file. This is accomplished by the '-v' flag in the example.
#Grab a small test SVS from the OpenSlide site
wget http://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/CMU-1-Small-Region.svs
sudo docker run --rm -e OPENSLIDE_DEBUG=detection -e G_MESSAGES_DEBUG=VIPS -v ${PWD}:/home metacell/libvips vips openslideload --associated thumbnail /home/HM_0597_Myelin_TO\ BE\ FLIPPED\ HORIZONTALLY.svs testflip
sudo docker run --rm -e OPENSLIDE_DEBUG=detection -e G_MESSAGES_DEBUG=VIPS -v ${PWD}:/home metacell/libvips vips --vips-progress flip /home/HM_0597_Myelin_TO\ BE\ FLIPPED\ HORIZONTALLY.svs /home/HM_0597_Myelin_FLIPPED\ HORIZONTALLY.tiff horizontalDeep Zoom
In this command, we have enabled progress reporting. We are making sure that the input path AND the output path includes /home as otherwise the resulting file will not get saved on the local system.
sudo docker run --rm -e OPENSLIDE_DEBUG=detection -e G_MESSAGES_DEBUG=VIPS -v ${PWD}:/home metacell/libvips vips --vips-progress dzsave /home/HM_0597_Myelin_FLIPPED\ HORIZONTALLY.tiff /home/HM_0597_Myelin_FLIPPED_HORIZONTALLY_DZ_tif
Coverting TIFs to PNGs (using ImageMagik & a different container)
sudo docker run -v /home/dockerx/test2/PEELED\ FIXED:/images --rm -it v4tech/imagemagick convert -monitor /images/HM\ BRAIN\ PEELED\ CEREBELLUM\ AND\ OCCIPTAL\ RULER.TIF /images/HM\ BRAIN\ PEELED\ CEREBELLUM\ AND\ OCCIPTAL\ RULER.pngLicense
Licensed under MIT