SVS-TIFF Tiler

Builds svs-tiff-tiler Docker image: This image uses libvips to convert OME-TIFF files to DeepZoom tiles for each image plane.

Build

docker build --tag=svs-tiler context .

Run

docker run \
    -rm \
    -e "PREFIX=your_prefix" \
    --mount "type=bind,src=YOUR_FILE.tif,dst=/input.ome.tif" \
    --mount "type=bind,src=YOUR_OUTPUT,dst=/output_dir" \
    ome-tiff-tiler

(Or gehlenborglab/ome-tiff-tiler:latest to pull from DockerHub.)

Two environment variables should be set:

• PREFIX: Prefix to prepend to tile filenames.

And two mounts should be provided:

• Replace YOUR_FILE.svs with absolute path of the SVS to tile.
• Replace YOUR_OUTPUT with absolute path of directory where the tiles should go.

Push to DockerHub

If tests pass, we're just pushing to DockerHub by hand:

# We should only push from master:
git checkout master
git pull

# First, set the new VERSION:
VERSION=v0.0.????
docker tag svs-tiler thomaslchan/svs-tiler:$VERSION
docker push thomaslchan/svs-tiler:$VERSION

# And also make a git tag:
git tag $VERSION
git push origin $VERSION