bisweb/tools repository overview

This container contains precompiled versions of the bioimagesuiteweb commandline tools.

First install using docker pull. To run use a script like the one below (let's call it dockerrun.sh)⁠

  #!/bin/bash
  DIR=${HOME}
  USERID=`id -u $USER`

  docker run -it --rm -p 8080:80 -p 24000:24000 \
      --mount src=${DIR},target=/data,type=bind \
      -e ORIG_DIR=${DIR} \
       -e LOCAL_USER_ID=${USERID} \
       -e LOCAL_USER=${USER} \
       --name biswebtools \
        bisweb/tools \
       "$@"

If you are using Windows: take a look at the script file dockerrun.bat⁠

This will map a directory ${DIR} -- by default the user's home directory as /data inside the container. If you run this simply as:

   dockerrun.sh

you will get an interactive bash shell. In this shell:

• To execute the bisweb JS command line tools type: biswebnode.

• To use the node.js library simply require('biswebnode')

• To execute the bisweb Python command line tools type: biswebpy

• To use the python3 library simply import biswebpython

• The web applications are available under localhost:8080 with a local biweb file server on port 24000

• To run the node.js regression tests simply type:

  biswebnode regressiontests --run 1
  

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• To run the python3 regression tests simply type:

  biswebpy regressiontests
  

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• Alternatively you run a command, for example the following will smooth an image:

  dockerrun.sh biswebnode smoothimage -i /data/input.nii.gz -o /data/output.nii.gz --sigma 3.0
  

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For more information on BioImage Suite Web see

• The source repository -- https://github.com/bioimagesuiteweb/bisweb⁠
• The actual web application -- https://bioimagesuiteweb.github.io/webapp/⁠

BioImage Suite Web (bisweb) is a web-based medical image analysis suite primarily geared towards Neuroimaging Analysis. We gratefully acknowledge support from the NIH Brain Initiative under grant R24 MH114805 (Papademetris X. and Scheinost D. PIs).