ITISFoundation / jupyter-medimproc

Docker image for a Jupyter Lab with a variety of Medical Image Processing packages installed

JupyterLab for Medical Image Processing (MedImProc)

This is the source code of the JupyterLab Medical Image Processing OSPARC service. It is mostly centered on MRI data, and contains the following packages: "JupyterLab with a variety of Medical Image Processing packages pre-installed, mostly centered on MRI data:

• FSL, a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.
• FreeSurfer, an open source neuroimaging toolkit for processing, analyzing, and visualizing human brain MR images-
• MRtrix3 provides a set of tools to perform various types of diffusion MRI analyses.
• Spinal Cord Toolbox, a comprehensive, free and open-source set of command-line tools dedicated to the processing and analysis of spinal cord MRI data.
• Synb0 Disco, for distortion correction of diffusion weighted MRI without reverse phase-encoding scans or field-maps.
• Python packages like nibabel, pyvista, fsleyes and cc3d.

Commands from these packages can be run either from a terminal or from Jupyter Lab (using ! before the command) thus also offering visualization possibilities. Either single commands can be run, or full .sh files.

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Information for developers of this o²S²PARC service

Building the docker image:

make build

Test the built image locally:

make run-local

Note that the validation directory will be mounted inside the service.

Raising the version can be achieved via one for three methods. The major,minor or patch can be bumped, for example:

make version-patch

If you already have a local copy of o²S²PARC running and wish to push data to the local registry:

make publish-local