Fractal is a framework to process high-content imaging data at scale and prepare it for interactive visualization.
Fractal provides distributed workflows that convert TBs of image data into OME-Zarr files. The platform then processes the 3D image data by applying tasks like illumination correction, maximum intensity projection, 3D segmentation using cellpose and measurements using napari workflows. The pyramidal OME-Zarr files enable interactive visualization in the napari viewer.
This is the repository that contains the Fractal client. Find more information about Fractal in general and the other repositories at the Fractal home page.
Documentation is not yet available.
For installation instructions, see below.
Simply
pip install fractal-client
Subsequently, you may invoke it as fractal. Note that you must provide
the following environment variables:
FRACTAL_SERVER: fully qualified URL to the Fractal server installationFRACTAL_USER,FRACTAL_PASSWORD: email and password used to log-in to the Fractal server
By default, fractal caches some information in ~/.cache/fractal. This destination
can be customized by setting FRACTAL_CACHE_PATH.
For ease of use, you may define an environment file .fractal.env in the
folder from which fractal is invoked.
Fractal is developed and maintained using poetry.
After cloning the repo, use
poetry install --with dev
to set up the development environment and all the dependencies and dev-dependencies. You may run the test suite with
poetry run pytest
Before release checklist:
- The
mainbranch is checked out - You reviewed dependencies and dev dependencies and the lock file is up to
date with
pyproject.toml. - The current
HEADof the main branch passes all the tests - Use
poetry run bumpver update --dry --[patch|minor] --tag-commit --commit
to test updating the version bump
- If the previous step looks good, use
poetry run bumpver update --[patch|minor] --tag-commit --commit
to actually bump the version and commit the changes locally.
- Test the build with
poetry build
- If the previous step was successful, push the version bump and tags:
git push && git push --tags
- Finally, publish the updated package to pypi with
poetry publish --dry-run
removing the --dry-run when you made sure that everything looks good.
Unless otherwise stated in each individual module, all Fractal components are released according to a BSD 3-Clause License, and Copyright is with Friedrich Miescher Institute for Biomedical Research and University of Zurich.
Fractal was conceived in the Liberali Lab at the Friedrich Miescher Institute for Biomedical Research and in the Pelkmans Lab at the University of Zurich (both in Switzerland). The project lead is with @gusqgm & @jluethi. The core development is done under contract by @mfranzon, @tcompa & @jacopo-exact from eXact lab S.r.l..