fractal-client 1.0.0a9

Client and common components of the Fractal analytics platform

Fractal Client

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

Documentation is not yet available.

For installation instructions, see below.

Installation

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 installation
• FRACTAL_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.

Development

Installation

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

Releasing

Before release checklist:

• The main branch is checked out
• You reviewed dependencies and dev dependencies and the lock file is up to date with pyproject.toml.
• The current HEAD of 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.

Contributors and license

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..