scMultipleX is a software package for feature extraction of microscopy imaging data. It provides workflows for feature extraction of segmentated objects (e.g. organoids) and single cells, and for linking of objects and cells over multiplexing rounds. It supports 2D and 3D imaging data, and single-round or multiplexed experiments. scMultipleX uses Prefect (v1.4) for parallelized processing, and assumes input data pre-proprecessed with Drogon.
The workflow consists of the following tasks:
- Task 0 Build Experiment: Initialize output data storage structure with FAIM-HCS (v0.1.1)
- Task 1 Feature Extraction: Perform 2D object-level and 3D single-cell-level feature extraction and nuclear to membrane linking
- Task 2 Organoid Multiplex: Link objects across multiplexing rounds
- Task 3 Nuclear Multiplex: Link nuclei within objects across multiplexing rounds
- Task 4 Aggregate Features: Output measured features for each round and objects type (e.g. organoids, nuclei, membranes)
- Task 5 Combine Nuclear and Membrane Features: Output combined nuclear and membrane features based on nuclear to membrane linking
- Task 6 Aggregate Organoid Multiplex: Output measured object features across multiplexing rounds
- Task 7 Aggregate Nuclear Multiplex: Output measured nuclear features across multiplexing rounds
See scMultipleX GitHub Wiki.
To make new releases, just create a Github release and create a semantic version tag upon release (e.g. v0.9.0). Make sure you include the "v" before the version number. The CI will add the whl files to the release for easier addition to Fractal server & making sure the package is listed on the Fractal task overview.
Alternatively, you can tag a specific commit in main (e.g. with v0.9.0) and push that tag to Github. The CI will take care of making a Github release and pushing it to PyPI.
git tag v0.9.0
git push origin v0.9.0
Unless otherwise stated in each individual module, all scMultipleX components are released according to a BSD 3-Clause License, and Copyright is with Friedrich Miescher Institute for Biomedical Research.
scMultipleX was conceived in the Prisca Liberali Lab at the Friedrich Miescher Institute for Biomedical Research, Switzerland. The project lead and development is with @nrepina, and refactor and development support is with @enricotagliavini and @tibuch.
The nuclear multiplexed linking algorithm is built on PlatyMatch (DOI) by Manan Lalit in the Florian Jug lab at the Human Technopole, Italy.