See our homepage here: cytomining.github.io
Cytomining is a software ecosystem that maintains essential tools, workflows, and best practices for single-cell image-based profiling and microscopy data analysis research. We are proud members of the CytoData scientific community.
| Tool | Description | |
|---|---|---|
 | pycytominer | Python package for image-based profiling bioinformatics |
 | CytoTable | Harmonize high-content image analysis tool outputs |
 | coSMicQC | Single-cell morphology quality control |
 | CytoDataFrame | In-memory data format for single-cell profiles alongside images |
| copairs | Find profile pairs and compute retrieval metrics | |
 | DeepProfiler | Morphological profiling using deep learning |
The following tools are under active development in the WayScience organization and represent the next generation of the Cytomining ecosystem.
| Tool | Description | |
|---|---|---|
 | buscar | Perturbation hit calling for high-content screening |
 | zedprofiler | CPU-first 3D image feature extraction for high-content profiling |
 | OME-arrow | OME specifications via Apache Arrow for fast, queryable bioimage data |
 | iceberg-bioimage | Format-agnostic framework for cataloging and querying bioimaging data |
See the links below to get started!
- 💬 Join the community on
Discord
- 📺 Watch image-based profiling videos at our
YouTube channel
- 😃 Check out our amazing community of contributors
- 🏫 Learn more about the CytoData community we are part of
- 📫 Subscribe to our mailing list
- 🌈 Please abide our community Code of Conduct
