pymaid: a Python-CATMAID interface

pymaid (short for “Python-CATMAID”) is a Python library for fetching, analyzing and visualisating data generated with CATMAID.

pymaid is built on top of navis and is fully compatible with its functions.

For a brief introduction to the library, you can read the tutorial. Visit the installation page page to see how to download the package. You can browse the example gallery and API reference to see what you can do with pymaid.

Pymaid is licensed under the GNU GPL v3+ license. The source code is hosted at Github. Feedback, feature requests and bug reports are very welcome and best placed in issues. If you have any questions, please don’t hesitate: pms70@cam.ac.uk

The package is stable but I recommend watching its Github repository for updates. Make sure that your pymaid.__version__ is up-to-date and check out the release notes.

Features

  • fetch data directly from CATMAID server
  • write data (e.g. annotations, tags, neurons) to the server
  • fully compatible with navis
  • high-level functions to analyze e.g. connectivity