pymaid: neuron analysis toolbox

Pymaid is a Python library for visualisation and analysis of neuron data generated with CATMAID. It allows you to fetch, analyse and plot neuron morpholgy and connectivity from a CATMAID server.

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.

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

Features

  • data fetching directly from CATMAID server
  • 2D (matplotlib) and 3D (vispy or plotly) plotting
  • virtual neuron surgery (cutting, stitching, pruning, rerooting)
  • R bindings (e.g. for libraries nat, nat.nblast and elmr)
  • interface with Blender 3D and Cytoscape
  • import/export from/to SWC
  • EM image data processing
  • data snapshots