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pymaid

Python-Catmaid - or "pymaid" - is a Python 3 library to interface with CATMAID servers.

Tested with CATMAID release version 2020.02.15 - if you are working with older versions you may run into issues due to API changes.

Features

  • pull and push data from/to a CATMAID server
  • visualize and analyse neuron morphology via navis
  • tools to analyse user stats (e.g. time-invested, project history)
  • clustering methods (e.g. by connectivity or synapse placement)

Documentation

Pymaid is on ReadTheDocs.

Getting started

See the documentation for detailed installation instructions, tutorials and examples. For the impatient:

pip3 install python-catmaid

Important: there is a pymaid package on PyPI which has nothing to do with this pymaid!

To install the bleeding edge from Github:

pip3 install git+https://github.com/navis-org/pymaid@master

Alternatively click on the launch binder badge above to try out pymaid hosted by mybinder!

pymaid example

License:

This code is under GNU GPL V3

References:

Pymaid implements/provides an interfaces with algorithms described in:

  1. Comparison of neurons based on connectivity: Science. 2012 Jul 27;337(6093):437-44. doi: 10.1126/science.1221762. The connectome of a decision-making neural network. Jarrell TA, Wang Y, Bloniarz AE, Brittin CA, Xu M, Thomson JN, Albertson DG, Hall DH, Emmons SW. link
  2. Comparison of neurons based on synapse distribution: eLife. doi: 10.7554/eLife.16799 Synaptic transmission parallels neuromodulation in a central food-intake circuit. Schlegel P, Texada MJ, Miroschnikow A, Schoofs A, Hueckesfeld S, Peters M, ... Pankratz MJ. link