Collection of Python 3 tools to work with neuron data from CATMAID servers
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README.md

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pymaid

Collection of Python 3 tools to interface with CATMAID servers. Tested with CATMAID release version 2018.07.19 - if you are working with older versions you may run into issues due to API changes.

Documentation

Pymaid is on ReadTheDocs.

Features

  • fetch data via CATMAID's API
  • custom neuron classes that perform on-demand data fetching
  • interactive 2D (matplotlib) and 3D (vispy or plotly) plotting of neurons
  • virtual neuron surgery: cutting, pruning, rerooting
  • clustering methods (e.g. by connectivity or synapse placement)
  • R bindings (e.g. for libraries nat, rcatmaid, elmr, catnat )
  • interface with NetworkX and iGraph
  • tools to analyse user stats (e.g. time-invested, project history)
  • interface with Blender 3D

Getting started

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

pip install git+git://github.com/schlegelp/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 morphology: Neuron. 2016 doi: 10.1016/j.neuron.2016.06.012 NBLAST: Rapid, Sensitive Comparison of Neuronal Structure and Construction of Neuron Family Databases. Costa M, Manton JD, Ostrovsky AD, Prohaska S, Jefferis GSXE. link
  2. 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
  3. 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, Hückesfeld S, Peters M, … Pankratz MJ. link
  4. Synapse flow centrality and segregation index: eLife. doi: 10.7554/eLife.12059 Quantitative neuroanatomy for connectomics in Drosophila. Schneider-Mizell CM, Gerhard S, Longair M, Kazimiers T, Li, Feng L, Zwart M … Cardona A. link