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!

License:

This code is under GNU GPL V3

References:

Pymaid implements/provides an interfaces with algorithms described in:

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
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
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
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

BrainCircuitsIO / pymaid