python-catmaid 2.0.0

Python interface to CATMAID servers

pymaid

Python-Catmaid - or pymaid - is a collection of Python 3 tools 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.

Documentation

Pymaid is on ReadTheDocs.

Features

• fetch data via CATMAID's API
• tools to analyse user stats (e.g. time-invested, project history)
• custom neuron classes that work with navis
• clustering methods (e.g. by connectivity or synapse placement)

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 bleeding edge from Github:

pip3 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:

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, Hueckesfeld 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