Tested with CATMAID release version 2020.02.15 - if you are working with older versions you may run into issues due to API changes.
- 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)
Pymaid is on ReadTheDocs.
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
To install the 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!
This code is under GNU GPL V3
Pymaid implements/provides an interfaces with algorithms described in:
- 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, Hueckesfeld S, Peters M, ... Pankratz MJ. link