Python interface to CATMAID servers
Project description
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 built on top of 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:
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
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Hashes for python_catmaid-1.1.2-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | abefecedcd0d6e9a735b19bdf17b8349da9f31bf335f146cad24fd842b8270f7 |
|
MD5 | 09506bdb77b31a6b32ae5ff76e55a04f |
|
BLAKE2b-256 | e3dbc7ee452df0a538c546243951dda91b1f00f59896d80e1a6c95b5d098d45c |