Metadata-Version: 2.1
Name: python-catmaid
Version: 1.1.2
Summary: Python interface to CATMAID servers
Home-page: https://github.com/schlegelp/pymaid
Author: Philipp Schlegel
Author-email: pms70@cam.ac.uk
License: GNU GPL V3
Keywords: CATMAID interface neuron navis
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Requires-Python: >=3.6
Description-Content-Type: text/markdown
Requires-Dist: navis (~=0.2)
Requires-Dist: numpy (>=1.16.3)
Requires-Dist: networkx (>=2.4)
Requires-Dist: pandas (~=1.0)
Requires-Dist: requests-futures (>=0.9.9)
Requires-Dist: requests (>=2.21.0)
Requires-Dist: setuptools (>=41.0.1)
Requires-Dist: scipy (>=1.3.0)
Requires-Dist: six (>=1.11.0)
Requires-Dist: tqdm (>=4.50.0)
Requires-Dist: psutil (>=5.4.3)
Provides-Extra: extras
Requires-Dist: fuzzywuzzy[speedup] (~=0.17.0) ; extra == 'extras'
Requires-Dist: ujson (~=1.35) ; extra == 'extras'

[![Documentation Status](https://readthedocs.org/projects/pymaid/badge/?version=latest)](http://pymaid.readthedocs.io/en/latest/?badge=latest) [![Build Status](https://travis-ci.org/schlegelp/pyMaid.svg?branch=master)](https://travis-ci.org/schlegelp/pyMaid) [![Coverage Status](https://coveralls.io/repos/github/schlegelp/pyMaid/badge.svg?branch=master)](https://coveralls.io/github/schlegelp/pyMaid?branch=master) [![Binder](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/schlegelp/pyMaid/master?urlpath=tree)

<img src="https://github.com/schlegelp/pyMaid/raw/master/docs/_static/favicon.png" height="30"> pymaid
======================================================================================================
Python-Catmaid - or pymaid - is a collection of [Python](http://www.python.org) 3 tools to interface with [CATMAID](https://github.com/catmaid/CATMAID "CATMAID Repo") 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](http://pymaid.readthedocs.io/ "pymaid 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](https://navis.readthedocs.io)
* clustering methods (e.g. by connectivity or synapse placement)

## Getting started
See the [documentation](http://pymaid.readthedocs.io/ "PyMaid ReadTheDocs") 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](https://mybinder.org)!

![pymaid example](https://user-images.githubusercontent.com/7161148/41200671-4e4320ec-6ca1-11e8-90a2-2feda2d9372d.gif)

## 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](https://www.cell.com/neuron/fulltext/S0896-6273(16)30265-3?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0896627316302653%3Fshowall%3Dtrue)
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](http://science.sciencemag.org/content/337/6093/437.long)
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](https://elifesciences.org/content/5/e16799)
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](https://elifesciences.org/articles/12059)


