Metadata-Version: 2.1
Name: python-catmaid
Version: 2.0.3
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
Description: [![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 that work with [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:
        
        ```bash
        pip3 install python-catmaid
        ```
        
        *Important*: there is a `pymaid` package on PyPI which has _nothing_ to do with
        this pymaid!
        
        To install the bleeding edge from Github:
        
        ```bash
        pip3 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, Hueckesfeld 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)
        
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
Provides-Extra: extras
