[](http://pymaid.readthedocs.io/en/latest/?badge=latest) [](https://github.com/navis-org/pymaid/actions/workflows/run-tests.yml) [](https://coveralls.io/github/navis-org/pymaid?branch=master) [](https://mybinder.org/v2/gh/navis-org/pymaid/master?urlpath=tree) [](https://zenodo.org/badge/latestdoi/78551448)
<img src="https://github.com/navis-org/pymaid/raw/master/docs/_static/favicon.png" height="30"> pymaid
======================================================================================================
Python-Catmaid - or "pymaid" - is a [Python](http://www.python.org) 3 library 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.
## Features
* pull and push data from/to a CATMAID server
* visualize and analyse neuron morphology via [navis](https://navis.readthedocs.io)
* tools to analyse user stats (e.g. time-invested, project history)
* clustering methods (e.g. by connectivity or synapse placement)
## Documentation
Pymaid is on [ReadTheDocs](http://pymaid.readthedocs.io/ "pymaid ReadTheDocs").
## 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+https://github.com/navis-org/pymaid@master
```
Alternatively click on the *launch binder* badge above to try out pymaid hosted by [mybinder](https://mybinder.org)!
## License:
This code is under GNU GPL V3
## References:
Pymaid implements/provides an interfaces with algorithms described in:
1. **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)
2. **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)
Raw data
{
"_id": null,
"home_page": "https://github.com/navis-org/pymaid",
"name": "python-catmaid",
"maintainer": "",
"docs_url": null,
"requires_python": ">=3.6",
"maintainer_email": "",
"keywords": "CATMAID interface neuron navis",
"author": "Philipp Schlegel",
"author_email": "pms70@cam.ac.uk",
"download_url": "https://files.pythonhosted.org/packages/64/1f/7d26cc9218c66cd85a10509c7c8ee3b9ed9a427d0bf38b283a2cb0a00303/python-catmaid-2.4.0.tar.gz",
"platform": null,
"description": "[](http://pymaid.readthedocs.io/en/latest/?badge=latest) [](https://github.com/navis-org/pymaid/actions/workflows/run-tests.yml) [](https://coveralls.io/github/navis-org/pymaid?branch=master) [](https://mybinder.org/v2/gh/navis-org/pymaid/master?urlpath=tree) [](https://zenodo.org/badge/latestdoi/78551448)\n\n<img src=\"https://github.com/navis-org/pymaid/raw/master/docs/_static/favicon.png\" height=\"30\"> pymaid\n======================================================================================================\nPython-Catmaid - or \"pymaid\" - is a [Python](http://www.python.org) 3 library to\ninterface with [CATMAID](https://github.com/catmaid/CATMAID \"CATMAID Repo\")\nservers.\n\nTested with CATMAID release version 2020.02.15 - if you are working with older\nversions you may run into issues due to API changes.\n\n## Features\n* pull and push data from/to a CATMAID server\n* visualize and analyse neuron morphology via [navis](https://navis.readthedocs.io)\n* tools to analyse user stats (e.g. time-invested, project history)\n* clustering methods (e.g. by connectivity or synapse placement)\n\n## Documentation\nPymaid is on [ReadTheDocs](http://pymaid.readthedocs.io/ \"pymaid ReadTheDocs\").\n\n## Getting started\nSee the [documentation](http://pymaid.readthedocs.io/ \"PyMaid ReadTheDocs\") for\ndetailed installation instructions, tutorials and examples. For the impatient:\n\n```bash\npip3 install python-catmaid\n```\n\n*Important*: there is a `pymaid` package on PyPI which has _nothing_ to do with\nthis pymaid!\n\nTo install the bleeding edge from Github:\n\n```bash\npip3 install git+https://github.com/navis-org/pymaid@master\n```\n\nAlternatively click on the *launch binder* badge above to try out pymaid hosted by [mybinder](https://mybinder.org)!\n\n\n\n## License:\nThis code is under GNU GPL V3\n\n## References:\nPymaid implements/provides an interfaces with algorithms described in:\n\n1. **Comparison of neurons based on connectivity**: Science. 2012 Jul 27;337(6093):437-44. doi: 10.1126/science.1221762.\n*The connectome of a decision-making neural network.*\nJarrell TA, Wang Y, Bloniarz AE, Brittin CA, Xu M, Thomson JN, Albertson DG, Hall DH, Emmons SW.\n[link](http://science.sciencemag.org/content/337/6093/437.long)\n2. **Comparison of neurons based on synapse distribution**: eLife. doi: 10.7554/eLife.16799\n*Synaptic transmission parallels neuromodulation in a central food-intake circuit.*\nSchlegel P, Texada MJ, Miroschnikow A, Schoofs A, Hueckesfeld S, Peters M, ... Pankratz MJ.\n[link](https://elifesciences.org/content/5/e16799)\n",
"bugtrack_url": null,
"license": "GNU GPL V3",
"summary": "Python interface to CATMAID servers",
"version": "2.4.0",
"split_keywords": [
"catmaid",
"interface",
"neuron",
"navis"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "fd1c4795166106f430958fc782ac6c234bd750b3b0f0df80ab1a58ef95aff4f8",
"md5": "bd2c0cb55a00556a599ee38ec52bfae8",
"sha256": "ab81535d704f5c4158ab5ce9e9fa271cc72240d48e336fa12959f342fd179d3d"
},
"downloads": -1,
"filename": "python_catmaid-2.4.0-py3-none-any.whl",
"has_sig": false,
"md5_digest": "bd2c0cb55a00556a599ee38ec52bfae8",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": ">=3.6",
"size": 177535,
"upload_time": "2023-04-27T15:37:44",
"upload_time_iso_8601": "2023-04-27T15:37:44.987179Z",
"url": "https://files.pythonhosted.org/packages/fd/1c/4795166106f430958fc782ac6c234bd750b3b0f0df80ab1a58ef95aff4f8/python_catmaid-2.4.0-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "641f7d26cc9218c66cd85a10509c7c8ee3b9ed9a427d0bf38b283a2cb0a00303",
"md5": "e367ad01dd416bbe868cf4c2bab9fe11",
"sha256": "04d34f60484b2b78d50907dbfb35446b8cc40d1994c0c246cba98a3362deb7d4"
},
"downloads": -1,
"filename": "python-catmaid-2.4.0.tar.gz",
"has_sig": false,
"md5_digest": "e367ad01dd416bbe868cf4c2bab9fe11",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.6",
"size": 169503,
"upload_time": "2023-04-27T15:37:46",
"upload_time_iso_8601": "2023-04-27T15:37:46.744106Z",
"url": "https://files.pythonhosted.org/packages/64/1f/7d26cc9218c66cd85a10509c7c8ee3b9ed9a427d0bf38b283a2cb0a00303/python-catmaid-2.4.0.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2023-04-27 15:37:46",
"github": true,
"gitlab": false,
"bitbucket": false,
"github_user": "navis-org",
"github_project": "pymaid",
"travis_ci": true,
"coveralls": true,
"github_actions": true,
"requirements": [
{
"name": "navis",
"specs": [
[
">=",
"1.0.0"
]
]
},
{
"name": "numpy",
"specs": [
[
">=",
"1.16.3"
]
]
},
{
"name": "networkx",
"specs": [
[
">=",
"2.4"
]
]
},
{
"name": "pandas",
"specs": [
[
">=",
"1.0"
]
]
},
{
"name": "requests-futures",
"specs": [
[
">=",
"0.9.9"
]
]
},
{
"name": "requests",
"specs": [
[
">=",
"2.21.0"
]
]
},
{
"name": "setuptools",
"specs": [
[
">=",
"41.0.1"
]
]
},
{
"name": "scipy",
"specs": [
[
">=",
"1.3.0"
]
]
},
{
"name": "six",
"specs": [
[
">=",
"1.11.0"
]
]
},
{
"name": "tqdm",
"specs": [
[
">=",
"4.50.0"
]
]
},
{
"name": "psutil",
"specs": [
[
">=",
"5.4.3"
]
]
}
],
"lcname": "python-catmaid"
}
JSON
