From 4a26a8706ee6d465d92b8bce76db445131bf0992 Mon Sep 17 00:00:00 2001 From: Philipp Schlegel Date: Wed, 28 Apr 2021 08:42:59 +0100 Subject: [PATCH] update README --- README.md | 31 ++++++++++++++----------------- 1 file changed, 14 insertions(+), 17 deletions(-) diff --git a/README.md b/README.md index 9076415..f48ff11 100644 --- a/README.md +++ b/README.md @@ -2,20 +2,25 @@ 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. +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. -## Documentation -Pymaid is on [ReadTheDocs](http://pymaid.readthedocs.io/ "pymaid ReadTheDocs"). +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 -* fetch data via CATMAID's API +* 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) -* custom neuron classes that work with [navis](https://navis.readthedocs.io) * 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: +See the [documentation](http://pymaid.readthedocs.io/ "PyMaid ReadTheDocs") for +detailed installation instructions, tutorials and examples. For the impatient: ```bash pip3 install python-catmaid @@ -40,19 +45,11 @@ 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. +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) -3. **Comparison of neurons based on synapse distribution**: eLife. doi: 10.7554/eLife.16799 +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) -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)