Metadata-Version: 2.1
Name: kcsd
Version: 2.0.1
Summary: kernel current source density methods
Home-page: https://github.com/Neuroinflab/kCSD-python
Author: Chaitanya Chintaluri et al
License: Modified BSD License
Keywords: Electrophysiology CSD LFP MEA
Classifier: Development Status :: 5 - Production/Stable
Classifier: License :: OSI Approved :: BSD License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Operating System :: OS Independent
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
Classifier: Intended Audience :: Science/Research
License-File: LICENSE.txt
Requires-Dist: numpy >=1.19
Requires-Dist: scipy >=1.8.0
Requires-Dist: matplotlib >=3.6
Provides-Extra: docs
Requires-Dist: numpydoc >=1.6.0 ; extra == 'docs'
Requires-Dist: sphinx >=5 ; extra == 'docs'

Kernel Current Source Density
=============================

This 2.0 version of kCSD method.

Only supported for python 3.



Relevant Papers
---------------

Paper 1: "Kernel Current Source Density
Method", J. Potworowski, W. Jakuczun, S. Łȩski, D. K. Wójcik; Neural
Comput 2012; 24 (2): 541–575, doi:
https://doi.org/10.1162/NECO_a_00236


Paper 2 : "What we can and what we cannot see with extracellular
multielectrodes", C. Chintaluri, M. Bejtka, W.
Średniawa, M. Czerwiński, J. M. Dzik, J.
Jędrzejewska-Szmek, K. Kondrakiewicz, E. Kublik, D. K. Wójcik; PLoS
Computational Biology (2021), 17(5): e1008615, doi:
https://doi.org/10.1371/journal.pcbi.1008615

Paper 3 : "kCSD-python, reliable current source density estimation
with quality
control", C. Chintaluri, M. Bejtka, W. Średniawa, M. Czerwiński, J. M. Dzik, J. Jędrzejewska-Szmek, D. K. Wójcik;
bioRxiv, doi: https://doi.org/10.1101/708511

Paper 1 is the original paper with software code in Matlab.
Paper 2 is an improvement and development of the paper 1.
Paper 3 is a feature showcase and walk-through of the method and its applications. 

Tutorials
---------

This library comes with three tutorials and **does not require any installation**.

1. `Basic tutorial <https://colab.research.google.com/drive/1M7fCR5iZ9c7SAZWWoq9WLfFpk7pCaufd?usp=sharing>`_
2. `Advanced tutorial <https://colab.research.google.com/drive/1gIuBJ2XzOGmgnRuxKguHevcYoE6eY_o1?usp=sharing>`_
3. `sKCSD tutorial <https://colab.research.google.com/drive/1tjOvC5-OTteiGT_f-MBQ3hqN7P3i1P8e?usp=sharing>`_
   
More information on the tutorials is provided here `Tutorials!`_

.. _Tutorials!: /docs/source/TUTORIALS.rst

You can also save these tutorials on your desktop, for this you will
need to install jupyter-notebook. Do this by

..  code-block:: bash

   pip install jupyter notebook


Figures
-------

This library includes all the necessary scripts to generate the figures for papers 2 and 3.

`Figures for Paper 2`_

.. _Figures for Paper 2: /figures/what_you_can_see_with_lfp/README.txt

`Figures for Paper 3`_

.. _Figures for Paper 3: /figures/kCSD_properties/README.txt

Installation
------------

..  code-block:: bash

   user:~/$ pip install kcsd

`More Installations`_

.. _More Installations : https://kcsd-python.readthedocs.io/en/latest/INSTALL.html


Documentation
-------------

Autogenerated documentation available from readthedocs:

`kCSD-python_Reference`_

.. _kCSD-python_Reference : https://kcsd-python.readthedocs.io/en/latest/

Also included here are authors and their contributions, citation policy, contacts etc.,


Earlier Stable versions
-----------------------
Please see git tags for earlier versions. These are not available as packages unfortunately.

- v1.2 corresponds to the first time kCSD-python released as a python package
- v1.0 corresponds to the version with the test cases written inside tests folder
- v1.1 corresponds to the elephant python library version - no tests here


Health Report
-------------

Continuous Integration (Travis):

.. image:: https://travis-ci.org/Neuroinflab/kCSD-python.png?branch=master
   :target: https://travis-ci.org/Neuroinflab/kCSD-python

Test Coverage :	   

.. image:: https://coveralls.io/repos/github/Neuroinflab/kCSD-python/badge.png?branch=master
   :target: https://coveralls.io/github/Neuroinflab/kCSD-python?branch=master

Documentation Status:

.. image:: https://readthedocs.org/projects/kcsd-python/badge/?version=latest
   :target: https://kcsd-python.readthedocs.io/en/latest/?badge=latest

  
License
-------
`Modified BSD License`_

.. _Modified BSD License: https://opensource.org/licenses/BSD-3-Clause



