Kernel Current Source Density

This is version 2.0 of kCSD-python implementing kCSD method and related functionality.

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