kcsd 2.0.1

kernel current source density methods

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

2. Advanced tutorial

3. sKCSD tutorial

More information on the tutorials is provided here Tutorials!

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

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 3

Installation

user:~/$ pip install kcsd

More Installations

Documentation

Autogenerated documentation available from readthedocs:

kCSD-python_Reference

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):

Test Coverage :

Documentation Status:

License

Modified BSD License