11Kernel Current Source Density
22=============================
33
4- This is python3 based library 2.0 version of kCSD inverse method proposed.
4+ This 2.0 version of kCSD inverse method proposed in python3
55
6- 1. J. Potworowski, W. Jakuczun, S. Łȩski, D. K. Wójcik
6+ Relevant Papers
7+ ---------------
8+
9+ # J. Potworowski, W. Jakuczun, S. Łȩski, D. K. Wójcik
710 "Kernel Current Source Density Method"
811 Neural Comput 2012; 24 (2): 541–575.
912 doi: https://doi.org/10.1162/NECO_a_00236
10-
11- 2. C. Chintaluri, M. Bejtka, W. Średniawa, M. Czerwiński, J. M. Dzik, J. Jędrzejewska-Szmek, K. Kondrakiewicz, E. Kublik, D. K. Wójcik
13+ ----
14+ # C. Chintaluri, M. Bejtka, W. Średniawa, M. Czerwiński, J. M. Dzik, J. Jędrzejewska-Szmek, K. Kondrakiewicz, E. Kublik, D. K. Wójcik
1215 "What we can and what we cannot see with extracellular multielectrodes"
1316 PLoS Computational Biology (2021), 17(5): e1008615.
1417 doi: https://doi.org/10.1371/journal.pcbi.1008615
15-
16- 3. C. Chintaluri, M. Bejtka, W. Średniawa, M. Czerwiński, J. M. Dzik, J. Jędrzejewska-Szmek, D. K. Wójck
18+ ----
19+ # C. Chintaluri, M. Bejtka, W. Średniawa, M. Czerwiński, J. M. Dzik, J. Jędrzejewska-Szmek, D. K. Wójck
1720 "kCSD-python, reliable current source density estimation with quality control"
1821 bioRxiv
1922 doi: https://doi.org/10.1101/708511
23+ ----
2024
2125Paper 1 is the original paper with software code in Matlab.
2226Paper 2 is an improvement and development of the paper 1.
2327Paper 3 is a feature showcase and walk-through of the method and its applications.
2428
25- Health Report
26- -------------
27-
28- Continuous Integration (Travis):
29-
30- .. image :: https://travis-ci.org/Neuroinflab/kCSD-python.png?branch=master
31- :target: https://travis-ci.org/Neuroinflab/kCSD-python
32-
33- Test Coverage :
34-
35- .. image :: https://coveralls.io/repos/github/Neuroinflab/kCSD-python/badge.png?branch=master
36- :target: https://coveralls.io/github/Neuroinflab/kCSD-python?branch=master
37-
38- Documentation Status:
39-
40- .. image :: https://readthedocs.org/projects/kcsd-python/badge/?version=latest
41- :target: https://kcsd-python.readthedocs.io/en/latest/?badge=latest
42-
4329Tutorials
4430---------
4531
4632This library comes with three tutorials that **do not require any installation **.
4733
48- 1. `Basic tutorial<https://colab.research.google.com/drive/1M7fCR5iZ9c7SAZWWoq9WLfFpk7pCaufd?usp=sharing> `_
49- 2. `Advanced tutorial<https://colab.research.google.com/drive/1gIuBJ2XzOGmgnRuxKguHevcYoE6eY_o1?usp=sharing> `_
50- 3. `sKCSD tutorial<https://colab.research.google.com/drive/1tjOvC5-OTteiGT_f-MBQ3hqN7P3i1P8e?usp=sharing> `_
34+ 1. `Basic tutorial <https://colab.research.google.com/drive/1M7fCR5iZ9c7SAZWWoq9WLfFpk7pCaufd?usp=sharing >`_
35+ 2. `Advanced tutorial <https://colab.research.google.com/drive/1gIuBJ2XzOGmgnRuxKguHevcYoE6eY_o1?usp=sharing >`_
36+ 3. `sKCSD tutorial <https://colab.research.google.com/drive/1tjOvC5-OTteiGT_f-MBQ3hqN7P3i1P8e?usp=sharing >`_
5137
52- More information on these **online only ** tutorials is provided here `Tutorials! `_
38+ More information on the **online and installed version ** of tutorials is provided here `Tutorials! `_
5339
5440.. _Tutorials! : /docs/source/TUTORIALS.rst
5541
5642To have these tutorials and saved on your desktop, you will also need jupyter-notebook installed
5743
5844.. code-block :: bash
45+
5946 pip install jupyterlab
6047
6148
@@ -64,15 +51,22 @@ Figures
6451
6552This library includes all the necessary scripts to generate the figures for papers 2 and 3.
6653
67- `Figures for Paper 2! `_
54+ `Figures for Paper 2 `_
6855
69- .. _Figures for Paper 2! : /figures/what_you_can_see_with_lfp/README.txt
56+ .. _Figures for Paper 2 : /figures/what_you_can_see_with_lfp/README.txt
7057
71- `Figures for Paper 3! `_
58+ `Figures for Paper 3 `_
59+
60+ .. _Figures for Paper 3 : /figures/kCSD_properties/README.txt
61+
62+ Installation
63+ ------------
64+
65+ `kCSD-python Installation `_
66+
67+ .. _kCSD-python Installation : https://kcsd-python.readthedocs.io/en/latest/INSTALL.html
7268
73- .. _Figures for Paper 3! : /figures/kCSD_properties/README.txt
7469
75-
7670Documentation
7771-------------
7872
@@ -82,8 +76,7 @@ Autogenerated documentation available from readthedocs:
8276
8377.. _kCSD-python_Reference : https://kcsd-python.readthedocs.io/en/latest/
8478
85- Also included here are installation instructions, authors and their
86- contributions, citation policy, contacts etc.,
79+ Also included here are authors and their contributions, citation policy, contacts etc.,
8780
8881
8982Earlier Stable versions
@@ -95,6 +88,25 @@ Please see git tags for earlier versions
9588- v1.1 corresponds to the elephant python library version - no tests here
9689
9790
91+ Health Report
92+ -------------
93+
94+ Continuous Integration (Travis):
95+
96+ .. image :: https://travis-ci.org/Neuroinflab/kCSD-python.png?branch=master
97+ :target: https://travis-ci.org/Neuroinflab/kCSD-python
98+
99+ Test Coverage :
100+
101+ .. image :: https://coveralls.io/repos/github/Neuroinflab/kCSD-python/badge.png?branch=master
102+ :target: https://coveralls.io/github/Neuroinflab/kCSD-python?branch=master
103+
104+ Documentation Status:
105+
106+ .. image :: https://readthedocs.org/projects/kcsd-python/badge/?version=latest
107+ :target: https://kcsd-python.readthedocs.io/en/latest/?badge=latest
108+
109+
98110License
99111-------
100112`Modified BSD License `_
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