Skip to content

Commit 45753b5

Browse files
m-kowalskam-kowalska
authored
Merge pull request #152 from Neuroinflab/readmefix
Tutorials visibility
2 parents 6676bae + 2e839fe commit 45753b5

2 files changed

Lines changed: 132 additions & 41 deletions

File tree

‎README.rst‎

Lines changed: 75 additions & 25 deletions
Original file line numberDiff line numberDiff line change
@@ -1,34 +1,72 @@
11
Kernel Current Source Density
22
=============================
33

4-
This is the 2.0 version of kCSD inverse method proposed in
4+
This 2.0 version of kCSD inverse method proposed in python3
55

6-
J. Potworowski, W. Jakuczun, S. Łęski, D. K. Wójcik
7-
"Kernel Current Source Density Method"
8-
Neural Computation 24 (2012), 541–575
6+
Relevant Papers
7+
---------------
98

10-
For details see the `bioRxiv pre-print`_
9+
Paper 1: "Kernel Current Source Density
10+
Method", J. Potworowski, W. Jakuczun, S. Łȩski, D. K. Wójcik; Neural
11+
Comput 2012; 24 (2): 541–575, doi:
12+
https://doi.org/10.1162/NECO_a_00236
1113

12-
.. _bioRxiv pre-print : https://doi.org/10.1101/708511
1314

15+
Paper 2 : "What we can and what we cannot see with extracellular
16+
multielectrodes", C. Chintaluri, M. Bejtka, W.
17+
Średniawa, M. Czerwiński, J. M. Dzik, J.
18+
Jędrzejewska-Szmek, K. Kondrakiewicz, E. Kublik, D. K. Wójcik; PLoS
19+
Computational Biology (2021), 17(5): e1008615, doi:
20+
https://doi.org/10.1371/journal.pcbi.1008615
1421

15-
Health Report
16-
-------------
22+
Paper 3 : "kCSD-python, reliable current source density estimation
23+
with quality
24+
control", C. Chintaluri, M. Bejtka, W. Średniawa, M. Czerwiński, J. M. Dzik, J. Jędrzejewska-Szmek, D. K. Wójcik;
25+
bioRxiv, doi: https://doi.org/10.1101/708511
1726

18-
Continuous Integration (Travis):
27+
Paper 1 is the original paper with software code in Matlab.
28+
Paper 2 is an improvement and development of the paper 1.
29+
Paper 3 is a feature showcase and walk-through of the method and its applications.
1930

20-
.. image:: https://travis-ci.org/Neuroinflab/kCSD-python.png?branch=master
21-
:target: https://travis-ci.org/Neuroinflab/kCSD-python
31+
Tutorials
32+
---------
2233

23-
Test Coverage :
34+
This library comes with three tutorials and **does not require any installation**.
2435

25-
.. image:: https://coveralls.io/repos/github/Neuroinflab/kCSD-python/badge.png?branch=master
26-
:target: https://coveralls.io/github/Neuroinflab/kCSD-python?branch=master
36+
1. `Basic tutorial <https://colab.research.google.com/drive/1M7fCR5iZ9c7SAZWWoq9WLfFpk7pCaufd?usp=sharing>`_
37+
2. `Advanced tutorial <https://colab.research.google.com/drive/1gIuBJ2XzOGmgnRuxKguHevcYoE6eY_o1?usp=sharing>`_
38+
3. `sKCSD tutorial <https://colab.research.google.com/drive/1tjOvC5-OTteiGT_f-MBQ3hqN7P3i1P8e?usp=sharing>`_
39+
40+
More information on the tutorials is provided here `Tutorials!`_
2741

28-
Documentation Status:
42+
.. _Tutorials!: /docs/source/TUTORIALS.rst
2943

30-
.. image:: https://readthedocs.org/projects/kcsd-python/badge/?version=latest
31-
:target: https://kcsd-python.readthedocs.io/en/latest/?badge=latest
44+
To have these tutorials and saved on your desktop, you will also need jupyter-notebook installed
45+
46+
.. code-block:: bash
47+
48+
pip install jupyterlab
49+
50+
51+
Figures
52+
-------
53+
54+
This library includes all the necessary scripts to generate the figures for papers 2 and 3.
55+
56+
`Figures for Paper 2`_
57+
58+
.. _Figures for Paper 2: /figures/what_you_can_see_with_lfp/README.txt
59+
60+
`Figures for Paper 3`_
61+
62+
.. _Figures for Paper 3: /figures/kCSD_properties/README.txt
63+
64+
Installation
65+
------------
66+
67+
`kCSD-python Installation`_
68+
69+
.. _kCSD-python Installation : https://kcsd-python.readthedocs.io/en/latest/INSTALL.html
3270

3371

3472
Documentation
@@ -40,16 +78,9 @@ Autogenerated documentation available from readthedocs:
4078

4179
.. _kCSD-python_Reference : https://kcsd-python.readthedocs.io/en/latest/
4280

43-
Also included here are installation instructions, authors and their
44-
contributions, citation policy, contacts etc.,
45-
46-
47-
Also included are `Tutorials!`_
48-
49-
.. _Tutorials!: /docs/source/TUTORIALS.rst
81+
Also included here are authors and their contributions, citation policy, contacts etc.,
5082

5183

52-
5384
Earlier Stable versions
5485
-----------------------
5586
Please see git tags for earlier versions
@@ -59,6 +90,25 @@ Please see git tags for earlier versions
5990
- v1.1 corresponds to the elephant python library version - no tests here
6091

6192

93+
Health Report
94+
-------------
95+
96+
Continuous Integration (Travis):
97+
98+
.. image:: https://travis-ci.org/Neuroinflab/kCSD-python.png?branch=master
99+
:target: https://travis-ci.org/Neuroinflab/kCSD-python
100+
101+
Test Coverage :
102+
103+
.. image:: https://coveralls.io/repos/github/Neuroinflab/kCSD-python/badge.png?branch=master
104+
:target: https://coveralls.io/github/Neuroinflab/kCSD-python?branch=master
105+
106+
Documentation Status:
107+
108+
.. image:: https://readthedocs.org/projects/kcsd-python/badge/?version=latest
109+
:target: https://kcsd-python.readthedocs.io/en/latest/?badge=latest
110+
111+
62112
License
63113
-------
64114
`Modified BSD License`_

‎docs/source/TUTORIALS.rst‎

Lines changed: 57 additions & 16 deletions
Original file line numberDiff line numberDiff line change
@@ -1,12 +1,33 @@
11
Tutorials
22
---------
33

4-
kcsd-python library comes with two extensive tutorials (at this
5-
moment, more soon). These can be tested using Jupyter notebook on your
6-
desktop after installing the kCSD-python package. Alternatively, they
7-
can be played around with without any installation on Binder in a
8-
web-browser. Note that in this case, the results from a browser are
9-
not saved, and cannot be retreived.
4+
kcsd-python library comes with three extensive tutorials. These
5+
tutorials can be explored online or installed on your desktop computer
6+
depending on your usage. To simple test it out try the online version
7+
first, and if required install the python package.
8+
9+
**Online version**
10+
11+
To play around with the library without any installation, you can run
12+
the tutorials on Google collaboratory in a web-browser. **Note:** the
13+
results from a browser are not saved and cannot be retreived. If you
14+
wish to have the results stored somewhere, please use the desktop
15+
version.
16+
17+
**Desktop version**
18+
19+
This requires you to install the kCSD-package and additionally to
20+
install jupyter notebook on your desktop.
21+
22+
.. code-block:: bash
23+
24+
git clone https://github.com/Neuroinflab/kCSD-python.git
25+
cd kCSD-python
26+
pip install .
27+
pip install jupyterlab
28+
29+
30+
1031
1132
Basic Features
1233
~~~~~~~~~~~~~~
@@ -22,15 +43,18 @@ and repeat the procedure. We also explore the situation when certain
2243
number of the electrode are broken, and how that would effect the
2344
reconstructions.
2445

25-
The tutorial is provided with Binder access, click the button below to
46+
The tutorial is provided with Google collaboratory, click the button below to
2647
interact with it in a browser, no installation necessary.
2748

28-
.. image:: https://mybinder.org/badge.svg
29-
:target: https://mybinder.org/v2/gh/Neuroinflab/kCSD-python/master?filepath=tutorials%2Ftutorial_basic.ipynb
49+
`Basic tutorial <https://colab.research.google.com/drive/1M7fCR5iZ9c7SAZWWoq9WLfFpk7pCaufd?usp=sharing>`_
50+
51+
..
52+
.. image:: https://mybinder.org/badge.svg
53+
:target: https://mybinder.org/v2/gh/Neuroinflab/kCSD-python/master?filepath=tutorials%2Ftutorial_basic.ipynb
3054
3155

32-
For a non-interactive version of this tutorial, see
33-
`Tutorail1<https://github.com/Neuroinflab/kCSD-python/blob/master/tutorials/tutorial_basic.ipynb>`_.
56+
For a non-interactive static version of this tutorial, see
57+
`Tutorial1 <https://github.com/Neuroinflab/kCSD-python/blob/master/tutorials/tutorial_basic.ipynb>`_.
3458

3559

3660

@@ -47,15 +71,32 @@ Features tutorial and expands it to the other dimensions. NOTE, the
4771
user might have to 'Reset this tutorial' before using to enable the
4872
buttons (Kernel>Restart & Run All).
4973

50-
The tutorial is provided with Binder access, click the button below to
74+
The tutorial is provided with Google collaboratory, click the button below to
5175
interact with it in a browser, no installation necessary.
5276

53-
.. image:: https://mybinder.org/badge.svg
54-
:target: https://mybinder.org/v2/gh/Neuroinflab/kCSD-python/master?filepath=tutorials%2Ftutorial_advanced.ipynb
77+
`Advanced tutorial <https://colab.research.google.com/drive/1gIuBJ2XzOGmgnRuxKguHevcYoE6eY_o1?usp=sharing>`_
78+
79+
..
80+
.. image:: https://mybinder.org/badge.svg
81+
:target: https://mybinder.org/v2/gh/Neuroinflab/kCSD-python/master?filepath=tutorials%2Ftutorial_advanced.ipynb
82+
83+
84+
For a non-interactive static version of this tutorial, see
85+
`Tutorial2 <https://github.com/Neuroinflab/kCSD-python/blob/master/tutorials/tutorial_advanced.ipynb>`_.
86+
87+
sKCSD Tutorial
88+
~~~~~~~~~~~~~~
89+
90+
This tutorial showcases the possibility to reconstruct the current sources
91+
of a single neuron provided the morphology of the said neuron is known.
92+
This methods has been described extensively here: https://doi.org/10.7554/eLife.29384
93+
94+
95+
`sKCSD tutorial <https://colab.research.google.com/drive/1tjOvC5-OTteiGT_f-MBQ3hqN7P3i1P8e?usp=sharing>`_
5596

5697

57-
For a non-inteactive version of this tutorial, see
58-
`Tutorail2<https://github.com/Neuroinflab/kCSD-python/blob/master/tutorials/tutorial_advanced.ipynb>`_.
98+
For a non-interactive static version of this tutorial, see
99+
`sKCSD Tutorial <https://github.com/Neuroinflab/kCSD-python/blob/master/tutorials/skcsd_tutorial.ipynb>`_
59100

60101

61102
More Tutorials

0 commit comments

Comments
 (0)