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README.txt
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README.txt
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Instructions for the figures from kCSD-python, reliable current source density estimation with quality control.
~~~~~~~~~~~~~~~~~~~~~~~
Figure 1 - Schematic
name: figure1.png
~~~~~~~~~~~~~~~~~~~~~~~
Figure 2 - L-curve method for regularization
You will need to run L_curve_simulation.py first.
figure_LC.py
~~~~~~~~~~~~~~~~~~~~~~~
Figure 3 - Error propagation map
error_propagation.py
colorblind_friendly.py
~~~~~~~~~~~~~~~~~~~~~~~
Figure 4 - Reliability map 2D
reliability_map_2d.py
Download kCSD_properties.zip file from here: http://bit.ly/kCSD-supplementary
and unzip the data
kCSD_properties/error_maps_2D/point_error_large_100_all_ele.npy
kCSD_properties/error_maps_2D/point_error_small_100_all_ele.npy
~~~~~~~~~~~~~~~~~~~~~~~
Figure 5 - Reliability map; Use case in a 2D dipolar large source
kCSD_with_reliability_map_2D.py
Download kCSD_properties.zip file from here http://bit.ly/kCSD-supplementary
and unzip the data
kCSD_properties/error_maps_2D/point_error_large_100_all_ele.npy
kCSD_properties/error_maps_2D/point_error_small_100_all_ele.npy
~~~~~~~~~~~~~~~~~~~~~~~
Figure 6 - Average Error (Diff) when broken electrode and loss in reconstruction quality
You will need to run tutorial3.py first or download kCSD_properties.zip file from here
http://bit.ly/kCSD-supplementary
tutorial_broken_electrodes_diff_err.py
~~~~~~~~~~~~~~~~~~~~~~~
Figure 7 - L-Curve and CV landscape
You will need to run L_curve_simulation.py first.
figure_LCandCV.py
~~~~~~~~~~~~~~~~~~~~~~~
Figure 8 - Basic features tutorial
You will need to run tutorial3.py first or download kCSD_properties.zip file from here
http://bit.ly/kCSD-supplementary
tutorial_basic.py
~~~~~~~~~~~~~~~~~~~~~~~
Figure 9 - Noisy electrodes tutorial
tutorial_noisy_electrodes.py
~~~~~~~~~~~~~~~~~~~~~~~
Figure 10 - Broken electrodes tutorial
Download kCSD_properties.zip file first from
http://bit.ly/kCSD-supplementary
(generated from tweaking tutorial3.py)
tutorial_broken_electrodes.py
~~~~~~~~~~~~~~~~~~~~~~~
Figure 11 - Error propagation maps for 1D
pots_propagation.py
~~~~~~~~~~~~~~~~~~~~~~~
Figure 12 - 3D source reconstruction
tutorial_basic_3d.py
~~~~~~~~~~~~~~~~~~~~~~~
Figure 13 - sKCSD example
You will need to install LFPy package first:
pip install lfpy
skcsd_and_l_curve_complex_morphology.py