Merge pull request #130 from m-kowalska/master

Correction of estimate_at method + new figures

Author: abukaj

figures/kCSD_properties/README.txt

@@ -3,7 +3,7 @@ Instructions for the figures from kCSD-revisited paper.
 ~~~~~~~~~~~~~~~~~~~~~~~
 Figure 1 - Schematic
 
-sources_electrodes.odg
+name: figure1.png
 
 ~~~~~~~~~~~~~~~~~~~~~~~
 Figure 2 - 1D spectral properties of kCSD method
@@ -23,22 +23,22 @@ figure_Tbasis_noise.py
 ~~~~~~~~~~~~~~~~~~~~~~~
 Figure 5 - L-curve method for regularization
 
-You will need to run L_curve_simulation.py first or download files from here:
-...
+You will need to run L_curve_simulation.py first.
+
 figure_LC.py
 
 ~~~~~~~~~~~~~~~~~~~~~~~
 Figure 6 - L-curve versus Cross-validation
 
-You will need to run L_curve_simulation.py first or download files from here:
-...
+You will need to run L_curve_simulation.py first.
+
 figure_LCandCVperformance.py
 
 ~~~~~~~~~~~~~~~~~~~~~~~
 Figure 7 - Error propagation map
 
 error_propagation.py
-colorblind_friendly.py 
+colorblind_friendly.py
 
 ~~~~~~~~~~~~~~~~~~~~~~~
 Figure 8 - Reliability map
@@ -65,53 +65,114 @@ https://www.dropbox.com/sh/6kykj4d3dx3fp5s/AAACtN49VCbAHA9otOfNXbnOa?dl=0
 tutorial_broken_electrodes_diff_err.py
 
 ~~~~~~~~~~~~~~~~~~~~~~~
-Figure 11 - Basic features tutorial
+Figure 11 - Simulated cortical recordings in Traubs's model
 
-You will need to run tutorial3.py first or download files from here
-https://www.dropbox.com/sh/6kykj4d3dx3fp5s/AAACtN49VCbAHA9otOfNXbnOa?dl=0
+You will need to download files from:
+https://repod.pon.edu.pl/dataset/thalamocortical-network/resource/6add09e1-bfe4-4082-b990-24b469756886
 
-tutorial_basic.py
+npx/traub_data_kcsd_column_figure.py
 
 ~~~~~~~~~~~~~~~~~~~~~~~
-Figure 12 - Noisy electrodes tutorial
+Figure 12 - LFP and CSD as a function of time - Traub's model
 
-tutorial_noisy_electrodes.py
+You will need to download files from:
+https://repod.pon.edu.pl/dataset/thalamocortical-network/resource/6add09e1-bfe4-4082-b990-24b469756886
 
-~~~~~~~~~~~~~~~~~~~~~~~~
-Figure 13 - Broken electrodes tutorial
+npx/figure_traub_timespace.py
 
-Download first from
-https://www.dropbox.com/sh/6kykj4d3dx3fp5s/AAACtN49VCbAHA9otOfNXbnOa?dl=0
-(generated from tweaking tutorial3.py)
+~~~~~~~~~~~~~~~~~~~~~~~
+Figure 13 - Six first eigensources for a single bank of a Neuropixels probe
 
-tutorial_broken_electrodes.py
+You will need to download files from:
+https://repod.pon.edu.pl/dataset/thalamocortical-network/resource/6add09e1-bfe4-4082-b990-24b469756886
+
+npx/figure_traub_eigensources.py
+
+~~~~~~~~~~~~~~~~~~~~~~~
+Figure 14 - LFP and CSD space profiles - experimental data from a single bank of a Neuropixels probe
+
+You will need to download files from:
+
+npx/kCSD2D_reconstruction_from_npx.py
+
+~~~~~~~~~~~~~~~~~~~~~~~
+Figure 15 - LFP and CSD as a function of time - experimental data
+
+You will need to download files from:
+
+npx/kCSD2D_reconstruction_from_npx.py
 
 ~~~~~~~~~~~~~~~~~~~~~~~~
-Figure 14 - L-Curve and CV landscape
+Figure 16 - L-Curve and CV landscape
+
+You will need to run L_curve_simulation.py first.
 
-You will need to run L_curve_simulation.py first or download files from here:
-...
 figure_LCandCV.py
 
+~~~~~~~~~~~~~~~~~~~~~~~
+Figure 17 - Schematic - location of Neuropixels bank 0
+
+name: figure17.png
+
 =====================
 Supplementary Figures
 =====================
+
 ~~~~~~~~~~~~~~~~~~~~~~~~~~
-Figure S1 / 15 - spectral properties of kCSD method for simple 2D case
+Figure 2-Figure supplement 1 - spectral properties of kCSD method for simple 2D case
 
 figure_eigensources_M_2D.py
 
 ~~~~~~~~~~~~~~~~~~~~~~~~~~
-Figure S2 / 16 - Error propagation maps for 1D
+Figure 7-Figure supplement 1 - Error propagation maps for 1D
 
 pots_propagation.py
 
 ~~~~~~~~~~~~~~~~~~~~~~~~~~
-Figure S3 / 17 - 3D source reconstruction
+Figure 13-Figure supplement 1 - Eigensurces 7-12 ('start=6', 'stop=12'),
+Figure 13-Figure supplement 2 - Eigensurces 13-18 ('start=12', 'stop=18'),
+Figure 13-Figure supplement 3 - Eigensurces 19-24 ('start=18', 'stop=24'),
+Figure 13-Figure supplement 4 - Eigensurces 25-30 ('start=24', 'stop=30'),
+Figure 13-Figure supplement 5 - Eigensurces 31-36 ('start=30', 'stop=36'),
+Figure 13-Figure supplement 6 - Eigensurces 37-42 ('start=36', 'stop=42'),
+Figure 13-Figure supplement 7 - Eigensurces 43-48 ('start=42', 'stop=48')
+
+All supplementary figures to Figure 13 were created using different
+'start' and 'stop'parameters at:
+npx/figure_traub_eigensources.py
+
+================
+Appendix Figures
+================
+
+~~~~~~~~~~~~~~~~~~~~~~~
+Appendix 1 Figure 1 - Basic features tutorial
+
+You will need to run tutorial3.py first or download files from here
+https://www.dropbox.com/sh/6kykj4d3dx3fp5s/AAACtN49VCbAHA9otOfNXbnOa?dl=0
+
+tutorial_basic.py
+
+~~~~~~~~~~~~~~~~~~~~~~~
+Appendix 1 Figure 2 - Noisy electrodes tutorial
+
+tutorial_noisy_electrodes.py
+
+~~~~~~~~~~~~~~~~~~~~~~~~
+Appendix 1 Figure 3 - Broken electrodes tutorial
+
+Download first from
+https://www.dropbox.com/sh/6kykj4d3dx3fp5s/AAACtN49VCbAHA9otOfNXbnOa?dl=0
+(generated from tweaking tutorial3.py)
+
+tutorial_broken_electrodes.py
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~
+Appendix 1 Figure 4 - 3D source reconstruction
 
 tutorial_basic_3d.py
 
 ~~~~~~~~~~~~~~~~~~~~~~~~~~
-Figure S4 / 18 - sKCSD example
+Appendix 1 Figure 5 - sKCSD example
 
 skcsd_and_l_curve_complex_morphology.py