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Francioni, Padamsey, Rochefort, eLife 2019

MATLAB code from the Rochefort lab used for analysis in this paper.

General notes

  • The code in the folder /Peaks_functions includes functions used to find peaks in deltaf traces (detect_df_peaks.m), extract the peak deltaf window (get_peakwindow_df.m) and peaks coincidence between two compartments (get_coincident_events.m).
  • A practical example is given for the apical tuft results presented in Figure 1 (main_fig1.m and /Fig1_functions folder). For all remaining figures, except for Electrophysiology in Figure 4, we refer to the relevant panels in Figure 1 which implement the same method.
  • The analysis functions may call other specific functions in the folder /Utilities, e.g. for data handling or plot.
  • Code downloaded from external sources can be found in the folder /external (licence in corresponding folder).

Below are the functions used for each figure in the paper. Letters on the left indicate the corresponding panel within each figure.

Data repository

Repository for electrophysiological and anatomical data included in the article:

https://datashare.ed.ac.uk/handle/10283/3873

3D Reconstructions of the neurons

The 3D reconstructions of 19 neurons included in the manuscript are freely available at:

http://neuromorpho.org/KeywordResult.jsp?count=19&keywords=%22rochefort%22

Figure 1

The main functions and plot scripts for each panel are called in main_fig1.m.

D) get_FOVtuft_peaks.m, detect_df_peaks.m, compute_FOVtuft_peak_corr.m (calls get_peakwindow_df.m)
F) see panel D
I) get_FOVtuft_peaks.m, detect_df_peaks.m, compute_FOVtuft_peak_corr.m (calls get_peakwindow_df.m)
J) get_FOVtuft_peaks.m, detect_df_peaks.m, get_FOVtuft_coincident_peaks.m (calls get_coincident_events.m)

Figure 1 - supplementary 2

For each panel see Fig1 panel J.

The same method is applied for various compartments, and two parameters can vary when calling get_FOVtuft_coincident_peaks.m: (i) the peak detection threshold (k_dfthresh) and (ii) the peak window size (k_window)

B,C) see Fig1 panel J, vary peak detection threshold
E,F) see Fig1 panel J, vary peak window size

Figure 2

D) see Fig1 panel D, between planes

Figure 2 - supplementary 2

B) see Fig1 panel J

Figure 3

B) get the frequency of events using detect_df_peaks.m ; see get_FOVtuft_peaks.m at the start of main_fig1.m
C) see Fig1 panel J, between planes

Figure 3 - supplementary 1

B) see Fig1 panel J
C) get the frequency of events using detect_df_peaks.m ; see get_FOVtuft_peaks.m at the start of main_fig1.m

Figure 4 & Figure 4 supplementary 1

exVivo_Extraction_Analysis.m 
ReadImageJRoi.m (external)

Data available as xlsx tables in folders /Fig4_Data and /Fig4S1_Data

Figure 5

A,B) see Fig1 panel J, between planes; vary condition (stim_action_state)

Figure 5 - supplementary 1 & 2

S1-A,B; S2-A) see Fig1 panel J, between planes; vary condition (stim_action_state)

Figure 6

D,L,M) see Fig1 panel D; select deltaf during specific stimulation (e.g. preferred orientation)