In vivo Ephys: Analysis Protocol

To plot the waveforms from one electrode of interest in the raw data (ex, Fig. 1c), run the Matlab code

plotRawTraces(electrode)
``` on the raw continuous data.

To analyze the sorted templates extracted from Spyking Circus,

Use the custom matlab code.

plotSpikes(chWithCell)

chWithCell = array of the electrode which has a cell for each template (ex [5 15 3]).

Calculates and plots spike amplitude, cumulative spikes, and firing rate in Hz for all the templates saved.

From the resulting Templates_data structure, save each row as an individual dat variable.

i.e., for ch 15 in the above example:

load Templates_data;
dat = Templates_data(2, :); %row 2 is channel 15 data
save(‘mouse_date_ch15_data’, ‘dat’);

Copy multiple channels into one folder for grouped analysis, and run

spikingAcrossCells
``` in this folder.

Referencing the control and experimental

allCells
``` data structures created from 

spikingAcrossCells

plotFeaturesAcrossTime

Use the features in the

allCells
``` data structure:

Calculate delta norm as (post-pre)/(post+pre) for each feature for each cell.

Input ddHTP values as

y1
``` and +HTP values as 

y2

TwoGroupsMeanDiff

Use GraphPad Prism to generate the plots in Ext. Fig 2d and h-l from the delta norm features.