For code related to running experiments, see https://github.com/murthylab/leap_rigs
This repository contains a notebook and the measurements required to create stimulus files for opto experiments in the leap rigs.
The goal of this repo is to make creating stimulus files easy and seamless, and to have a place to store the calibration data.
The document LEAP_Rig_Opto.pdf contains information about the setup of the opto, the measurements taken, along with a protocol to use for running experiments on the leap rigs with optogenetics.
The notebook called create_opto_stim.ipynb contains a function asking what power level you would like to use for experiments. It returns the voltage required to produce that power density for each specific rig. This is calculated by finding a line of best fit from measured datapoints
You can then create a stimulus file in the notebook or you can pass this voltage output in matlab and create the actual stimulus like this:
% matlab stimulus creation code:
voltage = 1.23456;
fs = 10000; % daq samplerate
stimLength = 5; % seconds
daqStimLength = fs * stimLength;
stim = [ones(daqStimLength,1)*voltage; zeros(10000, 1)];
save('opto_stims/example_stim.mat', 'stim');
REMEMBER: you need to save an rig specific .mat file onto each computer in "C:\code\leap_rigs\opto_stims"
If you have any feedback or questions please let me know! -Kyle