This repository is dedicated to processing and analysis regarding two photon imaging of brain activities.
The past two years as my first postdoc project I started building a two photon microscope and virtual reality setup. The setup runs in a close loop so the animal behaviour can be mapped to its brain activity. To extract the neurons activities I ended up using CaImAn package in Matlab. To ease my pain and build a smooth pipeline for my application I build a script that calls CaImAn function in a certian order. The script starts with a popup that ask for user input for essential parameters and then ask for the image file. At the end, after the script finishes it will clean up the unncessary variables and save the rest for the user's reference as a ".mat" file in the same directory.
CaImAn is a great work done by fine group of people. Please cite them and support them. For more details and learn about this package please visit their repository.
I have put together here my script and a striped down verstion of CaImAn with the hope that it might be of any assistance to anyone using CaImAn is a similar application.
Here is a test file for anyone to give it a try. One needs to only open and run "aaa_Extract_Calcium_Traces_04.m" which will promp for user input and the image file.