This collection of code is a toolbox that I wrote and adapted for 2P physiology experiments in mice in vivo.
The toolbox contains a collection of tools for data acquisition, preprocessing and analysis of all sorts of data present in a recording, and some code and infos on the software and hardware setup of the experimental setup. In particular:
This subfolder contains the code used to detect, track and analyze the pupil size during the recording
This subfolder contains 3D printable projects to print a monodimensional treadmill for mice. The setup is thought to integrate with a standard thorlabs rigid stand (available here) that can be easily mounted on an optical table and allows flexibility being at the same time standardized lab equipment. The rotational motion is picked up by a rotary encoder that can be attached to the side of the 3Dprinted parts. The folder also contains Arduino code that allows to correctly read the rotary encoder and to output an analog value representing the angular position of the wheel. This code requires a microcontroller capable of true digital-to-analog (DAC) conversion. it has being tested and used successfully on an arduino Zero, but should work also on others boards (e.g., Teensy3.5)
This subfolder contains functions of general utility that I used thoughout the rest of the toolbox
Deprecated pieces of code
No functioning GUIs are used in the toolbox at the moment. This folder contains GUIs that are either in development, deprecated or not useful anymore