Documents https://bhallalab.github.io/MouseBehaviour

A cmake based C++/Python pipeline to run behavioural experiment.

Protocols

A protocols must be listed in ./Protocols/BehaviourProtocols.csv. You must specify the right protocol code duging configuration. See section How to run the pipeline below.

How to run the pipeline

Both the arduino and the camera should be connected to the computer before starting the session.

Download and setup (done once)

This code will only work on Ubuntu-16.04. Install arduino, c++ compiler (gcc), cmake, and boost libraries.

Script bootstrap.sh will try to install all dependencies. Required libraries for PointGrey camera is in the source.

$ git clone  https://github.com/BhallaLab/MouseBehaviour.git
$ cd MouseBehaviour 
$ sudo -E ./bootstrap.sh  # on first time post login. If it fails, manual configuration is needed.

The script bootstap.sh will try to configure your system. You must have sudo permissions because we need to add to various groups (pgrimaging and dialout) before you can access camera and serial port. In case, something odd happens, raise an issue on github.

Once bootstrap is successful, logout and login. Changes made to your groups comes into effect only after a fresh login. To verify that you are in appropriate groups, type groups command in terminal. Make sure that pgrimaging and dialout appears in the group list. If not, things have not gone properly.

To build and upload to arduino:

$ mkdir _build 
$ cd _build
$ cmake -DANIMAL_NAME=k2 -DSESSION_NUM=1 -DPROTO_CODE=All1 ..
$ make run              # to run the whole setup, (arduino and camera both must be connected)or
$ make miniterm         # Just to test arduino board. (camera need to be connected)

On make run, a windows will appear with camera feed and couple of plots at the bottom.

Send commands to arduino

To send commands to arduino, make sure that you focus on the window first (click on it).

Press CTRL+C in terminal to close the session. To see the arduino output in the console, run make miniterm; and press CTRL+] to come out of miniterm.

CMake options

Port

If you need to change the arduino port, pass -DPORT=/path/to/port option to cmake. On a linux system, e.g.

 $ cmake -DPORT=/dev/ttyACM1 -DANIMAL_NAME=k2 -DSESSION_NUM=1 -DPROTO_CODE=A11 ..

Analysis

Analysis scripts are written in python and requires common numerical computational framework e.g., numpy, scipy, pandas and additionally tifflib.

• sudo apt install python-tifflib

Commands

• Puff : p
• Tone : t
• Led : l
• Start : s
• Shock : c
• Terminate : ctrl+c

What is being printed?

See function write_data_line in file src/main.ino for updated values.

How to analyze data

Go to directory ./analysis and read the README.md file there.

Extracting arduino data from tiff file.

Each tiff file contains one trial. The first row of each frame contains arduino data. You can extract that using the script ./analysis/get_data_line_from_tiff.py file.

To extract data run,

$ python ./analysis/get_data_line_from_tiff.py /path/to/session/trial01.tiff

It will print the csv files onto the terminal and also save it to a dat file in the same folder. A plot file is also generated.