PC Configuration for Experimental Mouse2AFC Bpod Protocol

Written for Poirazi Lab

See HERE for me info on the Bpod

Workspace Enviroment Setup

1. MATLAB 2018a (or newer)
2. Install psychtoolbox library
   • For Windows
     • Go to http://psychtoolbox.org/download#Windows (they have detailed instructions)
     • You download Psychtoolbox installer as written in Psychtoolbox-3; step 2
     • Create a folder “toolbox” under C:\ and extract DownloadPsychtoolbox.m zip folder here (you should end up with C:\toolbox\DownloadPsychtoolbox.m)
     • Download gStreamer as written in Psychtoolbox-3; step 3
     • Download TortoiseSVN from here
     • Run MATLAB as Administrator (you can go to C:\Program Files\MATLAB\R2018a\bin and right click to matlab.exe file
     • In MATLAB command line:

       >> cd('C:\toolbox\')
       >> DownloadPsychtoolbox('C:\toolbox')

       • A folder Psychtoolbox will be created under C:\toolbox\
   • For linux
     • Go to http://psychtoolbox.org/download.html#Linux
     • Their instructions should be enough
3. Install python (Suggested version == 3.7)
   • verify installation before proceeding
4. Install pip (https://phoenixnap.com/kb/install-pip-windows) (steps 1-3)
5. Copy and paste in command prompt to install the necesary libraries:

pip install numpy scipy matplotlib pandas scikit-learn statsmodels colour click

6. If you'll do random dots experiments, then you'll need Psychopy as well

pip install Psychopy

8. Download/unzip the Bpod software (from wetlab drive: software/Bpod_Gen2_live.zip) under C:

9. Download/unzip the Bpod protocols/files (from wetlab drive: software/BpodUser) under C:

   • Replace the files in BpodUser/Protocols/Mouse2AFC with the files from this repo
   • This repo will have a more up to date version than the one in the C: drive
   • As of writing this the most up to date version is named Mouse2AFC_2023_01_13

10. Install Arduino software for your OS

MATLAB Configuration

Then open MATLAB → go to SetPath (in the environment panel)→

1. Import all files from Bpod_Gen2_live: click to add with subfolders and chose the Bpod_Gen2_live folder and SAVE
2. Import all files from toolbox (Psychtoolbox): click to add with subfolders and chose the Psychtoolbox folder and SAVE - NOTE: Move the folder C:\toolbox\Psychtoolbox\PsychBasic\MatlabWindowsFilesR2007a\ before (up) the folder C:\toolbox\Psychtoolbox\PsychBasic\ and SAVE.
3. Import all files from BpodUser/Protocols/Mouse2AFC/Definitions folder and SAVE
   • As state previously, right now Mouse2AFC is named Mouse2AFC_2023_01_13
4. Import all files from BpodUser/Settings_Bpod2 folder and SAVE
5. import all files from the MATLAB folder in this repo and SAVE

Arduino Congifuration

Open Arduino software and

1. Connect Arduino to PC using the programming port (not native port)
   • Use the programming port to upload to the arduino and native port when running Bpod
2. Go to tools --> board --> board manager and search arduino due
3. Select Arduino Sam Boards(32-bits ARM Cortex-M3) and install the package
4. Upload the files found here to the arduino

Run Bpod in Matlab

1. Connect arduino to PC using the native port

2. Open MATLAB

3. Open arduino software

4. In tools, under Boards select the Native Port and under Port select the port (i.e. 'COM4' for Windows)

5. In MATLAB command line:

Bpod('COM4')

To start Bpod

Required Changes For Linux Users

1. Mouse2AFC: Line 63

createMMFile('c:\Bpoduser\', 'mmap_matlab_randomdot.dat', file_size);

Change c:\Bpoduser\ to reflect your system path to mmap_matlab_randomdot.dat

2. BpodObject: Line 116

 obj.Path.LocalDir = 'C:\BpodUser'; %fullfile(obj.Path.ParentDir, 'BpodUser');

Delete `C:\BpodUser' and uncomment the rest of the line

These instructions are a revised version of the ones found here: HenryJFlynn/mouse2afc#5

For any problems, first see HenryJFlynn/mouse2afc#2