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hsombehaviorsuite

Contains behavioral control files for use with MATLAB 2021B+ and Arduino

https://github.com/harvardschoolofmouse/hsombehaviorsuite

Science Score: 57.0%

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    Low similarity (10.1%) to scientific vocabulary
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Repository

Contains behavioral control files for use with MATLAB 2021B+ and Arduino

Basic Info
  • Host: GitHub
  • Owner: harvardschoolofmouse
  • License: mit
  • Language: MATLAB
  • Default Branch: master
  • Homepage:
  • Size: 270 KB
Statistics
  • Stars: 1
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 1
Created almost 6 years ago · Last pushed over 2 years ago
Metadata Files
Readme License Citation

README.md

HSOMbehaviorSuite v2.0 (9-23-23 release)

The Harvard School of Mouse Behavioral Control Suite

As used in Hamilos et al., eLife, 2021 (https://doi.org/10.7554/eLife.62583) and Hamilos and Assad, 2020 (https://doi.org/10.1101/2020.06.03.128272)

Contains behavioral control files for use with MATLAB 2021B+ and Arduino

The Harvard School of Mouse (HSOM) Behavioral Control Suite consists of an Arduino State System controller and MATLAB serial interface for setting parameters and collecting/viewing behavioral events on-line.

Authors:

Matlab Serial Interface: Ofer Mazor

Original Arduino State System Backbone: Lingfeng Hou

Matlab HSOM GUI Interface: Lingfeng Hou and Allison Hamilos

Harvard School of Mouse Arduino Controllers: Allison Hamilos

Last updated by Allison Hamilos on September 27, 2023. Please contact ahamilos{at}wi.mit.edu if you have questions or encounter issues.

New to version 2.0

  • Added TaskScheduler to run automated paramter changes (adapted from original version by Lingfeng Hou)
  • Fixed bugs in histogram function
  • Improved look and feel of plotting functions (e.g., now using makeStandardFigure and prettyHxg)
  • Default plot parameters can now be saved as DefaultPlotParams.mat to the folder with MouseBehaviorInterface

Equipment Needed

  • MATLAB2021B+
  • Arduino 1.8.12+ NB: If using Teensy controllers, you will also need to install Teensy add ons to Arduino from PRJC: https://www.pjrc.com/teensy/
  • 2 Arduino controllers (We use Teensy 3.2 or 3.6)
    • One controller is for behavior, the other is for optogenetics
  • LEDs and speakers

Toolboxes

  • Instrument Control Toolbox
  • Statistics and Machine Learning Toolbox

Instructions

  1. Clone or download the repo. Add the folders to your MATLAB 2021B+ path.
  2. You will need to configure each Arduino to match the pinouts annotated in the .ino files
  3. Upload the PhotometryandOptogeneticsController2019.ino Arduino file to the Behavior Controller Arduino
  4. Upload the Optogenetics_Controller4.ino Arduino file to the Optogenetics Controller Adruino
  5. Open MATLAB2021B+ and run MouseBehaviorInterface
    • Select the COM port for the Behavior Controller Arduino
      • You can now edit parameters of the behavior controller, start and save files, and track behavior with the plotting window
  6. For best results, open a new instance of Matlab to run the Optogenetics Controller, run: OptogeneticsController
    • Select the COM port of the Optogenetics Controller Arduino
      • You can now set stimulation parameters

Owner

  • Name: Allison E Hamilos
  • Login: harvardschoolofmouse
  • Kind: user
  • Location: Boston, MA
  • Company: Harvard Medical School

MD-PhD Neuroscientist | Harvard-MIT Program in Health Science and Technology

Citation (citation.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Hamilos"
  given-names: "Allison Elizabeth"
  orcid: "https://orcid.org/0000-0001-9486-0017"
- family-names: "Hou"
  given-names: "Lingfeng"
- family-names: "Mazor"
  given-names: "Ofer"
title: "The Harvard School of Mouse Behavioral Control Suite"
version: 2.0.0
date-released: 2023-09-23
url: "https://github.com/harvardschoolofmouse/HSOMbehaviorSuite"

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