behavython 0.6.0

To be used in conjunction with Bonsai-RX to extract behavior from video

To be used in conjunction with Bonsai-RX to extract behavior from video
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Table of Contents

1. About the project
   • Built With
2. Getting Started
   • Prerequisites
   • Installation
3. Usage
4. Contributing
5. License
6. Contact
7. Acknowledgments

About

• This software was developed to be used in conjunction with Bonsai-RX to extract behavior from video. It is a simple interface that allows the user to select the data and image files that were generated by Bonsai and then run the analysis. The results are saved in a csv file that can be used for further analysis.
• The software also implements bindings to the DeepLabCut package, allowwing users to run the analysis using pretrained models on their data.

Built With

• Python
• Qt Designer

Getting Started

Prerequisites

• deeplabcut
• seaborn
• pyside6
• openpyxl
• scikit-image
• pandas
• numpy
• matplotlib
• tk
• scipy

For a simple way to keep up to date with requirements, reference the requirements.txt file

Installation as a pip package

For the installation you need a simple command that you can get by one of two ways:

1. Copying and pasting from here:
   • "pip install behavython" (without quotation[""] marks)
2. Going to the Pypi site and copying from there:
   • PyPi frontpage

At the moment, Behavython was mainly tested on Windows

Usage

• Windows

1. Open the interface typing "behavython" on the command line
   • If you installed it as a pip package you can just type "behavython" on the command line
   • If you downloaded the source code you need to go to the folder where you downloaded it and type "python Bbehavython_front.py" on the command line

2. Select all the photo-data pairs that you want to analyze
   • In this step is important that you don't forget to verify that you got all the bonsai files, including the data and a image of the arena that you are analyzing

3. Wait for the program to finish the analysis
   • Currently the program looks like it freezed when running. It is expected behavior but we are looking into it. Right now you only need to wait a little bit.

4. When finished the progress bar will show 100% and a preview of the results will be available on the right

See the open issues for a full list of proposed features (and known issues).

Contributing

Contributions are what make the open source community such an amazing place to learn, inspire, and create. Any contributions you make are greatly appreciated. If you have a suggestion that would make this better, please fork the repo and create a pull request. You can also simply open an issue explaining what is the problem. Also, you can reach us by mail - listed at the end :)

License

Distributed under the GNU General Public License v3.0. See LICENSE.txt for more information.

Contact

João Pedro Carvalho Moreira - [e-mail]
Matheus Costa - [e-mail]

Acknowledgments

• Flávio Mourão:
  Github: Flávio Mourão Twitter: @F_Mourao_
• Lab:
  Núcleo de Neurociências

Developed at

Nucleo de Neurociencias - NNC
Universidade Federal de Minas Gerais - UFMG
Brazil