behavython
To be used in conjunction with Bonsai-RX to extract behavior from video
Science Score: 44.0%
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✓CITATION.cff file
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✓codemeta.json file
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✓.zenodo.json file
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○Scientific vocabulary similarity
Low similarity (16.5%) to scientific vocabulary
Keywords
Repository
To be used in conjunction with Bonsai-RX to extract behavior from video
Basic Info
Statistics
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 11
- Releases: 3
Topics
Metadata Files
README.md
To be used in conjunction with Deeplabcut to extract behavior from video
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About
- This software was developed to be used in conjunction with Deeplabcut to extract behavior from video. It is a interface that allows the user to select the data files that were generated by DLC and then run the analysis, allowwing users to run the analysis using pretrained models on their data. The results are saved in a csv file that can be used for further analysis.
Built With
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:
- Copying and pasting from here:
- "pip install behavython" (without quotation[""] marks)
- Going to the Pypi site and copying from there:
At the moment, Behavython was mainly tested on Windows
<!-- USAGE EXAMPLES -->
Usage
- Windows
- 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
- 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
- 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.
- 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 - mcjpedro@gmail.com
Matheus Costa - matheuscosta3004@gmail.com
Acknowledgments
- Flávio Mourão:
Github: Flávio Mourão - Lab:
Núcleo de Neurociências
Developed at
Nucleo de Neurociencias - NNC
Universidade Federal de Minas Gerais - UFMG
Brazil
Owner
- Name: Matheus C.
- Login: mrdrzit
- Kind: user
- Location: Brazil
- Company: Núcleo de Neurociências - NNC
- Repositories: 5
- Profile: https://github.com/mrdrzit
Learning neuroscience and a pint of signal/image processing along the way. Undergraduate Student at UFMG and member of NNC
Citation (CITATION.cff)
cff-version: 1.2.0
title: Behavyton
message: >-
If you use this software, please cite it using these
metadata.
type: software
authors:
- given-names: Matheus
name-particle: Costa
family-names: Passos
email: matheuscosta@gmail.com
affiliation: Universidade Federal de Minas Gerais
orcid: 'https://orcid.org/0009-0005-8838-9210'
- given-names: João
name-particle: Pedro
family-names: Carvalho Moreira
email: mcjpedro@gmail.com
affiliation: Universidade Federal de Minas Gerais
orcid: 'https://orcid.org/0000-0002-9208-4250'
repository-code: 'https://github.com/mrdrzit/behavython'
abstract: >-
Behavython is an open-source Python-based toolkit designed
for streamlined analysis and processing of behavioral
data, with a particular focus on social behavior and
phenotyping in neuroscience research. Its modular
framework includes tools for video processing, machine
learning-based behavior tracking (such as DeepLabCut
integration), and bout analysis to facilitate rigorous
data management and analysis workflows. Behavython aims to
simplify complex behavioral analysis tasks, offering a
user-friendly GUI and a multi-threaded backend to improve
performance.
keywords:
- Phenotyping
- Machine Learning
- Behavioral analysis
- Neuroscience
license: GPL-3.0
commit: 29b051677ef2e81c882241761557760a5c0a3fa1
version: 0.7.0
date-released: '2024-02-13'
GitHub Events
Total
- Push event: 18
- Create event: 1
Last Year
- Push event: 18
- Create event: 1
Packages
- Total packages: 1
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Total downloads:
- pypi 46 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 6
- Total maintainers: 1
pypi.org: behavython
To be used in conjunction with Bonsai-RX to extract behavior from video
- Homepage: https://github.com/mrdrzit/Behavython
- Documentation: https://behavython.readthedocs.io/
- License: GPL-3.0
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Latest release: 0.6.3
published about 2 years ago