Skip to content

add about.md for CV Zebrafish project #207

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
wants to merge 2 commits into
base: main
Choose a base branch
from
Open
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
51 changes: 51 additions & 0 deletions docs/projects/cv_zebrafish/README.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,51 @@
# CV Zebrafish

## Overview

The CV Zebrafish project aims to develop an interactive, user-friendly software tool to track and analyze zebrafish body parts and movements from high-resolution, high-speed imaging data. It will integrate with machine learning outputs like DeepLabCut to process large datasets and generate detailed metrics, including speed, fin angles, movement timing, phase synchronization, and behavior classification. The modular design will make it adaptable for researchers at SLU and beyond, supporting diverse movement analysis and visualization needs in aquatic behavioral studies

The project is part of the [Saint Louis University Open Source Software (OSS)](https://github.com/oss-slu) initiative and is being developed in collaboration with Mohini Sengupta, Ph.D.

---

## Features

<!-- - **Automated Zebrafish Tracking** – Detect and track single or multiple zebrafish in video recordings.
- **Behavioral Analysis** – Extract metrics such as swimming speed, direction changes, and grouping behavior.
- **Multi-Fish Support** – Accurate tracking even in group settings.
- **Data Visualization** – Generate plots and charts for movement patterns.
- **Exportable Results** – Save analysis outputs in CSV/JSON formats for further research.
- **Modular Design** – Extend functionality with custom behavioral metrics or machine learning models. -->

---

## Tech Stack

- **Programming Language:** Python
- **Core Libraries:** OpenCV, NumPy, Pandas, Matplotlib
- **Machine Learning Frameworks:** PyTorch / TensorFlow (planned)
- **Web Interface (optional):** Flask / React
- **Version Control:** Git & GitHub

---

## Getting Started

### Prerequisites
- Python 3.9+
- pip package manager
- Git

### Installation
```bash
# Clone the repository
git clone https://github.com/oss-slu/cv_zebrafish.git
cd cv_zebrafish

# Create a virtual environment (optional but recommended)
python -m venv venv
source venv/bin/activate # Linux/Mac
venv\Scripts\activate # Windows

# Install dependencies
pip install -r requirements.txt
63 changes: 63 additions & 0 deletions docs/projects/cv_zebrafish/about.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,63 @@
---
id: about
title: CV Zebrafish
custom_edit_url: null
---

<!-- Optional header image -->
<!-- ![Header Alt Text](header.png) -->

## Overview

The CV Zebrafish project aims to develop an interactive, user-friendly software tool to track and analyze zebrafish body parts and movements from high-resolution, high-speed imaging data. It will integrate with machine learning outputs like DeepLabCut to process large datasets and generate detailed metrics, including speed, fin angles, movement timing, phase synchronization, and behavior classification. The modular design will make it adaptable for researchers at SLU and beyond, supporting diverse movement analysis and visualization needs in aquatic behavioral studies.

### Information

- **Source Code:** [https://github.com/oss-slu/cv_zebrafish](https://github.com/oss-slu/cv_zebrafish) [<img src="/img/git-alt.svg" alt="git" width="25" height="25" />](https://github.com/oss-slu/cv_zebrafish)
- **Client:** Mohini Sengupta, Ph.D.
- **Current Tech Lead:** Shahid Malik [<img src="/img/github.svg" alt="github" width="25" height="25" />](https://github.com/Shahid1Malik)
- **Developers:**
- [Developer 1 Name] [<img src="/img/github.svg" alt="github" width="25" height="25" />](https://github.com/USERNAME) [<img src="/img/linkedin.svg" alt="linkedin" width="25" height="25" />](https://www.linkedin.com/in/USERNAME/)
Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I like that you're thinking ahead. Let's comment these out until we have team members identified on/around August 25.

- [Developer 2 Name] [<img src="/img/github.svg" alt="github" width="25" height="25" />](https://github.com/USERNAME) [<img src="/img/linkedin.svg" alt="linkedin" width="25" height="25" />](https://www.linkedin.com/in/USERNAME/)
- **Start Date:** Aug, 2025
Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

You can put August 11 here. That's when you stared working on it.

- **Technologies Used:**
- Python (OpenCV, NumPy, Pandas)
- Flask / React (for web interface, if applicable)
- Machine Learning frameworks (e.g., PyTorch or TensorFlow)
- **Type:** Computer Vision Application
- **License:** MIT (https://opensource.org/license/mit)

## Technical Information

### Development Priorities

#### Zebrafish Tracking and Analysis

<!-- - **From Manual Observation to Automated Analysis:** The current zebrafish tracking process often involves manual observation or semi-automated tools. This project will replace these with a fully automated, computer vision–driven system.

- **Features of the Planned CV Zebrafish Tool:**
Includes motion tracking, behavioral pattern recognition, and data visualization to help researchers quantify zebrafish activity.

Key planned features include: -->

<!-- - **Automated Tracking:**
Detect and track individual zebrafish in video recordings with high accuracy.

- **Behavior Analysis:**
Identify and log patterns such as swimming speed, direction changes, grouping behavior, and inactivity.

- **Data Visualization & Export:**
Provide visual plots and allow exporting metrics for further statistical analysis.

- **Multi-Fish Support:**
Handle scenarios with multiple zebrafish in the same tank without losing tracking accuracy.

- **User-Friendly Interface:**
Clean, intuitive controls for loading videos, starting analysis, and reviewing results.

- **Adaptable for Research Needs:**
Modular design to allow additional behavioral metrics or machine learning models. -->

## Get Involved

If you would like to contribute to this project, please visit our [GitHub page](https://github.com/oss-slu/cv_zebrafish) to create issues or pull requests.