# CoralNet-Toolbox 🪸🧰
<div align="center">
<p>
<img src="https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/CoralNet_Toolbox.png" alt="CoralNet-Toolbox" width="400">
</p>
<h3>🌊 <em>Empowering Coral Reef Research with AI-Powered Annotation Tools</em> 🌊</h3>
<p><strong>An unofficial toolkit to supercharge your <a href="https://coralnet.ucsd.edu/">CoralNet</a> workflows with cutting-edge computer vision</strong></p>
</div>
---
## 📊 Project Stats
<div align="center">
[](https://pypi.org/project/CoralNet-Toolbox)
[](https://pypi.python.org/pypi/CoralNet-Toolbox)
[](https://pepy.tech/project/coralnet-toolbox)
[](https://pypi.org/project/CoralNet-Toolbox)
[](https://pypi.org/project/CoralNet-Toolbox)
[](https://pypi.org/project/CoralNet-Toolbox)
[](https://pypi.org/project/CoralNet-Toolbox)
</div>
---
## ✨ Why CoralNet-Toolbox?
<div align="center">
| 🎯 **Smart Annotation** | 🤖 **AI-Powered** | 🚀 **Complete Pipeline** |
|:---:|:---:|:---:|
| Create patches, rectangles, and polygons with intelligent assistance | Leverage SAM, YOLO, and foundation models | From data collection to deployment |
| *Precision meets efficiency* | *Cutting-edge AI at your fingertips* | *End-to-end workflow automation* |
</div>
---
## ⚡ Quick Start
Get up and running in seconds:
```bash
# 💻 Installation
pip install coralnet-toolbox
# 🚀 Launch
coralnet-toolbox
```
> **🎉 That's it!** The toolbox will open and you're ready to start annotating!
For a complete installation guide (including CUDA setup), see the [Installation Documentation](https://jordan-pierce.github.io/CoralNet-Toolbox/installation).
---
## 📚 Documentation Hub
<div align="center">
| 📖 Guide | 🎯 Purpose | 🔗 Link |
|:---:|:---:|:---:|
| **Overview** | Get the big picture | [📋 Read More](https://jordan-pierce.github.io/CoralNet-Toolbox/overview) |
| **Installation** | Detailed setup instructions | [⚙️ Setup Guide](https://jordan-pierce.github.io/CoralNet-Toolbox/installation) |
| **Usage** | Learn the tools | [🛠️ User Manual](https://jordan-pierce.github.io/CoralNet-Toolbox/usage) |
| **Hot Keys** | Keyboard shortcuts | [⌨️ Shortcuts](https://jordan-pierce.github.io/CoralNet-Toolbox/hot-keys) |
| **Classification** | Community tutorial | [🧠 AI Tutorial](https://jordan-pierce.github.io/CoralNet-Toolbox/classify) |
</div>
---
## 🎥 Video Demonstrations
<details open>
<summary><h3>📺 <strong>Watch the Complete Tutorial Series</strong></h3></summary>
<div align="center">
<a href="https://youtube.com/playlist?list=PLG5z9IbwhS5NQT3B2jrg3hxQgilDeZak9&feature=shared">
<img src="https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/toolbox_qt.PNG" alt="Video Tutorial Series" width="80%" style="border-radius: 10px; box-shadow: 0 4px 8px rgba(0,0,0,0.1);">
</a>
<p><strong>🎬 Complete playlist covering all major features and workflows</strong></p>
</div>
</details>
---
## 🤖 AI Model Arsenal
The toolbox integrates state-of-the-art models for efficient annotation workflows:
<div align="center">
### 🏋️ **Trainable Models**
| **YOLO Family** | **Versions Available** |
|:---:|:---:|
| 🦾 **Legacy** | YOLOv3 • YOLOv4 • YOLOv5 |
| 🚀 **Modern** | YOLOv6 • YOLOv7 • YOLOv8 |
| ⚡ **Latest** | YOLOv9 • YOLOv10 • YOLO11 • YOLO12 |
*Powered by the [Ultralytics](https://ultralytics.com/) ecosystem*
</div>
<div align="center">
### 🎯 **Segment Anything Models**
| **Model** | **Specialty** | **Use Case** |
|:---:|:---:|:---:|
| 🪸 **SAM** | General segmentation | High-quality masks |
| 🌊 **CoralSCOP** | Coral-specific | Marine biology focus |
| ⚡ **FastSAM** | Speed optimized | Real-time annotation |
| 📱 **MobileSAM** | Mobile-friendly | Edge deployment |
| ✂️ **EdgeSAM** | Efficient | Resource-constrained |
| 🔍 **RepViT-SAM** | Vision transformers | Advanced features |
*Powered by our [xSAM](https://Github.com/Jordan-Pierce/xSAM) integration*
</div>
<div align="center">
### 👁️ **Visual Prompting & Foundation Models**
| **Framework** | **Models** | **Capability** |
|:---:|:---:|:---:|
| **YOLOE** | See Anything | Visual prompt detection |
| **Transformers** | Grounding DINO • OWLViT • OmDetTurbo | Zero-shot detection |
</div>
---
## 🛠️ Feature Showcase
<div align="center">
### 📝 **Core Annotation Tools**
| <img src="https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/tools/Patches.gif" alt="Patch Annotation" width="250" style="border-radius: 8px;"/><br>**🎯 Patch Annotation** | <img src="https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/tools/Rectangles.gif" alt="Rectangle Annotation" width="250" style="border-radius: 8px;"/><br>**📐 Rectangle Annotation** | <img src="https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/tools/Polygons.gif" alt="Polygon Annotation" width="250" style="border-radius: 8px;"/><br>**🔷 Multi-Polygon Annotation** |
|:---:|:---:|:---:|
### 🤖 **AI-Powered Analysis**
| <img src="https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/tools/Classification.gif" alt="Classification" width="250" style="border-radius: 8px;"/><br>**🧠 Image Classification** | <img src="https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/tools/Object_Detection.gif" alt="Object Detection" width="250" style="border-radius: 8px;"/><br>**🎯 Object Detection** | <img src="https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/tools/Instance_Segmentation.gif" alt="Instance Segmentation" width="250" style="border-radius: 8px;"/><br>**🎭 Instance Segmentation** |
|:---:|:---:|:---:|
### 🔬 **Advanced Capabilities**
| <img src="https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/tools/Segment_Anything.gif" alt="SAM" width="250" style="border-radius: 8px;"/><br>**🪸 Segment Anything (SAM)** | <img src="https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/tools/Classifying_Polygons.gif" alt="Polygon Classification" width="250" style="border-radius: 8px;"/><br>**🔍 Polygon Classification** | <img src="https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/tools/Work_Areas.gif" alt="Work Areas" width="250" style="border-radius: 8px;"/><br>**📍 Region-based Detection** |
|:---:|:---:|:---:|
### ✂️ **Editing & Processing Tools**
| <img src="https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/tools/Cut.gif" alt="Cut Tool" width="250" style="border-radius: 8px;"/><br>**✂️ Cut** | <img src="https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/tools/Combine.gif" alt="Combine Tool" width="250" style="border-radius: 8px;"/><br>**🔗 Combine** | <img src="https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/tools/Simplify.gif" alt="Simplify Tool" width="250" style="border-radius: 8px;"/><br>**🎨 Simplify** |
|:---:|:---:|:---:|
### 🌟 **Specialized Features**
| <img src="https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/tools/See_Anything.gif" alt="YOLOE" width="400" style="border-radius: 8px;"/><br>**👁️ See Anything (YOLOE)** | <img src="https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/tools/Classifying_Orthomosaics.gif" alt="LAI Classification" width="400" style="border-radius: 8px;"/><br>**🗺️ LAI Classification** |
|:---:|:---:|
### 📊 **Analysis & Exploration**
| <img src="https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/tools/Analytics.gif" alt="Video Analysis" width="400" style="border-radius: 8px;"/><br>**🎬 Video Inference & Analytics** | <img src="https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/tools/Explorer.gif" alt="Data Explorer" width="400" style="border-radius: 8px;"/><br>**🔍 Data Explorer & Clustering** |
|:---:|:---:|
</div>
---
## 🔧 Complete Workflow Pipeline
### 📥 **Data Input**
- **🔥 CoralNet Download**: Retrieve source data and annotations
- **🎬 Video Processing**: Extract frames from video files
- **📸 Image Import**: Support for various image formats
### ✏️ **Annotation & Labeling**
- **👆 Manual Annotation**: Intuitive point, rectangle, and polygon tools
- **🤖 AI-Assisted**: SAM, YOLO, and visual prompting models
- **📐 Precision Editing**: Cut, combine, subtract, and simplify shapes
### 🧠 **Machine Learning**
- **🔬 Hyperparameter Tuning**: Optimize training conditions
- **🚀 Model Training**: Build custom classifiers and detectors
- **⚡ Model Optimization**: Production-ready deployment
### 📊 **Analysis & Export**
- **📈 Performance Evaluation**: Comprehensive model metrics
- **🎯 Batch Inference**: Process multiple images automatically
- **🎥 Video Analysis**: Real-time processing with analytics
- **📋 Multi-format Export**: CoralNet, Viscore, TagLab, GeoJSON
---
## 📋 Roadmap
*See the current tickets and planned features on the [GitHub Issues Page](https://github.com/Jordan-Pierce/CoralNet-Toolbox/issues)*
---
## 💻 Installation Guide
### 🐍 **Step 1: Environment Setup**
```bash
# Create a dedicated environment (recommended)
conda create --name coralnet10 python=3.10 -y
conda activate coralnet10
```
### ⚡ **Step 2: Fast Installation with UV**
```bash
# Install UV for faster package management
pip install uv
# Install CoralNet-Toolbox
uv pip install coralnet-toolbox
```
> **Fallback**: If UV fails, use regular pip: `pip install coralnet-toolbox`
### 🚀 **Step 3: GPU Acceleration (Optional)**
For CUDA-enabled systems:
```bash
# Example for CUDA 12.9
# Install PyTorch with CUDA support
uv pip install torch torchvision --index-url https://download.pytorch.org/whl/cu129 --upgrade
```
### 🏃♂️ **Step 4: Launch**
```bash
coralnet-toolbox
```
### 🎯 **GPU Status Indicators**
- **🐢** CPU only
- **🐇** Single GPU
- **🚀** Multiple GPUs
- **🍎** Mac Metal (Apple Silicon)
*Click the icon in the bottom-left to see available devices*
### 🔄 **Upgrading**
```bash
# When updates are available
uv pip install -U coralnet-toolbox==[latest_version]
```
---
### 🏗️ **Repository Structure**
<div align="center">
<a href="https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/diagram.svg">
<img src="https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/diagram.svg" alt="Visualization of the codebase" width="80%">
</a>
</div>
---
## 🌊 Success Stories
> **Using CoralNet-Toolbox in your research?**
>
> We'd love to feature your work! Share your success stories to help others learn and get inspired.
---
## 🌍 About CoralNet
<div align="center">
<p><em>🪸 Protecting our oceans, one annotation at a time 🪸</em></p>
</div>
Coral reefs are among Earth's most biodiverse ecosystems, supporting marine life and coastal communities worldwide. However, they face unprecedented threats from climate change, pollution, and human activities.
**[CoralNet](https://coralnet.ucsd.edu/)** is a revolutionary platform enabling researchers to:
- Upload and analyze coral reef photographs
- Create detailed species annotations
- Build AI-powered classification models
- Collaborate with the global research community
The **CoralNet-Toolbox** extends this mission by providing advanced AI tools that accelerate research and improve annotation quality.
---
## 📄 Citation
If you use CoralNet-Toolbox in your research, please cite:
```bibtex
@misc{CoralNet-Toolbox,
author = {Pierce, Jordan and Battista, Tim},
title = {CoralNet-Toolbox: AI-Powered Tools for Coral Reef Research},
year = {2025},
howpublished = {\url{https://github.com/Jordan-Pierce/CoralNet-Toolbox}},
note = {GitHub repository}
}
```
---
## ⚖️ Legal & Licensing
<div align="center">
### ⚠️ **Disclaimer**
*This is a scientific product and not official communication of NOAA or the US Department of Commerce. All code is provided 'as is' - users assume responsibility for its use.*
### 📋 **License**
*Software created by US Government employees is not subject to copyright in the United States (17 U.S.C. §105). The Department of Commerce reserves rights to seek copyright protection in other countries.*
</div>
---
<div align="center">
<p><strong>🌊 Built with ❤️ for coral reef conservation 🌊</strong></p>
<p><em>Empowering researchers • Protecting ecosystems • Advancing science</em></p>
</div>
Raw data
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"description": "# CoralNet-Toolbox \ud83e\udeb8\ud83e\uddf0\n\n<div align=\"center\">\n <p>\n <img src=\"https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/CoralNet_Toolbox.png\" alt=\"CoralNet-Toolbox\" width=\"400\">\n </p>\n \n <h3>\ud83c\udf0a <em>Empowering Coral Reef Research with AI-Powered Annotation Tools</em> \ud83c\udf0a</h3>\n \n <p><strong>An unofficial toolkit to supercharge your <a href=\"https://coralnet.ucsd.edu/\">CoralNet</a> workflows with cutting-edge computer vision</strong></p>\n</div>\n\n---\n\n## \ud83d\udcca Project Stats\n\n<div align=\"center\">\n\n[](https://pypi.org/project/CoralNet-Toolbox)\n[](https://pypi.python.org/pypi/CoralNet-Toolbox)\n[](https://pepy.tech/project/coralnet-toolbox)\n\n[](https://pypi.org/project/CoralNet-Toolbox)\n[](https://pypi.org/project/CoralNet-Toolbox)\n[](https://pypi.org/project/CoralNet-Toolbox)\n[](https://pypi.org/project/CoralNet-Toolbox)\n\n</div>\n\n---\n\n## \u2728 Why CoralNet-Toolbox?\n\n<div align=\"center\">\n \n| \ud83c\udfaf **Smart Annotation** | \ud83e\udd16 **AI-Powered** | \ud83d\ude80 **Complete Pipeline** |\n|:---:|:---:|:---:|\n| Create patches, rectangles, and polygons with intelligent assistance | Leverage SAM, YOLO, and foundation models | From data collection to deployment |\n| *Precision meets efficiency* | *Cutting-edge AI at your fingertips* | *End-to-end workflow automation* |\n\n</div>\n\n---\n\n## \u26a1 Quick Start\n\nGet up and running in seconds:\n\n```bash\n# \ud83d\udcbb Installation\npip install coralnet-toolbox\n\n# \ud83d\ude80 Launch\ncoralnet-toolbox\n```\n\n> **\ud83c\udf89 That's it!** The toolbox will open and you're ready to start annotating! \n\nFor a complete installation guide (including CUDA setup), see the [Installation Documentation](https://jordan-pierce.github.io/CoralNet-Toolbox/installation).\n\n---\n\n## \ud83d\udcda Documentation Hub\n\n<div align=\"center\">\n\n| \ud83d\udcd6 Guide | \ud83c\udfaf Purpose | \ud83d\udd17 Link |\n|:---:|:---:|:---:|\n| **Overview** | Get the big picture | [\ud83d\udccb Read More](https://jordan-pierce.github.io/CoralNet-Toolbox/overview) |\n| **Installation** | Detailed setup instructions | [\u2699\ufe0f Setup Guide](https://jordan-pierce.github.io/CoralNet-Toolbox/installation) |\n| **Usage** | Learn the tools | [\ud83d\udee0\ufe0f User Manual](https://jordan-pierce.github.io/CoralNet-Toolbox/usage) |\n| **Hot Keys** | Keyboard shortcuts | [\u2328\ufe0f Shortcuts](https://jordan-pierce.github.io/CoralNet-Toolbox/hot-keys) |\n| **Classification** | Community tutorial | [\ud83e\udde0 AI Tutorial](https://jordan-pierce.github.io/CoralNet-Toolbox/classify) |\n\n</div>\n\n---\n\n## \ud83c\udfa5 Video Demonstrations\n\n<details open>\n<summary><h3>\ud83d\udcfa <strong>Watch the Complete Tutorial Series</strong></h3></summary>\n\n<div align=\"center\">\n <a href=\"https://youtube.com/playlist?list=PLG5z9IbwhS5NQT3B2jrg3hxQgilDeZak9&feature=shared\">\n <img src=\"https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/toolbox_qt.PNG\" alt=\"Video Tutorial Series\" width=\"80%\" style=\"border-radius: 10px; box-shadow: 0 4px 8px rgba(0,0,0,0.1);\">\n </a>\n \n <p><strong>\ud83c\udfac Complete playlist covering all major features and workflows</strong></p>\n</div>\n\n</details>\n\n---\n\n## \ud83e\udd16 AI Model Arsenal\n\nThe toolbox integrates state-of-the-art models for efficient annotation workflows:\n\n<div align=\"center\">\n\n### \ud83c\udfcb\ufe0f **Trainable Models**\n\n| **YOLO Family** | **Versions Available** |\n|:---:|:---:|\n| \ud83e\uddbe **Legacy** | YOLOv3 \u2022 YOLOv4 \u2022 YOLOv5 |\n| \ud83d\ude80 **Modern** | YOLOv6 \u2022 YOLOv7 \u2022 YOLOv8 |\n| \u26a1 **Latest** | YOLOv9 \u2022 YOLOv10 \u2022 YOLO11 \u2022 YOLO12 |\n\n*Powered by the [Ultralytics](https://ultralytics.com/) ecosystem*\n\n</div>\n\n<div align=\"center\">\n\n### \ud83c\udfaf **Segment Anything Models**\n\n| **Model** | **Specialty** | **Use Case** |\n|:---:|:---:|:---:|\n| \ud83e\udeb8 **SAM** | General segmentation | High-quality masks |\n| \ud83c\udf0a **CoralSCOP** | Coral-specific | Marine biology focus |\n| \u26a1 **FastSAM** | Speed optimized | Real-time annotation |\n| \ud83d\udcf1 **MobileSAM** | Mobile-friendly | Edge deployment |\n| \u2702\ufe0f **EdgeSAM** | Efficient | Resource-constrained |\n| \ud83d\udd0d **RepViT-SAM** | Vision transformers | Advanced features |\n\n*Powered by our [xSAM](https://Github.com/Jordan-Pierce/xSAM) integration*\n\n</div>\n\n<div align=\"center\">\n\n### \ud83d\udc41\ufe0f **Visual Prompting & Foundation Models**\n\n| **Framework** | **Models** | **Capability** |\n|:---:|:---:|:---:|\n| **YOLOE** | See Anything | Visual prompt detection |\n| **Transformers** | Grounding DINO \u2022 OWLViT \u2022 OmDetTurbo | Zero-shot detection |\n\n</div>\n\n---\n\n## \ud83d\udee0\ufe0f Feature Showcase\n\n<div align=\"center\">\n\n### \ud83d\udcdd **Core Annotation Tools**\n\n| <img src=\"https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/tools/Patches.gif\" alt=\"Patch Annotation\" width=\"250\" style=\"border-radius: 8px;\"/><br>**\ud83c\udfaf Patch Annotation** | <img src=\"https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/tools/Rectangles.gif\" alt=\"Rectangle Annotation\" width=\"250\" style=\"border-radius: 8px;\"/><br>**\ud83d\udcd0 Rectangle Annotation** | <img src=\"https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/tools/Polygons.gif\" alt=\"Polygon Annotation\" width=\"250\" style=\"border-radius: 8px;\"/><br>**\ud83d\udd37 Multi-Polygon Annotation** |\n|:---:|:---:|:---:|\n\n### \ud83e\udd16 **AI-Powered Analysis**\n\n| <img src=\"https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/tools/Classification.gif\" alt=\"Classification\" width=\"250\" style=\"border-radius: 8px;\"/><br>**\ud83e\udde0 Image Classification** | <img src=\"https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/tools/Object_Detection.gif\" alt=\"Object Detection\" width=\"250\" style=\"border-radius: 8px;\"/><br>**\ud83c\udfaf Object Detection** | <img src=\"https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/tools/Instance_Segmentation.gif\" alt=\"Instance Segmentation\" width=\"250\" style=\"border-radius: 8px;\"/><br>**\ud83c\udfad Instance Segmentation** |\n|:---:|:---:|:---:|\n\n### \ud83d\udd2c **Advanced Capabilities**\n\n| <img src=\"https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/tools/Segment_Anything.gif\" alt=\"SAM\" width=\"250\" style=\"border-radius: 8px;\"/><br>**\ud83e\udeb8 Segment Anything (SAM)** | <img src=\"https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/tools/Classifying_Polygons.gif\" alt=\"Polygon Classification\" width=\"250\" style=\"border-radius: 8px;\"/><br>**\ud83d\udd0d Polygon Classification** | <img src=\"https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/tools/Work_Areas.gif\" alt=\"Work Areas\" width=\"250\" style=\"border-radius: 8px;\"/><br>**\ud83d\udccd Region-based Detection** |\n|:---:|:---:|:---:|\n\n### \u2702\ufe0f **Editing & Processing Tools**\n\n| <img src=\"https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/tools/Cut.gif\" alt=\"Cut Tool\" width=\"250\" style=\"border-radius: 8px;\"/><br>**\u2702\ufe0f Cut** | <img src=\"https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/tools/Combine.gif\" alt=\"Combine Tool\" width=\"250\" style=\"border-radius: 8px;\"/><br>**\ud83d\udd17 Combine** | <img src=\"https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/tools/Simplify.gif\" alt=\"Simplify Tool\" width=\"250\" style=\"border-radius: 8px;\"/><br>**\ud83c\udfa8 Simplify** |\n|:---:|:---:|:---:|\n\n### \ud83c\udf1f **Specialized Features**\n\n| <img src=\"https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/tools/See_Anything.gif\" alt=\"YOLOE\" width=\"400\" style=\"border-radius: 8px;\"/><br>**\ud83d\udc41\ufe0f See Anything (YOLOE)** | <img src=\"https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/tools/Classifying_Orthomosaics.gif\" alt=\"LAI Classification\" width=\"400\" style=\"border-radius: 8px;\"/><br>**\ud83d\uddfa\ufe0f LAI Classification** |\n|:---:|:---:|\n\n### \ud83d\udcca **Analysis & Exploration**\n\n| <img src=\"https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/tools/Analytics.gif\" alt=\"Video Analysis\" width=\"400\" style=\"border-radius: 8px;\"/><br>**\ud83c\udfac Video Inference & Analytics** | <img src=\"https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/tools/Explorer.gif\" alt=\"Data Explorer\" width=\"400\" style=\"border-radius: 8px;\"/><br>**\ud83d\udd0d Data Explorer & Clustering** |\n|:---:|:---:|\n\n</div>\n\n---\n\n## \ud83d\udd27 Complete Workflow Pipeline\n\n### \ud83d\udce5 **Data Input**\n- **\ud83d\udd25 CoralNet Download**: Retrieve source data and annotations\n- **\ud83c\udfac Video Processing**: Extract frames from video files\n- **\ud83d\udcf8 Image Import**: Support for various image formats\n\n### \u270f\ufe0f **Annotation & Labeling**\n- **\ud83d\udc46 Manual Annotation**: Intuitive point, rectangle, and polygon tools\n- **\ud83e\udd16 AI-Assisted**: SAM, YOLO, and visual prompting models\n- **\ud83d\udcd0 Precision Editing**: Cut, combine, subtract, and simplify shapes\n\n### \ud83e\udde0 **Machine Learning**\n- **\ud83d\udd2c Hyperparameter Tuning**: Optimize training conditions\n- **\ud83d\ude80 Model Training**: Build custom classifiers and detectors\n- **\u26a1 Model Optimization**: Production-ready deployment\n\n### \ud83d\udcca **Analysis & Export**\n- **\ud83d\udcc8 Performance Evaluation**: Comprehensive model metrics\n- **\ud83c\udfaf Batch Inference**: Process multiple images automatically\n- **\ud83c\udfa5 Video Analysis**: Real-time processing with analytics\n- **\ud83d\udccb Multi-format Export**: CoralNet, Viscore, TagLab, GeoJSON\n\n---\n\n## \ud83d\udccb Roadmap\n\n*See the current tickets and planned features on the [GitHub Issues Page](https://github.com/Jordan-Pierce/CoralNet-Toolbox/issues)*\n\n---\n\n## \ud83d\udcbb Installation Guide\n\n### \ud83d\udc0d **Step 1: Environment Setup**\n```bash\n# Create a dedicated environment (recommended)\nconda create --name coralnet10 python=3.10 -y\nconda activate coralnet10\n```\n\n### \u26a1 **Step 2: Fast Installation with UV**\n```bash\n# Install UV for faster package management\npip install uv\n\n# Install CoralNet-Toolbox\nuv pip install coralnet-toolbox\n```\n\n> **Fallback**: If UV fails, use regular pip: `pip install coralnet-toolbox`\n\n### \ud83d\ude80 **Step 3: GPU Acceleration (Optional)**\nFor CUDA-enabled systems:\n```bash\n# Example for CUDA 12.9\n# Install PyTorch with CUDA support\nuv pip install torch torchvision --index-url https://download.pytorch.org/whl/cu129 --upgrade\n```\n\n### \ud83c\udfc3\u200d\u2642\ufe0f **Step 4: Launch**\n```bash\ncoralnet-toolbox\n```\n\n### \ud83c\udfaf **GPU Status Indicators**\n- **\ud83d\udc22** CPU only\n- **\ud83d\udc07** Single GPU\n- **\ud83d\ude80** Multiple GPUs \n- **\ud83c\udf4e** Mac Metal (Apple Silicon)\n\n*Click the icon in the bottom-left to see available devices*\n\n### \ud83d\udd04 **Upgrading**\n```bash\n# When updates are available\nuv pip install -U coralnet-toolbox==[latest_version]\n```\n\n---\n\n### \ud83c\udfd7\ufe0f **Repository Structure**\n\n<div align=\"center\">\n <a href=\"https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/diagram.svg\">\n <img src=\"https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/diagram.svg\" alt=\"Visualization of the codebase\" width=\"80%\">\n </a>\n</div>\n\n---\n\n## \ud83c\udf0a Success Stories\n\n> **Using CoralNet-Toolbox in your research?** \n> \n> We'd love to feature your work! Share your success stories to help others learn and get inspired.\n\n---\n\n## \ud83c\udf0d About CoralNet\n\n<div align=\"center\">\n <p><em>\ud83e\udeb8 Protecting our oceans, one annotation at a time \ud83e\udeb8</em></p>\n</div>\n\nCoral reefs are among Earth's most biodiverse ecosystems, supporting marine life and coastal communities worldwide. However, they face unprecedented threats from climate change, pollution, and human activities.\n\n**[CoralNet](https://coralnet.ucsd.edu/)** is a revolutionary platform enabling researchers to:\n- Upload and analyze coral reef photographs\n- Create detailed species annotations\n- Build AI-powered classification models\n- Collaborate with the global research community\n\nThe **CoralNet-Toolbox** extends this mission by providing advanced AI tools that accelerate research and improve annotation quality.\n\n---\n\n## \ud83d\udcc4 Citation\n\nIf you use CoralNet-Toolbox in your research, please cite:\n\n```bibtex\n@misc{CoralNet-Toolbox,\n author = {Pierce, Jordan and Battista, Tim},\n title = {CoralNet-Toolbox: AI-Powered Tools for Coral Reef Research},\n year = {2025},\n howpublished = {\\url{https://github.com/Jordan-Pierce/CoralNet-Toolbox}},\n note = {GitHub repository}\n}\n```\n\n---\n\n## \u2696\ufe0f Legal & Licensing\n\n<div align=\"center\">\n\n### \u26a0\ufe0f **Disclaimer**\n*This is a scientific product and not official communication of NOAA or the US Department of Commerce. All code is provided 'as is' - users assume responsibility for its use.*\n\n### \ud83d\udccb **License**\n*Software created by US Government employees is not subject to copyright in the United States (17 U.S.C. \u00a7105). The Department of Commerce reserves rights to seek copyright protection in other countries.*\n\n</div>\n\n---\n\n<div align=\"center\">\n <p><strong>\ud83c\udf0a Built with \u2764\ufe0f for coral reef conservation \ud83c\udf0a</strong></p>\n <p><em>Empowering researchers \u2022 Protecting ecosystems \u2022 Advancing science</em></p>\n</div>\n",
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