Merge pull request #1 from Annotation-Garden/agi-branding-high-priority

Add AGI branding and update repository references

Author: neuromechanist

.gitignore

@@ -1,30 +1,125 @@
-# Dependencies
-node_modules/
-venv/
-__pycache__/
-*.pyc
-
-# Build artifacts
-dist/
-build/
-*.egg-info/
+# Development context (local workflow docs)
+.context/
+.rules/
 
-# IDE
+# IDE and tools
 .vscode/
 .idea/
+.cursor/
+.claude/
+CLAUDE.md
 *.swp
 *.swo
-
-# OS files
 .DS_Store
-Thumbs.db
 
 # Environment
 .env
 .env.local
+.env.development
+.env.production
+
+# Python
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+.Python
+build/
+develop-eggs/
+dist/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+.pytest_cache/
+.coverage
+htmlcov/
+.mypy_cache/
+.ruff_cache/
+.tox/
+*.cover
+.hypothesis/
+
+# Node
+node_modules/
+npm-debug.log*
+yarn-debug.log*
+yarn-error.log*
+.pnpm-debug.log*
+.next/
+out/
+.nuxt/
+.cache/
+
+# Virtual environments
+venv/
+ENV/
+env/
+.venv
+
+# Logs
+*.log
+logs/
+
+# Temporary files
+tmp/
+temp/
+*.tmp
+*.bak
+
+# Database
+*.db
+*.sqlite
+*.sqlite3
+
+# Image processing
+processed_images/
+# thumbnails/  # Keep thumbnails in git for frontend
+optimized/
+
+# API Keys and secrets
+api_keys.json
+secrets.json
+
+# Model outputs
+outputs/
+results/
+
+# OLLAMA models
+models/
+
+# Cache
+.cache/
+cache/
+
+# OS
+Thumbs.db
+ehthumbs.db
+
+# Jupyter
+.ipynb_checkpoints/
+*.ipynb
+
+# Testing
+test_outputs/
+test_results/
+
+# Frontend public assets (copied for deployment)
+frontend/public/*
+!frontend/public/AGI-square.svg
+!frontend/public/AGI-square.png
+!frontend/public/favicon.ico
+
+# Image files (but keep README, and downsampled)
+images/original/*.png
 
-# Data (annotations should be version controlled separately)
-data/
-annotations/
-!data/.gitkeep
-!annotations/.gitkeep
+# Test annotations only (keep real annotations)
+annotations/test/

README.md

@@ -1,14 +1,20 @@
-# The Annotation Garden Project
+# Image Annotation Tool - Annotation Garden Initiative
 
-🌐 **[View Live Dashboard](https://neuromechanist.github.io/image-annotation)**
+🌐 **Part of the [Annotation Garden Initiative](https://annotation.garden)**
 
-A VLM-based image annotation system for Natural Scene Dataset (NSD) using multiple Vision-Language Models (VLMs).
+A VLM-based image annotation system adapted for the Annotation Garden ecosystem. This tool provides collaborative annotation capabilities for static image datasets, starting with the Natural Scene Dataset (NSD).
+
+## About Annotation Garden
+
+The Annotation Garden Initiative (AGI) establishes an open infrastructure for collaborative, multi-layered annotation of stimuli used in neuroscience research. This tool serves as the primary interface for annotating static image datasets in the AGI ecosystem.
 
 ## Key Features
 
 - **Multi-model support**: OLLAMA, OpenAI GPT-4V, Anthropic Claude
 - **Batch processing**: Handle 25k+ annotations with real-time progress
-- **Web dashboard**: Interactive visualization and analysis interface
+- **Web dashboard**: Interactive visualization with AGI branding
+- **HED integration**: Hierarchical Event Descriptors for semantic annotations
+- **BIDS-compliant**: Output follows stimuli-BIDS specifications
 - **Annotation tools**: Reorder, filter, export, and manipulate annotations
 - **Research-ready**: Structured JSON output with comprehensive metrics
 
@@ -24,9 +30,9 @@ A VLM-based image annotation system for Natural Scene Dataset (NSD) using multip
 ### Installation
 
 ```bash
-# Clone and setup
-git clone https://github.com/neuromechanist/hed-image-annotation.git
-cd hed-image-annotation
+# Clone from Annotation Garden
+git clone https://github.com/Annotation-Garden/image-annotation.git
+cd image-annotation
 
 # Python environment
 conda activate torch-312  # or create: conda create -n torch-312 python=3.12
@@ -45,19 +51,38 @@ ollama serve
 # Test VLM service
 python -m image_annotation.services.vlm_service
 
-# Run frontend dashboard
+# Run frontend dashboard (with AGI branding)
 cd frontend && npm run dev
 # Visit http://localhost:3000
 
 # Configuration
 cp config/config.example.json config/config.json
-# Edit config.json with API keys and NSD image paths
+# Edit config.json with API keys and image paths
 ```
 
+## AGI Integration
+
+### Design Elements
+- AGI logo positioned top-left in all interfaces
+- AGI color theme throughout dashboard
+- Consistent with annotation.garden website design
+
+### HED Integration
+This tool includes enhanced support for Hierarchical Event Descriptors (HED):
+- HED tag suggestions during annotation
+- HED validation for annotations
+- Export annotations with HED tags
+
+### BIDS Compliance
+Annotations follow stimuli-BIDS specifications:
+- Standardized events.tsv format
+- JSON sidecars with annotation schema
+- Compatible with neuroimaging datasets
+
 ## Architecture
 
 - **Backend**: FastAPI with OLLAMA/OpenAI/Anthropic integration
-- **Frontend**: Next.js dashboard with real-time progress tracking  
+- **Frontend**: Next.js dashboard with AGI branding
 - **Storage**: JSON files with database support for large datasets
 - **Processing**: Stateless VLM calls with comprehensive metrics
 
@@ -107,7 +132,6 @@ pytest tests/ --cov
 ruff check --fix . && ruff format .
 ```
 
-
 ## NSD Research Usage
 
 1. **Download NSD images** to `/path/to/NSD_stimuli/shared1000/`
@@ -116,17 +140,25 @@ ruff check --fix . && ruff format .
 4. **Post-process** with annotation tools
 5. **Export results** to CSV for analysis
 
-See [CONTRIBUTING.md](CONTRIBUTING.md) for detailed research workflows.
+See [CONTRIBUTING.md](https://github.com/Annotation-Garden/management/blob/main/CONTRIBUTING.md) for detailed research workflows.
 
 ## Contributing
 
-See [CONTRIBUTING.md](CONTRIBUTING.md) for development setup, standards, and submission process.
+See [CONTRIBUTING.md](https://github.com/Annotation-Garden/management/blob/main/CONTRIBUTING.md) in the management repository for AGI contribution guidelines.
+
+## Related Repositories
+
+- [Management](https://github.com/Annotation-Garden/management): Organizational documentation
+- [Assets](https://github.com/Annotation-Garden/assets): AGI branding and design guidelines
+- [Website](https://github.com/Annotation-Garden/annotation-garden.github.io): Main AGI website
 
 ## License
 
-This project is licensed under CC-BY-NC-SA 4.0 - see the [LICENSE](LICENSE) file for details.
+This project is licensed under CC-BY-NC-SA 4.0 - see the [LICENSE](LICENSE.md) file for details.
 
 ## Acknowledgments
 
 - Natural Scene Dataset (NSD) team
-- LangChain and OLLAMA communities
+- Annotation Garden Initiative community
+- LangChain and OLLAMA communities
+- Original tool by neuromechanist

SETUP.md

@@ -6,7 +6,7 @@ This repository will be populated by cloning and adapting the existing image ann
 
 ```bash
 # Clone the source repository
-git clone https://github.com/neuromechanist/image-annotation.git temp-image-annotation
+git clone https://github.com/Annotation-Garden/image-annotation.git temp-image-annotation
 
 # Copy relevant files to this directory
 cp -r temp-image-annotation/* .

frontend/README.md

@@ -38,7 +38,7 @@ npm run build:static
 npm run deploy
 ```
 
-The site will be available at: https://neuromechanist.github.io/image-annotation
+The site will be available at: https://annotation-garden.github.io/image-annotation
 
 ## 🛠️ Available Scripts
 

frontend/app/page.tsx

@@ -278,16 +278,15 @@ export default function Dashboard() {
         <footer className="bg-black/30 backdrop-blur-xl border-t border-purple-500/20 px-6 py-3">
           <div className="text-center text-sm text-gray-400">
             © 2025{' '}
-            <a 
-              href="https://neuromechanist.github.io" 
-              target="_blank" 
+<a
+              href="https://annotation.garden"
+              target="_blank"
               rel="noopener noreferrer"
               className="text-purple-400 hover:text-purple-300 transition-colors inline-flex items-center gap-1"
             >
-              Seyed Yahya Shirazi
+              Annotation Garden Initiative
               <ExternalLink className="w-3 h-3" />
             </a>
-            , Swartz Center for Computational Neuroscience, UC San Diego
           </div>
         </footer>
       </main>