Revert comprehensive CellMap overview - awaiting access to experimental repositories for train setup analysis

README.md

@@ -1,2 +1,87 @@
 # exp-overview
 an overview and reference for the experimental projects
+
+## CellMap Experimental Projects
+
+This repository provides an overview of the current experimental setups and projects within the CellMap initiative at Janelia Research Campus.
+
+## Current Experimental Projects
+
+| Project | Repository | Status | Dataset(s) | Organelles/Targets | ML Framework | Description | Key Tools |
+|---------|------------|--------|------------|-------------------|--------------|-------------|-----------|
+| **C. elegans Expression** | [expr_c-elegans](https://github.com/janelia-cellmap/expr_c-elegans) | 🔶 Archived | jrc_c-elegans-op50-1<br/>jrc_c-elegans-bw-1<br/>jrc_c-elegans-comma-1 | Mitochondria [mito]<br/>Lipid droplets [ld] | DaCapo + UNet | C. elegans organelle segmentation experiments | DaCapo, process-blockwise |
+
+## Core CellMap Infrastructure
+
+| Component | Repository | Purpose | Key Features |
+|-----------|------------|---------|--------------|
+| **Data Loading** | [cellmap-data](https://github.com/janelia-cellmap/cellmap-data) | PyTorch data loading for ML training | Multi-class segmentation, spatial transforms, efficient streaming |
+| **Model Repository** | [cellmap-models](https://github.com/janelia-cellmap/cellmap-models) | Pre-trained segmentation models | COSEM models, whole-cell organelle segmentation |
+| **Segmentation Challenge** | [cellmap-segmentation-challenge](https://github.com/janelia-cellmap/cellmap-segmentation-challenge) | Competition framework and toolbox | Data access, training, prediction, evaluation |
+| **Data Analysis** | [cellmap-analyze](https://github.com/janelia-cellmap/cellmap-analyze) | Analysis utilities | Post-processing and metrics |
+| **Nucleus Segmentation** | [cellmap-nuclei](https://github.com/janelia-cellmap/cellmap-nuclei) | Nucleus segmentation for FIB-SEM | Specialized nucleus detection |
+| **Visualization** | [cellmap-flow](https://github.com/janelia-cellmap/cellmap-flow) | Results visualization | Neuroglancer integration |
+
+## Experimental Setup Details
+
+### C. elegans Expression Project
+- **Datasets**: 
+  - `jrc_c-elegans-op50-1` and `jrc_c-elegans-bw-1` (similar characteristics, combined for training)
+  - `jrc_c-elegans-comma-1` (different characteristics, limited crops available)
+- **Target Organelles**: 
+  - Mitochondria using full pipeline
+  - Lipid droplets using lightweight U-Net (large, round, easy to identify)
+- **ML Framework**: [DaCapo](https://github.com/janelia-cellmap/dacapo) for training
+- **Inference**: [process-blockwise](https://github.com/janelia-cellmap/process-blockwise)
+- **Status**: Archived (completed experimental phase)
+
+## Data Format and Storage
+- **Primary Format**: OME-NGFF/Zarr with multiscale support
+- **Storage**: Local filesystem and cloud (S3/GCS) via TensorStore
+- **Visualization**: Neuroglancer for 3D volume inspection
+
+## Common Tools and Workflows
+
+### Training Pipeline
+1. **Data Preparation**: cellmap-data for efficient loading and augmentation
+2. **Model Training**: DaCapo framework with configurable architectures
+3. **Inference**: process-blockwise for large-volume prediction
+4. **Visualization**: cellmap-flow with Neuroglancer integration
+
+### Model Architectures
+- **U-Net variants**: 2D and 3D configurations
+- **Multi-class segmentation**: Support for mutually exclusive classes
+- **Pre-trained models**: Available via cellmap-models
+
+## Getting Started
+
+To work with CellMap experimental data:
+
+1. **Install core packages**:
+   ```bash
+   pip install cellmap-data cellmap-models
+   ```
+
+2. **Download challenge data**:
+   ```bash
+   pip install cellmap-segmentation-challenge
+   csc fetch-data
+   ```
+
+3. **Explore existing experiments**:
+   - Review the [expr_c-elegans](https://github.com/janelia-cellmap/expr_c-elegans) repository for C. elegans workflows
+   - Check [cellmap-segmentation-challenge](https://github.com/janelia-cellmap/cellmap-segmentation-challenge) for training examples
+
+## Contributing
+
+To add a new experimental project:
+1. Create a repository following the `expr_*` naming convention
+2. Include a comprehensive README with dataset and organelle information
+3. Document the ML frameworks and tools used
+4. Update this overview table with your project details
+
+## Resources
+
+- [CellMap Project Page](https://www.janelia.org/project-team/cellmap)
+- [CellMap Segmentation Challenge](https://cellmapchallenge.janelia.org/)
+- [DaCapo Documentation](https://github.com/janelia-cellmap/dacapo)