```markdown
# microgen3D

[![Code](https://img.shields.io/badge/GitHub-Code-black?logo=github)](https://github.com/baskargroup/MicroGen3D)

## Dataset Summary

**microgen3D** is a dataset of 3D voxelized microstructures designed for training, evaluation, and benchmarking of generative models—especially Conditional Latent Diffusion Models (LDMs). It includes both synthetic (Cahn-Hilliard) and experimental microstructures with multiple phases (2 to 3). The voxel grids range from `64³` up to `128×128×64`.

The dataset consists of three microstructure types:
- **Experimental microstructures**
- **2-phase Cahn-Hilliard microstructures**
- **3-phase Cahn-Hilliard microstructures**

The two Cahn-Hilliard datasets are thresholded versions of the same simulation source. For each dataset type, we also provide pretrained generative model weights, comprising:
- `vae.ckpt` – Variational Autoencoder
- `fp.ckpt` – Feature Predictor
- `ddpm.ckpt` – Denoising Diffusion Probabilistic Model

---

## 📁 Repository Structure

```
microgen3D/
├── data/
│   └── sample_data.h5                 # Experimental or synthetic HDF5 microstructure file
├── models/
│   └── weights/
│       ├── experimental/
│       │   ├── vae.ckpt
│       │   ├── fp.ckpt
│       │   └── ddpm.ckpt
│       ├── two_phase/
│       └── three_phase/
└── ...
```

---

## 🚀 Quick Start

### 🔧 Setup Instructions

```bash
# 1. Clone the repo
git clone https://github.com/baskargroup/MicroGen3D.git
cd MicroGen3D

# 2. Set up environment
python -m venv venv
source venv/bin/activate  # On Windows use: venv\Scripts\activate

# 3. Install dependencies
pip install -r requirements.txt

# 4. Download dataset and weights (Hugging Face)
# Make sure HF CLI is installed and you're logged in: `huggingface-cli login`
```

```python
from huggingface_hub import hf_hub_download

# Download sample data
hf_hub_download(repo_id="BGLab/microgen3D", filename="sample_data.h5", repo_type="dataset", local_dir="data")

# Download model weights
hf_hub_download(repo_id="BGLab/microgen3D", filename="vae.ckpt", local_dir="models/weights/experimental")
hf_hub_download(repo_id="BGLab/microgen3D", filename="fp.ckpt", local_dir="models/weights/experimental")
hf_hub_download(repo_id="BGLab/microgen3D", filename="ddpm.ckpt", local_dir="models/weights/experimental")
```

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## 📜 Citation

If you use this dataset or models, please cite:

```
@article{baishnab2025microgen3d,
  title={3D Multiphase Heterogeneous Microstructure Generation Using Conditional Latent Diffusion Models},
  author={Baishnab, Nirmal and Herron, Ethan and Balu, Aditya and Sarkar, Soumik and Krishnamurthy, Adarsh and Ganapathysubramanian, Baskar},
  journal={arXiv preprint arXiv:2503.10711},
  year={2025}
}
```

---

## ⚖️ License

This project is licensed under the **MIT License**.

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