Update README.md

README.md

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-license: cc-by-4.0
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+# EMcopilot: Your label-free copilot for automated electron microscopy image analysis
+
+
+## Training and Code Details
+
+For detailed training procedures and source code, please refer to our GitHub repository:  
+[EMcopilot GitHub Repository](https://github.com/WenhaoYuan337/EMcopilot)
+
+
+
+## Usage
+
+1. **Train and predict segmentation models**:
+     * `00_01_sam_binary_masking.py` -  Generates coarse masks using the SAM model.
+3. **Generate and analyze synthetic masks**:
+     * `02_01_sam_mask_analysis.py` - Analyzes SAM mask properties and extracts morphology prior.
+     * `02_02_random_mask_generate.py` - Generates synthetic masks by augmenting existing masks.
+5. **Generate and evaluate images**:
+     * `03_01_p2p_train.py` - Trains a Pix2Pix model for mask-to-EMimage translation.
+     * `04_01_pix2pix_predict.py` - Runs inference using the trained Pix2Pix model.
+6. **Domain Adaptation**:
+     * `05_01_domain_adaptation.py` - Applies domain adaptation, including noise and contrast augmentation.
+7. **UNet++ Training and Inference**:
+     * `06_01_unet++_train.py` - Trains a CBAM-enhanced UNet++ model for segmentation.
+     * `07_01_unet++_predict.py` - Performs inference using the trained UNet++ model.
+8. **Analyze DM4 microscopy data**:
+     * `08_01_in_situ_analysis.py` - Analyze HAADF-STEM images of supported nanoparticles in real time.
+
+## Installation
+
+Install required packages using:
+```bash
+pip install -r requirements.txt
+```
+## Citation
+If you find our code or data useful in your research, please cite our paper:
+```
+@misc{yuan2024deepgenerativemodelsassistedautomated,
+      title={Deep Generative Models-Assisted Automated Labeling for Electron Microscopy Images Segmentation}, 
+      author={Wenhao Yuan and Bingqing Yao and Shengdong Tan and Fengqi You and Qian He},
+      year={2024},
+      eprint={2407.19544},
+      archivePrefix={arXiv},
+      primaryClass={cond-mat.mtrl-sci},
+      url={https://arxiv.org/abs/2407.19544}, 
+}
+```
+Copyright | 2025 Qian's Lab@NUS 
+