Update README.md

README.md

@@ -17,7 +17,7 @@ language:
   - en
 ---
 
-```markdown
+
 # microgen3D
 
 [![Code](https://img.shields.io/badge/GitHub-Code-black?logo=github)](https://github.com/baskargroup/MicroGen3D)
@@ -89,6 +89,73 @@ hf_hub_download(repo_id="BGLab/microgen3D", filename="fp.ckpt", local_dir="model
 hf_hub_download(repo_id="BGLab/microgen3D", filename="ddpm.ckpt", local_dir="models/weights/experimental")
 ```
 
+## ⚙️ Configuration
+
+### Training Config (`config.yaml`)
+- **task**: Auto-generated if left null  
+- **data_path**: Path to training dataset (`../data/sample_train.h5`)  
+- **model_dir**: Directory to save model weights  
+- **batch_size**: Batch size for training  
+- **image_shape**: Shape of the 3D images `[C, D, H, W]`  
+
+#### VAE Settings:
+- `latent_dim_channels`: Latent space channels size.  
+- `kld_loss_weight`: Weight of KL divergence loss  
+- `max_epochs`: Training epochs  
+- `pretrained`: Whether to use pretrained VAE  
+- `pretrained_path`: Path to pretrained VAE model  
+
+#### FP Settings:
+- `dropout`: Dropout rate  
+- `max_epochs`: Training epochs  
+- `pretrained`: Whether to use pretrained FP  
+- `pretrained_path`: Path to pretrained FP model  
+
+#### DDPM Settings:
+- `timesteps`: Number of diffusion timesteps  
+- `n_feat`: Number of feature channels for Unet. Higher the channels more model capacity. 
+- `learning_rate`: Learning rate  
+- `max_epochs`: Training epochs  
+
+### Inference Parameters (`params.yaml`)
+- **data_path**: Path to inference/test dataset (`../data/sample_test.h5`)  
+
+#### Training (for model init only):
+- `batch_size`, `num_batches`, `num_timesteps`, `learning_rate`, `max_epochs`  : Optional parameters
+
+#### Model:
+- `latent_dim_channels`: Latent space channels size.  
+- `n_feat`: Number of feature channels for Unet.
+- `image_shape`: Expected image input shape  
+
+#### Attributes:
+- List of features/targets to predict:
+  - `ABS_f_D`
+  - `CT_f_D_tort1`
+  - `CT_f_A_tort1`
+
+#### Paths:
+- `ddpm_path`: Path to trained DDPM model  
+- `vae_path`: Path to trained VAE model  
+- `fc_path`: Path to trained FP model  
+- `output_dir`: Where to store inference results  
+
+## 🏋️ Training
+
+Navigate to the training folder and run:
+```bash
+cd training
+python training.py
+```
+
+## 🧠 Inference
+
+After training, switch to the inference folder and run:
+```bash
+cd ../inference
+python inference.py
+```
+
 ---
 
 ## 📜 Citation