Update README.md

README.md

@@ -6,19 +6,43 @@ During theinference, generation time steps are set to T = 500. The naturalizatio
 The implementation of CVDM can be found on the GitHub page (G. Della Maggiora, L. A. Croquevielle, N. Deshpande, H. Horsley, T. Heinis, A. Yaki-movich, Conditional variational diffusion models, https://github.com/casus/cvdm)2023. 
 The Naturalness Factor information and documentation (including a guide on installation of the Mosaic Suite plugin) can be found in  MOSAIC group, MosaicSuite documentation, https://sbalzarinilab.org/MosaicSuiteDoc/index.html.
 
-##How to use the images?
+**How to use the images?**
 
 Every folder contains 100 TIFF images representing four biological structures from the **BioSR dataset**, 25 images for each structure.
 
-- **CCP** (Clathrin-Coated Pits)  
-- **ER** (Endoplasmic Reticulum)  
-- **F-actin** (Filamentous Actin)  
-- **MT** (Microtubules)
+- **CCP** (Clathrin-Coated Pits) from image_1 to image_25 
+- **ER** (Endoplasmic Reticulum)  from image_26 to image_50 
+- **F-actin** (Filamentous Actin)  from image_51 to image_75 
+- **MT** (Microtubules) from image_76 to image_100 
 
 The **BioSR_low_resolution_images** folder contains low-resolution images.
+
 The **BioSR_high_resolution_images** folder contains the high-resolution grond truth images.
-The **naturalized_BioSR_high_resolution_images** folder contains the naturalized high-resolution grond truth images, which are obtained by naturalize the images in **BioSR_high_resolution_images** using ImageJ Mosaic Suite plugin.
-The **CVDM_inference** folder contains CVDM generated images during the inference time with images from **BioSR_low_resolution_images** as input.
+
+The **naturalized_BioSR_high_resolution_images** folder contains the naturalized high-resolution ground truth images, which are obtained by naturalizing the images in **BioSR_high_resolution_images** using ImageJ Mosaic Suite plugin.
+
+The **CVDM_inference** folder contains CVDM generated images during inference, using images from **BioSR_low_resolution_images** as input.
+
+The **CVDM+N_inference** folder contains images obtained by natrualizing all images in the **CVDM_inference** folder using ImageJ Mosaic Suite plugin.
+
+The **NCVDM_inference** folder contains images generated by NCVDM model.
+
+**How to use the metric code?**
+
+To calculate **CVDM experiment metrics**:
+
+- Use images from the **BioSR_high_resolution_images** folder and the **CVDM_inference** folder as pairs to compute **MS-SSIM, MAE, and PSNR**.
+- Use images from the **CVDM_inference** folder to compute **RMS Contrast** and **Naturalness Factor**.
+
+To calculate **CVDM+N experiment metrics**:
+
+- Use images from the **naturalized_BioSR_high_resolution_images** folder and the **CVDM+N_inference** folder as pairs to compute **MS-SSIM, MAE, and PSNR**.
+- Use images from the **CVDM+N_inference** folder to compute **RMS Contrast** and **Naturalness Factor**.
+
+To calculate **NCVDM experiment metrics**:
+
+- Use images from the **naturalized_BioSR_high_resolution_images** folder and the **NCVDM_inference** folder as pairs to compute **MS-SSIM, MAE, and PSNR**.
+- Use images from the **NCVDM_inference** folder to compute **RMS Contrast** and **Naturalness Factor**.