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README.md

Nf-as-a-metric-for-quantifying-and-improving-super-resolution-microscopy-image-reconstruction

We trained a Conditional Variational Diffusion Model (CVDM) (G. Della Maggiora, 2023) using the BioSR dataset (Qiao & Li, 2020) (DOI: 10.6084/m9.figshare.13264793.v9). To evaluate if the model can generate natural images similar to the gtound truth, we assessed the Naturalness Factor(Gong, Y., & Sbalzarini, I. F. 2014) at two stages: prior learning (before training) and post-processing (after applying the model's output enhancements).

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 naturalization of images is done with the ImageJ Mosaic Suite plugin. 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 are experiments done?

CVDM:The CVDM model is trained for 10 epochs with a batch size of 2. Overall, the model is trained for 500,000 iterations, with generation time step T = 200, learning rate 0.0001. During theinference, generation time steps are set to T = 500.

CVDM+N: naturalize the output of the CVDM model using ImageJ Mosaic Suite plugin.

NCVDM: train a new CVDM model on pairs of low-resolution and naturalized high-resolution BioSR images using the same training dataset and training parameters of CVDM.

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) 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 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.