pix2pix_HUVEC_juctions_dataset

This repository contains a Pix2Pix deep learning model to generate synthetic PECAM-1 staining from brightfield images. The model was trained on an initial dataset of 484 paired brightfield and fluorescent microscopy images, which was computationally augmented by a factor of 6 to enhance model performance. The training was conducted over 245 epochs with a patch size of 512x512, a batch size of 1, and a vanilla GAN loss function. The final model was selected based on quality metric scores and visual comparison to ground truth images, achieving an average SSIM score of 0.273 and an LPIPS score of 0.360 on the test dataset.

Specifications

Model: Pix2Pix for generating synthetic PECAM staining from brightfield images

Training Dataset:

Original Dataset: 484 paired brightfield and fluorescent microscopy images

Augmented Dataset: Expanded to 2,904 paired images through computational augmentation

Microscope: Nikon Eclipse Ti2-E, brightfield/fluorescence microscope with a 20x objective

Data Type: Brightfield and fluorescent microscopy images

File Format: TIFF (.tif), 16-bit

Image Size: 1024 x 1022 pixels (Pixel size: 650 nm)

Training Parameters:

Epochs: 245

Patch Size: 512 x 512 pixels

Batch Size: 1

Loss Function: Vanilla GAN loss function

Model Performance:

SSIM Score: 0.273

LPIPS Score: 0.360

Model Selection: The best model was chosen based on quality metric scores and visual inspection compared to ground truth images.

Model Training: Conducted using ZeroCostDL4Mic (https://github.com/HenriquesLab/ZeroCostDL4Mic/wiki)

Reference

Fast label-free live imaging reveals key roles of flow dynamics and CD44-HA interaction in cancer cell arrest on endothelial monolayers

Gautier Follain, Sujan Ghimire, Joanna W. Pylvänäinen, Monika Vaitkevičiūtė, Diana Wurzinger, Camilo Guzmán, James RW Conway, Michal Dibus, Sanna Oikari, Kirsi Rilla, Marko Salmi, Johanna Ivaska, Guillaume Jacquemet

bioRxiv 2024.09.30.615654; doi: https://doi.org/10.1101/2024.09.30.615654