pix2pix_HUVEC_nuclei_immuno_cells_dataset

This repository contains a Pix2Pix deep learning model designed to generate synthetic nuclear staining from brightfield images of circulating immune cells. The model was trained on a dataset of 226 paired brightfield and fluorescent microscopy images, which were augmented computationally by a factor of 8 to enhance model performance. The model was trained over 400 epochs using 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 0.756 and an LPIPS score of 0.130.

Specifications

• Model: Pix2Pix for generating synthetic nuclear staining from brightfield images of circulating immune cells

• Training Dataset:

• Immune Cells: 226 paired brightfield and fluorescent microscopy images

• 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: 400

• Patch Size: 512 x 512 pixels

• Batch Size: 1

• Loss Function: Vanilla GAN loss function

• Model Performance:

• Immune Cells:

• SSIM Score: 0.756

• LPIPS Score: 0.130

• Model Selection: Models were 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)