Published February 5, 2024 | Version v1
Dataset Open

pix2pix_HUVEC_nuclei_cancer_cells_dataset

  • 1. University of Turku
  • 2. ROR icon Åbo Akademi University

Description

This repository contains a Pix2Pix deep learning model to generate synthetic nuclear staining from brightfield images. The model was trained on 258 paired brightfield and fluorescent microscopy images of circulating cancer cells perfused over an endothelial cell monolayer. To improve performance, the dataset was augmented computationally by a factor of 8. 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 its performance metrics and visual fidelity when compared to ground truth images, achieving an average SSIM score of 0.755 and an LPIPS score of 0.120.

Specifications

  • Model: Pix2Pix for generating synthetic nuclear staining from brightfield images

  • Training Dataset:

    • Cancer Cells: 258 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:

    • Circulating Cancer Cells:

      • SSIM Score: 0.755

      • LPIPS Score: 0.120

  • Model Selection: Models were selected 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

 

Files

pix2pix_HUVEC_nuclei_cancer_cells_dataset.zip

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