Data from: Segmentation of dense and multi-species bacterial colonies using models trained on synthetic microscopy images

This repository contains the relevant data and code for the article "Segmentation of dense and multi-species bacterial colonies using models trained on synthetic microscopy images" by Vincent Hickl, Abid Khan, René M. Rossi, Bruno F. B. Silva, and Katharina Maniura-Weber (arXiv version 3): Raw synthetic images of rod-shaped and circular cells Confocal microscopy images of densely packed colonies of Pseduomonas aeruginosa, and of mixed colonies of P. aeruginosa and Staphylococcus aureus Brigthfield microscopy images of rod-shaped and circular cells The code for processing raw synthetic images using CycleGAN can be found at https://github.com/abid1214/cyclegan Further relevant code can be found at https://github.com/vhickl/synth-bacteria-segmentation, including code to: generate raw synthetic images of rod-shaped and spherical bacteria analyze orientational order in densely-packed colonies of rod-shaped cells quantitatively compare segmentation masks of bacterial colonies