BPCIS (Bacterial Phase Contrast for Instance Segementation)

BPCIS is collection of 364 bacterial phase contrast images and corresponding label matrices for instance segmentation. Labels were made according to fluorescence channels where possible. Prior to manual annotation, images were automatically cropped into microcolonies and tiled into ensemble images to reduce the empty (non-cell) image regions for training and testing. Subsequent to annotation, we performed non-rigid registration of phase contrast to cell masks.

Species include Escherichia coli, Shigella flexneri, Francisella tularensis subsp. novicida, Acinetobacter baylyi, Burkholderia thailandensis, Helicobacter pylori, Caulobacter crescentus , Streptomyces pristinaespiralis, Vibrio cholerae, Serratia proteamaculans, Pseudomonas aeruginosa, Staphylococcus aureus, and Bacillus subtilis. E. coli mutant CS703-1 and H. pylori were treated with Aztreonam. Included are independent treatments of S. flexneri with cephalexin and A22. Also included are mixtures of E. coli and S. protreamaculans, mixtures of P. aeruginosa and S. aureus, and P. aeruginosa, S. aureus, V. cholerae, and B. subtilis.

This dataset represents a wide range of morphological and optical phenotypes both common and uncommon to bacterial microscopy. All manual annotaton was performed by Kevin J. Cutler. Micrographs were captured by Kevin J. Cutler, Teresa Lo, Paul A. Wiggins, and Maxime Jacq.