omnipose
a high-precision morphology-independent solution for bacterial cell segmentation



Kevin John Cutler and colleagues created Omnipose, which provides robust segmentation of bacteria and other elongated cell shapes.
Read the paper, and also try out the segmentation in cellpose with the --omni flag and the new "bact_omni" model!
Omnipose was trained on a large database of bacterial images, download the data here.