Code to segment yeast cells using a pre-trained mask-rcnn model. We've tested this with yeast cells imaged in fluorescent images and brightfield images, and gotten good results with both modalities. This code implements an user-friendly script that hides all of the messy implementation details and parameters. Simply put all of your images to be segmented into the same directory, and then plug and go.

has function

automated open-source image acquisition and on-the-fly analysis pipeline (initially developped for analysis of mitotic defects in fission yeast)

maars workflow from publication



Spotsizer is a software tool that automates analysis of large volumes of photographic images of growing microbes.

screenshot of the spotsizer gui