Shown in the GUI is an image from the test set, zoomed in on an area of interest, and segmented using Cellpose. The GUI serves two main purposes: 1) easily run Cellpose ‘out-of-the-box’ on new images and visualize the results in an interactive mode; 2) manually segment new images, to provide training data for Cellpose. The image view can be changed between image channels, cellpose vector flows and cellpose predicted pixel probabilities. Similarly, the mask overlays can be changed between outlines, transparent masks or both. The size calibration procedure can be run to estimate cell size, or the user can directly input the cell diameter, with an image overlay of a red disk shown as an aid for visual calibration. Dense, complete manual segmentations can be uploaded to our server with one button press, and the latest trained model can be downloaded from the drop-down menu.