Active contour tracking

Dear everyone,

I am measuring the pixel intensity of bacteria living on a microscope. So far, I can segment them with an excellent resolution for every frame. However, I was wondering if there is a way to correlate the binary mask of one frame with the next one. The cells don’t move or move very little, so a function like active contour as in icy would be optimal. I tried TrackMate, but ROIs are circular instead of the bacteria-mask shape. I have also seen similar applications with the skimage library of python, but as far as I know, that package is not available within the fiji/jython environment.

Enclosed I upload a example of my images.