AFMSlicer

AFMSlicer is a program for processing and analysing Atomic Force Microscopy images of bacterial cell walls.

It leverages the TopoStats package for loading and flattening/filtering images and as such follows a similar structure in terms of configuration and design patterns.

After filtering/flattening of an image it is then "sliced" into an 3-D numpy array of masks which are analysed to obtain statistics on the structure of images at different heights.