The goal of this project was to solve a major bottleneck in our lab, which was the large number of microscope slides that needed tiled acquisitions done across multiple color channels and then stitched together for a final tiled output image of the whole slide. The whole process was slow, inefficient, difficult to learn, and easy to mess up.

The solution I came up with here is a program that handles all of the complex features of both Micro-Manager and Fiji all behind the scenes, and gives the user a clean and easy to understand interface to quickly scan all their slides.

The entire application is written in python, including the GUI which is using the Tkinter library. It utilizes Micro-Manager’s API to control all the microscope and acquisition settings.

Once the slide has been scanned it then uses Fiji and its ability to run scripts via python to process and stitch the TIFF stack that was output from the acquisition step.