releasing final state of development phase

This release contains all files as they were used in the analysis of the image data and to prepare the manuscript.
At this stage, to run the analysis, paths to images and csv files need to be set manually in order to work on your system. Also several TODOs and comments from the development phase are left inside some files, to enable easier continuation of development work at a later point.

Feel free to open issues, if you are experiencing problems using the code.