Start with the bigextractscript.m file. This is the file that finds and organizes all of the data I took for the density paper project.
In bigextractscript, there are calls to different functions (e.g. extractalldata, extractalldata_heterokaryon, etc). All of these functions are found in the LittleExtractScripts folder.
All of the software used to do anything is in the SoftwareFreeze folder. The volume code is in "VOLUME CODE NEW". A new version of the volume code is also up on the bitbucket, and it works with new image objects (and has its own wiki).