The folder MFMSoftware is a copy from the scripts that are used to process the raw Multi-focus microscopy data and track molecules in 3D. The source of these scripts can be found here: https://github.com/aicjanelia/MFM
visitor-maarten-paul contains the scripts to interpolate the reference mask images and to correlate with the 3D tracking data. The orignal scripts that were the basis of these scripts can be found at https://gitlab.com/aicjanelia/visitor-maarten-paul
To run the above scripts you will need to install the following dependencies:
https://github.com/aicjanelia/hmm-bayes
https://github.com/ericwait/matlab-utilities
https://github.com/ericwait/hydra-image-processor