Dockerfile addition, some fixes for newer modules
- updated dependencies with latest version of scikit image and modules for reading CZI files
- added command line ability to set result folder, needed to be able to run on mulitple different sequences in parallel
- added back in catalog so that current .ini file works, however this might not be necessary
- note as well that "entropy_cell_map_margin" is now a required parameter in the ini file and the program will fail (late) if this isn't set
- adding Dockerfile for running this pipeline on Docker
- newer versions of phase_cross_correlation always return 3 arguments; added logic to handle the two cases (older vs newer behavior)