Reboot of Andrea Rau's 2019 analysis for Sumona Dhara's Zebrafish Optic Regen project.

Some of the tools used in the original 2019 analysis have been abandoned. This reboot utilizes newer tools and newer versions of previous used tools, as well as the latest Zebrafish build (GRCz11-105).

The primary motivation for this analysis, however, is the test the robustness of the CNC-EMDiff analysis scripts and expose opportunities for greater generalization to new data sets. The results have been encouraging, with only trivial changes needed to re-analyze the Zebrafish data.

CNC-EMDiff was itself originally modeled on Andrea Rau's OpticRegen analysis and later revamped to use the latest tools and simplify the scripts.