required software and plugins

To run the workflow, first you need to install:

• Fiji

Fiji plugins

Macros require the following plugins to be installed:

• Correlescence version 0.0.7
• BigTrace version either between 0.5.2 and 0.6.0 or above 0.8.3
• AveragingND version 0.1.0
• FeatureJ version 2.0.0
• UnequalTiffs version >= 0.1.0 (optional, for the inspection of tiff files)
• Radial Profile Angle or take jar from here

For the optional initial automatic ROIs detection at (part 1) Step 0: auto ROIs generation,
we gonna need multi-template matching plugin
(see installation instructions via the link, it requires IJ-OpenCV update site).