FIJI Spheroid Morphological Signature Scripts

Please review the README file for full details on the macros and their usage.
The repository contains FIJI macros as featured in the manuscript Shape Factor Analysis as a Quantitative Framework for Assessing Spheroid and Organoid Morphology and Invasiveness. The convexity macro stands alone in calculating the shape factor convexity for ROI(s) in FIJI. The perimeter points calculator and the interpolation macro are useful for preparing ROIs for the MATLAB radial length analysis also featured our manuscript. These macros are not required for editing the ROIs for radial length analysis but are useful for the applications we describe.

FIJI (ImageJ) Macros in this repository

1. ConvexityMacro.ijm = calculates the convexity (the convex perimeter divided by the perimeter) for each ROI open in the ROI manager
2. perimeter_points.ijm = counts the number of perimeter points defining an ROI. Useful in preparing ROIs for radial length analysis in MATLAB
3. interpolation.ijm = creates additional perimeter points to define an ROI by interpolating to a 1 pixel interval. Useful for preparing ROIs for radial length analysis in MATLAB
   .ijm files can be downloaded and opened directly in FIJI