This is a Python script for performing the compactness analysis on biological sample images described in Zaforas et al. (Bioactive Materials, vol. 47, pp 32-50, 2025) The script relies on matplotlib, PIL, sklearn, PyQt5 and numpy. A window menu will drive users through the analysis, prompting the user for the necessary data (image) and options. Results will be displayed as figures that can be saved to png or printed directly.