Contour Analysis Tool: an interactive tool for background and morphology analysis

Abstract

We introduce the Contour Analysis Tool (CAT), a Python toolkit aimed at identifying and analyzing structural elements in density maps. CAT employs various contouring techniques, including the lowest-closed contour (LCC), linear and logarithmic Otsu thresholding, and average gradient thresholding. These contours can aid in foreground and background segmentation, providing natural limits for both, as well as edge detection and structure identification. Additionally, CAT provides image processing methods such as smoothing, background removal, and image masking. The toolkit features an interactive suite of controls designed for Jupyter environments, enabling users to promptly visualize the effects of different methods and parameters. We describe, test, and demonstrate the performance of CAT, highlighting its potential use cases. CAT is publicly available on GitHub, promoting accessibility and collaboration.