arXiv subjects

Benjamin Evert Himberg

Publications and source records attributed to Benjamin Evert Himberg.

2 recordsLinked to original sources

arXiv2026

A geometry-first tutorial for time-resolved morphological analysis with PyPETANA

We present a step-by-step, reproducible tutorial for PyPETANA, an open-source Python framework for geometry-first, time-resolved quantification of evolving morphology from image data. Starting from time-lapse video input, the tutorial demonstrates how to extract binary masks, compute time-resolved geometric observables including area, perimeter, circularity, and effective fractal dimensions, and analyze their temporal evolution. The workflow emphasizes direct reconstruction of morphology from images without assuming microscopic growth mechanisms. In addition to compactness-sensitive geometric descriptors, the framework supports multiscale boundary analysis through supersampled box-counting methods applied to filled morphologies and finite-width boundary bands. The benchmark suite further demonstrates applicability to invasive tumor morphologies and multiscale boundary evolution in time-resolved cancer-growth interfaces. This tutorial accompanies the computational workflow underlying arXiv:2602.05958 and provides a reproducible foundation for geometry-based analysis of evolving non-equilibrium morphologies.

cond-mat.soft↗

arXiv2026

Geometry and dynamical morphology of growing bacterial colonies

We study non-equilibrium bacterial colony growth using a geometry-first, time-resolved analysis of morphology. From time-lapse microscopy data, we track the coupled evolution of area, perimeter, and boundary-sensitive shape descriptors along the full growth history. We find that non-equilibrium growth can exhibit extended intervals of compact area--perimeter scaling with exponent $α\approx 2$, consistent with growth governed by a single effective geometric length scale, as well as time-localized breakdowns of this scaling during ongoing growth. These breakdowns coincide with transient boundary reorganization while bulk area growth remains sustained. Our results demonstrate that visually distinct morphologies can arise within the same geometric growth regime, and that departures from single-scale behavior reflect intrinsic dynamical restructuring rather than growth arrest. More broadly, this work establishes time-resolved geometry as a coarse-grained framework for identifying when non-equilibrium growth departs from single-scale geometric constraints in living systems.

cond-mat.soft↗