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An Analytical Tool that Quantifies Cellular Morphology Changes from Three-dimensional Fluorescence Images

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Published on: August 31, 2012

FoamQuant: a Python package for time-resolved 3D image quantification of cellular materials.

Florian Schott¹, Benjamin Dollet², Stéphane Santucci³

¹Division of Solid Mechanics, LTH, Lund University, Lund, Sweden.

Journal of Synchrotron Radiation

|August 22, 2025

Summary

This summary is machine-generated.

We developed FoamQuant, a free software for analyzing 4D X-ray tomography data of cellular materials. This tool quantifies bubble properties and mechanical behavior in dynamic foam structures.

Keywords:

cellular materials image analysis tomography

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Area of Science:

Materials Science
Physics
Biotechnology

Background:

X-ray tomography is crucial for 3D structural analysis.
Dynamic 4D datasets from time-resolved X-ray tomography present significant image analysis challenges.
Existing tools struggle with the complexity of 4D cellular material data.

Purpose of the Study:

To introduce FoamQuant, a novel, free, and open-source software package.
To provide a dedicated platform for batch processing and quantitative analysis of 4D cellular or foam-like materials.
To enable detailed characterization of evolving material structures over time.

Main Methods:

Development of FoamQuant, a modular and user-friendly software package.
Implementation of algorithms for batch processing of large 4D time-series datasets.
Application of FoamQuant to analyze liquid foam dynamics and bubble coarsening.

Main Results:

FoamQuant successfully extracts key parameters like liquid fraction (porosity) and individual bubble volume.
Advanced characterization of mechanical properties, including elastic strain and stress fields, is achieved.
Individual cell rearrangements and plastic events in flowing foams are quantified.

Conclusions:

FoamQuant addresses the urgent need for specialized 4D image analysis tools for cellular materials.
The software facilitates in-depth understanding of material evolution, mechanical properties, and dynamic processes.
Demonstrated utility through case studies on liquid foams and coarsening albumin foams.