New Open-Source Tool for 3D Migration Analysis in Organoids and Spheroids

ImageJ Macro available at:

https://gitlab.fi.muni.cz/cbia/cellinvasion

Article in ACS Measurement Science Au:

https://pubs.acs.org/doi/10.1021/acsmeasuresciau.5c00121

Přikryl, M., Rousová, A., Acimovic, I., Vaňhara, P., Jan, L., Beneš, P., Šmarda, J., Kozubek, M., Štěpka, K., & Navrátilová, J. (2025). Cell Invasion Analysis of Tumor Spheroids Using 2D Image Data. ACS Measurement Science Au. https://doi.org/10.1021/acsmeasuresciau.5c00121

We introduce a software tool designed for the quantitative analysis of cell migration from fluorescently labeled 3D models such as spheroids and organoids. This tool enables researchers to measure invasive behavior by detecting cells or cell clusters that move beyond the original spheroid core, making it suitable for studies of cancer invasion, drug response, and tissue modeling. The software supports different morphologies, including compact spheroids and models that rapidly lose their boundaries after embedding in extracellular matrix. It automatically computes a core mask, identifies migrating cells based on fluorescence images with variable backgrounds, and provides visual overlays for easy verification. While largely automated, the workflow includes intuitive options for manual parameter adjustment, ensuring flexibility and accuracy for diverse experimental setups.