Imaging In Depth

3D lab-grown assembled cell models like organoids and tumoroids are becoming ever more complex to better mimic real life, and ever more popular as a go-to system for convenience to scrutinise how cells interact and tissues develop. Here, a user-friendly package in Python called Tapenade has been developed to quantify spatial patterns of gene activity [gene expression] and record the shapes of cell nuclei in such 3D cell assemblies, revealing how local cell deformations and gene co-expression relate to tissue-scale organisation.

Read the published research article here

Written by Lindsey Goff

Lindsey Goff

Editor-in-Chief

Formerly immunologist for Cancer Research UK, Lindsey has since moved into the field of scientific publishing. She looks after all BPoD editorial matters.

• Video from work by Alice Gros, Jules Vanaret and Valentin Dunsing-Eichenauer, and colleagues
• Aix Marseille Univ, CNRS IBDM (UMR 7288), Turing Centre for Living Systems, France
• Video originally published with a Creative Commons Attribution 4.0 International (CC BY 4.0)
• Published in eLife, May 2026