A quantitative pipeline for whole-mount deep imaging and analysis of multi-layered organoids across scales
Alice Gros, Jules Vanaret, Valentin Dunsing-Eichenauer, Agathe Rostan, Philippe Roudot, Pierre-François Lenne, Léo Guignard, Sham Tlili, Rio Sugimura, Alice Gros, Jules Vanaret, Valentin Dunsing-Eichenauer, Agathe Rostan, Philippe Roudot, Pierre-François Lenne, Léo Guignard, Sham Tlili · 2026
Read A quantitative pipeline for whole-mount deep imaging and analysis of multi-layered organoids across scales by Alice Gros, Jules Vanaret, Valentin Dunsing-Eichenauer, Agathe Rostan, Philippe Roudot, Pierre-François Lenne, Léo Guignard, Sham Tlili, Rio Sugimura, Alice Gros, Jules Vanaret, Valentin Dunsing-Eichenauer, Agathe Rostan, Philippe Roudot, Pierre-François Lenne, Léo Guignard, Sham Tlili (2026) in the Tower of Babel, a free online library of public-domain works preserved in clean, searchable text. No sign-up. The full text is served as a plain-text file at a predictable URL, where text is present: https://antarctic-labs.com/tower-of-babel/pmc-13197165.txt.
Description
Alice Gros and colleagues present a 2026 imaging pipeline for organoids, tiny lab-grown tissue models. Whole-mount imaging can show organoid structure in three dimensions, but dense cell packing blocks deep views and cell counts. Their pipeline joins lab imaging with software steps to fix that gap.
The lab part uses two-photon imaging, a deep-penetrating light method, on stained organoids. The software part corrects image flaws, outlines each cell core, and measures gene activity. It ships as a free Python package with viewer plug-ins. Tests on gastruloids, early embryo-like models, showed how local cell shape links to broad tissue order. The tools should transfer to other layered models.
Catalog record
| CREATOR | Alice Gros, Jules Vanaret, Valentin Dunsing-Eichenauer, Agathe Rostan, Philippe Roudot, Pierre-François Lenne, Léo Guignard, Sham Tlili, Rio Sugimura, Alice Gros, Jules Vanaret, Valentin Dunsing-Eichenauer, Agathe Rostan, Philippe Roudot, Pierre-François Lenne, Léo Guignard, Sham Tlili |
|---|---|
| YEAR | 2026 |
| COLLECTION | PAPERS |
| FORMAT | TXT |
| FILE SIZE | 180 KB |
| VERSION | 1.0 |
| LICENSE | CC BY 4.0 |
| RIGHTS | CC BY |
| SOURCE | Europe PMC |