Multiscale light-sheet organoid imaging framework

Gustavo Medeiros, Raphael Ortiz, Petr Strnad (), Andrea Boni, Franziska Moos, Nicole Repina, Ludivine Challet Meylan, Francisca Maurer and Prisca Liberali ()
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Gustavo Medeiros: Friedrich Miescher Institute for Biomedical Research (FMI) Maulbeerstrasse 66
Raphael Ortiz: Friedrich Miescher Institute for Biomedical Research (FMI) Maulbeerstrasse 66
Petr Strnad: Friedrich Miescher Institute for Biomedical Research (FMI) Maulbeerstrasse 66
Andrea Boni: Friedrich Miescher Institute for Biomedical Research (FMI) Maulbeerstrasse 66
Franziska Moos: Friedrich Miescher Institute for Biomedical Research (FMI) Maulbeerstrasse 66
Nicole Repina: Friedrich Miescher Institute for Biomedical Research (FMI) Maulbeerstrasse 66
Ludivine Challet Meylan: Friedrich Miescher Institute for Biomedical Research (FMI) Maulbeerstrasse 66
Francisca Maurer: Friedrich Miescher Institute for Biomedical Research (FMI) Maulbeerstrasse 66
Prisca Liberali: Friedrich Miescher Institute for Biomedical Research (FMI) Maulbeerstrasse 66

Nature Communications, 2022, vol. 13, issue 1, 1-14

Abstract: Abstract Organoids provide an accessible in vitro system to mimic the dynamics of tissue regeneration and development. However, long-term live-imaging of organoids remains challenging. Here we present an experimental and image-processing framework capable of turning long-term light-sheet imaging of intestinal organoids into digital organoids. The framework combines specific imaging optimization combined with data processing via deep learning techniques to segment single organoids, their lumen, cells and nuclei in 3D over long periods of time. By linking lineage trees with corresponding 3D segmentation meshes for each organoid, the extracted information is visualized using a web-based “Digital Organoid Viewer” tool allowing combined understanding of the multivariate and multiscale data. We also show backtracking of cells of interest, providing detailed information about their history within entire organoid contexts. Furthermore, we show cytokinesis failure of regenerative cells and that these cells never reside in the intestinal crypt, hinting at a tissue scale control on cellular fidelity.

Date: 2022
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DOI: 10.1038/s41467-022-32465-z

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