Comparison of different clearing and acquisition methods for 3D imaging of murine intestinal organoids


  • Louison Lallemant Cell Imaging Platform of Structure Fédérative de Recherche Necker INSERM-US24-CNRS UMS 3633
  • Corinne Lebreton Université de Paris, Imagine Institute, Laboratory of Intestinal Immunity, INSERM UMR1163
  • Meriem Garfa-Traoré Cell Imaging Platform of Structure Fédérative de Recherche Necker INSERM-US24-CNRS UMS 3633



Clearing, Intestinal organoids, Three-dimension imaging.


An organoid is a three-dimensional multicellular structure that shows realistic micro-anatomy of an organ. This in vitro model mimics the in vivo environment, architecture and multi-lineage differentiation of the original organs and allows to answer many interesting biological questions. For these reasons, they are widely used in stem cell, regenerative medicine, toxicology, pharmacology, and host-microbe interactions research. In order to study organoids, microscopy is very useful: It is possible to make three-dimensional reconstruction of serial sections but it is time consuming and error-prone. Here we propose an alternative solution: Tissue clearing reduces the dispersion of light because it homogenizes the refractive index of the tissue, allowing sample observation throughout its thickness. We have compared different clearing techniques on mouse intestinal organoids using different acquisition methods.


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How to Cite

Lallemant L, Lebreton C, Garfa-Traoré M. Comparison of different clearing and acquisition methods for 3D imaging of murine intestinal organoids. J Biol Methods [Internet]. 2020Dec.28 [cited 2021May18];7(4):e141. Available from: