PT  - JOURNAL ARTICLE
AU  - Sylvain Lempereur
AU  - Elodie Machado
AU  - Fabrice Licata
AU  - Lilian Buzer
AU  - Isabelle Robineau
AU  - Julien Hémon
AU  - Payel Banerjee
AU  - Noémie De Crozé
AU  - Marc Léonard
AU  - Pierre Affaticati
AU  - Arnim Jenett
AU  - Hugues Talbot
AU  - Jean-Stéphane Joly
TI  - ZeBraInspector, a whole organism screening platform enabling volumetric analysis of zebrafish brain white matter
AID  - 10.1101/2020.10.26.353656
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.10.26.353656
4099  - http://biorxiv.org/content/early/2020/10/26/2020.10.26.353656.short
4100  - http://biorxiv.org/content/early/2020/10/26/2020.10.26.353656.full
AB  - In recent years, zebrafish have become well established for the study of fundamental biology, toxicology and drug discovery. Here we propose fast, standardized protocols for high-throughput and high-content 3D imaging of 5dpf zebrafish EE using a confocal laser scanning microscope. Using a lipophilic fluorescent dye, we generated a reference labeling in cleared fish. We developed a mounting method based on 3D-printed stamps used to create a grid of wells in an agarose cast. We demonstrate that the quality and homogeneity of the fluorescence signal allows an unequivocal segmentation of the whole specimen and the white matter. From there, we built an automated image registration and analysis pipeline for the volumetric analysis of morphological defects. The platform, termed ZeBraInspector, is focused on the analysis of the shape of the whole EE or the white-matter of the central nervous system. A user-friendly software to visualize at large scale registered and segmented 3D images can be downloaded from https://tefor.net/portfolio/zebrainspector. We finally provide two examples of application: the characterization of a phenotype associated with a neuro-developmental mutation, and the defects caused by treatments with a toxic anti-cancer compound. ZeBraInspector can be adapted to a wide variety of high-content analyses.websites: TEFOR Paris-Saclay – Research and Development for the Tefor InfrastructureZeBraInspector – TeforZeBraInspector – Gitlab repositoryCompeting Interest StatementThe authors have declared no competing interest.