ZeBraInspector, a platform for the automated segmentation and analysis of body and brain volumes in whole 5 days post-fertilization zebrafish following simultaneous visualization with identical orientations
Lempereur, Sylvain | Machado, Elodie | Licata, Fabrice | Simion, Matthieu | Buzer, Lilian | Robineau, Isabelle | Hémon, Julien | Banerjee, Payel | de Crozé, Noémie | Léonard, Marc | Affaticati, Pierre | Talbot, Hugues | Joly, Jean-Stéphane | Laboratoire d'Informatique Gaspard-Monge (LIGM) ; École nationale des ponts et chaussées (ENPC)-Centre National de la Recherche Scientifique (CNRS)-Université Gustave Eiffel | Transgénèse pour les Etudes Fonctionnelles sur les Organismes Modèles (TEFOR Paris-Saclay) ; Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) | L'Oréal Recherche France (L'Oréal Recherche) ; L'OREAL | Ecole Supérieure d'Electricité - SUPELEC (FRANCE) | Centre Inria de Saclay ; Institut National de Recherche en Informatique et en Automatique (Inria) | Université Paris-Saclay | This work was supported by ANR-TEFOR-”Investissement d’avenir” (ANR–II–INBS-0014), ANR Fish-RNAvax (ANR-16-CE20-0002-01), ANR FEATS (ANR-19 -CE34-0005-05) and institutional grants from the CNRS and INRAE. We warmly thank the Leducq foundation for the RETP grant and constant support, which was central to the development of the ZBI platform. SL received a PhD grant from Université Paris-Est. | ANR-11-INBS-0014,TEFOR,Transgenèse pour les Etudes Fonctionnelles sur les Organismes modèles(2011) | ANR-16-CE20-0002,Fish-RNAvax,Vaccins ARN éco-compatibles pour l'induction de réponses immunitaires protectrices chez le poisson d'élevage(2016) | ANR-19-CE34-0005,FEATS,Utilisation des embryons de poisson zèbre pour l'évaluation du risque toxicologique: cas des perturbateurs endocriniens agissant sur l'aromatase cérébrale(2019)
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Показать больше [+] Меньше [-]Английский. In recent years, the zebrafish has become a well-established laboratory model. We describe here the ZeBraInspector (ZBI) platform for high-content 3D imaging (HCI) of 5 days post-fertilization zebrafish eleuthero-embryos (EEs). This platform includes a mounting method based on 3D-printed stamps to create a grid of wells in an agarose cast, facilitating batch acquisitions with a fast-confocal laser scanning microscope. We describe reference labeling in cleared fish with a fluorescent lipophilic dye. Based on this labeling, the ZBI software registers. EE 3D images, making it possible to visualize numerous identically oriented EEs on a single screen, and to compare their morphologies and any fluorescent patterns at a glance. High-resolution 2D snapshots can be extracted. ZBI software is therefore useful for diverse high-content analyses (HCAs). Following automated segmentation of the lipophilic dye signal, the ZBI software performs volumetric analyses on whole EEs and their nervous system white matter. Through two examples, we illustrate the power of these analyses for obtaining statistically significant results from a small number of samples: the characterization of a phenotype associated with a neurodevelopmental mutation, and of the defects caused by treatments with a toxic anti-cancer compound.
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