ZeBraInspector, a platform for the automated segmentation and analysis of body and brain volumes in whole 5 dpf zebrafish following simultaneous visualization with identical orientations - Archive ouverte HAL Accéder directement au contenu
Pré-Publication, Document De Travail Année : 2020

ZeBraInspector, a platform for the automated segmentation and analysis of body and brain volumes in whole 5 dpf zebrafish following simultaneous visualization with identical orientations

Matthieu Simion
  • Fonction : Auteur
Elodie Machado
  • Fonction : Auteur
Fabrice Licata
  • Fonction : Auteur
Lilian Buzer
  • Fonction : Auteur
Isabelle Robineau
  • Fonction : Auteur
Julien Hémon
  • Fonction : Auteur
Payel Banerjee
  • Fonction : Auteur
Noémie de Crozé
  • Fonction : Auteur
Marc Léonard
  • Fonction : Auteur
Pierre Affaticati
  • Fonction : Auteur
Arnim Jenett
  • Fonction : Auteur
Jean-Stéphane Joly
  • Fonction : Auteur

Résumé

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 dpf 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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Dates et versions

hal-04580401 , version 1 (20-05-2024)

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Sylvain Lempereur, Matthieu Simion, Elodie Machado, Fabrice Licata, Lilian Buzer, et al.. ZeBraInspector, a platform for the automated segmentation and analysis of body and brain volumes in whole 5 dpf zebrafish following simultaneous visualization with identical orientations. 2024. ⟨hal-04580401⟩
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