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 - École des Ponts ParisTech Access content directly
Preprints, Working Papers, ... Year : 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
  • Function : Author
Elodie Machado
  • Function : Author
Fabrice Licata
  • Function : Author
Lilian Buzer
  • Function : Author
Isabelle Robineau
  • Function : Author
Julien Hémon
  • Function : Author
Payel Banerjee
  • Function : Author
Noémie de Crozé
  • Function : Author
Marc Léonard
  • Function : Author
Pierre Affaticati
  • Function : Author
Arnim Jenett
  • Function : Author
Jean-Stéphane Joly
  • Function : Author

Abstract

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 and 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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