PUBLICATION
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
- Authors
- Lempereur, S., Machado, E., Licata, F., Simion, M., Buzer, L., Robineau, I., Hémon, J., Banerjee, P., De Crozé, N., Léonard, M., Affaticati, P., Talbot, H., Joly, J.S.
- ID
- ZDB-PUB-220717-7
- Date
- 2022
- Source
- Developmental Biology 490: 86-99 (Journal)
- Registered Authors
- Affaticati, Pierre, Banerjee, Payel, Joly, Jean-Stephane, Lempereur, Sylvain, Licata, Fabrice, Machado, Elodie, Simion, Matthieu
- Keywords
- Computer vision, Confocal imaging, Fish, Morphometry, Teratology, Tissue clearing
- MeSH Terms
-
- Animals
- Brain/diagnostic imaging
- Fertilization
- Imaging, Three-Dimensional*
- Microscopy, Confocal/methods
- Zebrafish*/genetics
- PubMed
- 35841952 Full text @ Dev. Biol.
Citation
Lempereur, S., Machado, E., Licata, F., Simion, M., Buzer, L., Robineau, I., Hémon, J., Banerjee, P., De Crozé, N., Léonard, M., Affaticati, P., Talbot, H., Joly, J.S. (2022) 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. Developmental Biology. 490:86-99.
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 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.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping