Protocol for brain and ventricle volume comparison after clearing and light-sheet microscopy in mice

Abstract

Analysis of brain and ventricular volumes provides insights into the physiological and pathological progression of brain development and aging, but accessible and cost-effective approaches are lacking. Here, we present a workflow to quantify relative brain and ventricular volumes in unsectioned cleared mouse brains following fluorescent detection of brain tissue and ventricle lining. We describe steps for brain harvesting, clearing, imaging by light-sheet microscopy, image resampling, and ventricle annotation, and comparing brains from adult, neonate, germ-free, and hydrocephalic mouse models.

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BibTeX RIS

BibTeX

@article{blasmedina2026protocol,
  title = {{Protocol for brain and ventricle volume comparison after clearing and light-sheet microscopy in mice}},
  author = {Ana Blas-Medina and Minh Son Phan and Samir Ali-Moussa and Nathalie Spassky and Julien Fernandes and Jean-Yves Tinevez and Aleksandra Deczkowska and Laetitia Travier},
  journal = {STAR Protocols},
  year = {2026},
  month = oct,
  doi = {10.1016/j.xpro.2026.104877},
  url = {https://pasteur.hal.science/pasteur-05835981v1},
  note = {CC BY 4.0},
}

RIS

TY  - JOUR
TI  - Protocol for brain and ventricle volume comparison after clearing and light-sheet microscopy in mice
AU  - Ana Blas-Medina
AU  - Minh Son Phan
AU  - Samir Ali-Moussa
AU  - Nathalie Spassky
AU  - Julien Fernandes
AU  - Jean-Yves Tinevez
AU  - Aleksandra Deczkowska
AU  - Laetitia Travier
PY  - 2026
DA  - 2026/10/22
JO  - STAR Protocols
DO  - 10.1016/j.xpro.2026.104877
UR  - https://pasteur.hal.science/pasteur-05835981v1
AB  - Analysis of brain and ventricular volumes provides insights into the physiological and pathological progression of brain development and aging, but accessible and cost-effective approaches are lacking. Here, we present a workflow to quantify relative brain and ventricular volumes in unsectioned cleared mouse brains following fluorescent detection of brain tissue and ventricle lining. We describe steps for brain harvesting, clearing, imaging by light-sheet microscopy, image resampling, and ventricle annotation, and comparing brains from adult, neonate, germ-free, and hydrocephalic mouse models.
SN  - 2666-1667
ER  -

Abstract

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