2023 journal article
COMBINe enables automated detection and classification of neurons and astrocytes in tissue-cleared mouse brains
CELL REPORTS METHODS, 3(4).
MeSH headings : Animals; Mice; Astrocytes; Excipients; Microscopy, Fluorescence; Neurons; Prosencephalon
TL;DR:
An automated workflow to map sparsely labeled neurons and astrocytes in genetically distinct mouse forebrains using mosaic analysis with double markers (MADM) is presented and the regional and subregional effects of MADM-based deletion of the epidermal growth factor receptor (EGFR) are quantitatively analyzed.
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open access via doi.org (publisher)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: May 30, 2023
Tissue clearing renders entire organs transparent to accelerate whole-tissue imaging; for example, with light-sheet fluorescence microscopy. Yet, challenges remain in analyzing the large resulting 3D datasets that consist of terabytes of images and information on millions of labeled cells. Previous work has established pipelines for automated analysis of tissue-cleared mouse brains, but the focus there was on single-color channels and/or detection of nuclear localized signals in relatively low-resolution images. Here, we present an automated workflow (COMBINe, Cell detectiOn in Mouse BraIN) to map sparsely labeled neurons and astrocytes in genetically distinct mouse forebrains using mosaic analysis with double markers (MADM). COMBINe blends modules from multiple pipelines with RetinaNet at its core. We quantitatively analyzed the regional and subregional effects of MADM-based deletion of the epidermal growth factor receptor (EGFR) on neuronal and astrocyte populations in the mouse forebrain.