ArticleCell reports methods2023
COMBINe enables automated detection and classification of neurons and astrocytes in tissue-cleared mouse brains.
Article in Cell reports methods, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed, 8 citations in OpenAlex.
- CellPheno: A High-throughput Computational Platform for Quantifying Cellular Resolution Whole Brain Microscopy Images.bioRxiv : the preprint server for biology · 2026Article
- Spiner, deep learning-based automated detection of spiral ganglion neurons in intact cochleae.iScience · 2025Article
- A deep learning pipeline for three-dimensional brain-wide mapping of local neuronal ensembles in teravoxel light-sheet microscopy.Nature methods · 2025Article
- Intelligent Beam Optimization for Light-Sheet Fluorescence Microscopy through Deep Learning.Intelligent computing (Washington, D.C.) · 2024Article
- Enhancing Light-Sheet Fluorescence Microscopy Illumination Beams through Deep Design Optimization.bioRxiv : the preprint server for biology · 2023Article
- Deep learning-based adaptive optics for light sheet fluorescence microscopy.Biomedical optics express · 2023Article
- Bulk and mosaic deletions ofiScience · 2023Article
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
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.
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