ArticlePLoS computational biology2021
A deep learning algorithm for 3D cell detection in whole mouse brain image datasets.
Article in PLoS computational biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed, 99 citations in OpenAlex.
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- VASCilia is an open-source, deep learning-based tool for 3D analysis of cochlear hair cell stereocilia bundles.PLoS biology · 2026Article
- A Computational Protocol for Whole Brain Histology Imaging.Methods in molecular biology (Clifton, N.J.) · 2026Article
- VASCilia (Vision Analysis StereoCilia): A Napari Plugin for Deep Learning-Based 3D Analysis of Cochlear Hair Cell Stereocilia Bundles.bioRxiv : the preprint server for biology · 2025Article
- Sexually dimorphic mechanisms of VGLUT-mediated protection from dopaminergic neurodegeneration.bioRxiv : the preprint server for biology · 2025Article
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- Brain-wide 3D neuron detection and mapping with deep learning.Neurophotonics · 2025Article
- Layer 6 corticocortical neurons are a major route for intra- and interhemispheric feedback.eLife · 2025Article
- A deep learning pipeline for three-dimensional brain-wide mapping of local neuronal ensembles in teravoxel light-sheet microscopy.Nature methods · 2025Article
- ClearFinder: a Python GUI for annotating cells in cleared mouse brain.BMC bioinformatics · 2025Article
- Cutting-edge AI tools revolutionizing scientific research in life sciences.Biotechnologia · 2025Review
- Software and pipelines for registration and analyses of rodent brain image data in reference atlas space.Frontiers in neuroinformatics · 2025Article
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 3 countries.
Funding
Abstract
Understanding the function of the nervous system necessitates mapping the spatial distributions of its constituent cells defined by function, anatomy or gene expression. Recently, developments in tissue preparation and microscopy allow cellular populations to be imaged throughout the entire rodent brain. However, mapping these neurons manually is prone to bias and is often impractically time consuming. Here we present an open-source algorithm for fully automated 3D detection of neuronal somata in mouse whole-brain microscopy images using standard desktop computer hardware. We demonstrate the applicability and power of our approach by mapping the brain-wide locations of large populations of cells labeled with cytoplasmic fluorescent proteins expressed via retrograde trans-synaptic viral infection.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.