ArticleProceedings of the National Academy of Sciences of the United States of America2020
Mapping mesoscale axonal projections in the mouse brain using a 3D convolutional network.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
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Who cites it
59 citing papers in PubMed, 99 citations in OpenAlex.
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- Spatial and network principles behind neural generation of locomotion.Nature communications · 2026Article
- Glycogen drives the sensory activation of POMC neurons.Nature metabolism · 2026Article
- The prefrontal cortex controls memory organization in the hippocampus.Nature neuroscience · 2026Article
- DMC-BrainMap is an open-source, end-to-end tool for multi-feature brain mapping in different species.Cell reports methods · 2026Article
- Sex and Stress Govern the Function and Innervation of a Basolateral Amygdala to Nucleus Accumbens Corticotropin-Releasing Hormone/GABA-Expressing Projection.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2026Article
- Whole-brain cFos mapping reveals the paraventricular thalamus as a key node for stress-enhanced fear learning.Frontiers in behavioral neuroscience · 2026Article
- BVLab-analyzer: a unified visual toolbox for terabyte-scale whole-brain cell detection, neuron reconstruction, and vascular network extraction.Frontiers in neuroinformatics · 2026Article
- Reconstructing the human brain's wiring diagram from axons up.Trends in neurosciences · 2026Review
- Quantitative profiling of whole-brain connectomes at single-axon resolution using deep learning and high-resolution light sheet microscopy.bioRxiv : the preprint server for biology · 2025Article
- Chemoarchitectural studies of the rat hypothalamus and zona incerta.bioRxiv : the preprint server for biology · 2025Article
- Automatic and accurate reconstruction of long-range axonal projections of single-neuron in mouse brain.eLife · 2025Article
- Concerted actions of distinct serotonin neurons orchestrate female pup care behavior.Research square · 2025Article
- Concerted actions of distinct serotonin neurons orchestrate female pup care behavior.bioRxiv : the preprint server for biology · 2025Article
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- Organization and development of bilateral somatosensory feedback projections in mice.iScience · 2025Article
- AxoDen: An Algorithm for the Automated Quantification of Axonal Density in Defined Brain Regions.eNeuro · 2025Article
Corrections and comments
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
Abstract
The projection targets of a neuronal population are a key feature of its anatomical characteristics. Historically, tissue sectioning, confocal microscopy, and manual scoring of specific regions of interest have been used to generate coarse summaries of mesoscale projectomes. We present here TrailMap, a three-dimensional (3D) convolutional network for extracting axonal projections from intact cleared mouse brains imaged by light-sheet microscopy. TrailMap allows region-based quantification of total axon content in large and complex 3D structures after registration to a standard reference atlas. The identification of axonal structures as thin as one voxel benefits from data augmentation but also requires a loss function that tolerates errors in annotation. A network trained with volumes of serotonergic axons in all major brain regions can be generalized to map and quantify axons from thalamocortical, deep cerebellar, and cortical projection neurons, validating transfer learning as a tool to adapt the model to novel categories of axonal morphology. Speed of training, ease of use, and accuracy improve over existing tools without a need for specialized computing hardware. Given the recent emphasis on genetically and functionally defining cell types in neural circuit analysis, TrailMap will facilitate automated extraction and quantification of axons from these specific cell types at the scale of the entire mouse brain, an essential component of deciphering their connectivity.
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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.