ReviewFrontiers in neuroanatomy2021
Seeing the Forest and Its Trees Together: Implementing 3D Light Microscopy Pipelines for Cell Type Mapping in the Mouse Brain.
Review in Frontiers in neuroanatomy, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
17 citing papers in PubMed, 20 citations in OpenAlex.
- Stroke drives glioma progression through the emergence of tumor-associated astrocytes with reduced CaNature cancer · 2026Article
- Dendritome mapping reveals the spatial organization of striatal neuron morphology.Nature neuroscience · 2025Article
- epDevAtlas: mapping GABAergic cells and microglia in the early postnatal mouse brain.Nature communications · 2025Article
- Chemoarchitectural studies of the rat hypothalamus and zona incerta.bioRxiv : the preprint server for biology · 2025Article
- Traditions of Excellence: neuroanatomy at the forefront of the new era.Anatomical science international · 2025Review
- Brain-wide connectivity and novelty response of the dorsal endopiriform nucleus in mice.Cell reports · 2025Article
- Developmental mouse brain common coordinate framework.Nature communications · 2024Article
- Current and future applications of light-sheet imaging for identifying molecular and developmental processes in autism spectrum disorders.Molecular psychiatry · 2024Review
- epDevAtlas: Mapping GABAergic cells and microglia in postnatal mouse brains.bioRxiv : the preprint server for biology · 2023Article
- Successful 3D imaging of cleared biological samples with light sheet fluorescence microscopy.The Journal of cell biology · 2023Review
- Developmental Mouse Brain Common Coordinate Framework.bioRxiv : the preprint server for biology · 2023Article
- AtOM, an ontology model to standardize use of brain atlases in tools, workflows, and data infrastructures.Scientific data · 2023Article
- Combining tissue clearing and Fluoro-Jade C labeling for neurotoxicity assessments.Experimental biology and medicine (Maywood, N.J.) · 2023Article
- Building bridges: simultaneous multimodal neuroimaging approaches for exploring the organization of brain networks.Neurophotonics · 2022Review
- Advancements in the Quest to Map, Monitor, and Manipulate Neural Circuitry.Frontiers in neural circuits · 2022Review
- Fluorescent transgenic mouse models for whole-brain imaging in health and disease.Frontiers in molecular neuroscience · 2022Review
- Digital Brain Maps and Virtual Neuroscience: An Emerging Role for Light-Sheet Fluorescence Microscopy in Drug Development.Frontiers in neuroscience · 2022Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
The brain is composed of diverse neuronal and non-neuronal cell types with complex regional connectivity patterns that create the anatomical infrastructure underlying cognition. Remarkable advances in neuroscience techniques enable labeling and imaging of these individual cell types and their interactions throughout intact mammalian brains at a cellular resolution allowing neuroscientists to examine microscopic details in macroscopic brain circuits. Nevertheless, implementing these tools is fraught with many technical and analytical challenges with a need for high-level data analysis. Here we review key technical considerations for implementing a brain mapping pipeline using the mouse brain as a primary model system. Specifically, we provide practical details for choosing methods including cell type specific labeling, sample preparation (e.g., tissue clearing), microscopy modalities, image processing, and data analysis (e.g., image registration to standard atlases). We also highlight the need to develop better 3D atlases with standardized anatomical labels and nomenclature across species and developmental time points to extend the mapping to other species including humans and to facilitate data sharing, confederation, and integrative analysis. In summary, this review provides key elements and currently available resources to consider while developing and implementing high-resolution mapping methods.
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What OpenQuestion holds
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.