ArticleeLife2021
Constructing and optimizing 3D atlases from 2D data with application to the developing mouse brain.
Article in eLife, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Spatial transcriptomics implicates the thalamus and cortex in autism and schizophrenia.bioRxiv : the preprint server for biology · 2026Article
- epDevAtlas: mapping GABAergic cells and microglia in the early postnatal mouse brain.Nature communications · 2025Article
- scBSP: a fast and accurate tool for identifying spatially variable features from high-resolution spatial omics data.Bioinformatics (Oxford, England) · 2025Article
- Article
- DeMBA: a developmental atlas for navigating the mouse brain in space and time.Nature communications · 2025Article
- scBSP: A fast and accurate tool for identifying spatially variable features from high-resolution spatial omics data.bioRxiv : the preprint server for biology · 2025Article
- An extended and improved CCFv3 annotation and Nissl atlas of the entire mouse brain.Imaging neuroscience (Cambridge, Mass.) · 2025Article
- Sialic acid and PirB are not required for targeting of neural circuits by neurotropic mammalian orthoreovirus.mSphere · 2024Article
- Developmental mouse brain common coordinate framework.Nature communications · 2024Article
- Connecto-informatics at the mesoscale: current advances in image processing and analysis for mapping the brain connectivity.Brain informatics · 2024Review
- Prenatal delivery of a therapeutic antisense oligonucleotide achieves broad biodistribution in the brain and ameliorates Angelman syndrome phenotype in mice.Molecular therapy : the journal of the American Society of Gene Therapy · 2024Article
- epDevAtlas: Mapping GABAergic cells and microglia in postnatal mouse brains.bioRxiv : the preprint server for biology · 2023Article
- Dimension-agnostic and granularity-based spatially variable gene identification using BSP.Nature communications · 2023Article
- Developmental Mouse Brain Common Coordinate Framework.bioRxiv : the preprint server for biology · 2023Article
- Pinpoint: trajectory planning for multi-probe electrophysiology and injections in an interactive web-based 3D environment.bioRxiv : the preprint server for biology · 2023Article
- Dimension-agnostic and granularity-based spatially variable gene identification.bioRxiv : the preprint server for biology · 2023Article
- Dimension-agnostic and granularity-based spatially variable gene identification.Research square · 2023Article
- A neuroscientist's guide to using murine brain atlases for efficient analysis and transparent reporting.Frontiers in neuroinformatics · 2023Article
- A Critical Review of Zebrafish Neurological Disease Models-1. The Premise: Neuroanatomical, Cellular and Genetic Homology and Experimental Tractability.Oxford open neuroscience · 2023Article
- Whole-Brain Single-Cell Imaging and Analysis of Intact Neonatal Mouse Brains Using MRI, Tissue Clearing, and Light-Sheet Microscopy.Journal of visualized experiments : JoVE · 2022Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
3D imaging data necessitate 3D reference atlases for accurate quantitative interpretation. Existing computational methods to generate 3D atlases from 2D-derived atlases result in extensive artifacts, while manual curation approaches are labor-intensive. We present a computational approach for 3D atlas construction that substantially reduces artifacts by identifying anatomical boundaries in the underlying imaging data and using these to guide 3D transformation. Anatomical boundaries also allow extension of atlases to complete edge regions. Applying these methods to the eight developmental stages in the Allen Developing Mouse Brain Atlas (ADMBA) led to more comprehensive and accurate atlases. We generated imaging data from 15 whole mouse brains to validate atlas performance and observed qualitative and quantitative improvement (37% greater alignment between atlas and anatomical boundaries). We provide the pipeline as the MagellanMapper software and the eight 3D reconstructed ADMBA atlases. These resources facilitate whole-organ quantitative analysis between samples and across development.
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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.