ArticleFrontiers in neuroinformatics2018
Mapping Histological Slice Sequences to the Allen Mouse Brain Atlas Without 3D Reconstruction.
Article in Frontiers in neuroinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Article
- Integrating optogenetic fMRI and spatial transcriptomics to reveal circuit-specific gene signatures in fronto- and hippo-thalamic networks.Nature communications · 2026Article
- Biophysical simulation enables segmentation and nervous system atlas mapping for image first spatial omics.NPJ systems biology and applications · 2025Article
- Solving the where problem and quantifying geometric variation in neuroanatomy using generative diffeomorphic mapping.Nature communications · 2025Article
- Mapping brain-wide activity networks: brainways as a tool for neurobiological discovery.Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology · 2025Article
- Deconstruction of a spino-brain-spinal cord circuit drives chronic mechanical pain.Research square · 2025Article
- Bell Jar: A Semiautomated Registration and Cell Counting Tool for Mouse Neurohistology Analysis.eNeuro · 2025Article
- An extended and improved CCFv3 annotation and Nissl atlas of the entire mouse brain.Imaging neuroscience (Cambridge, Mass.) · 2025Article
- Multimodal Mass Spectrometry Imaging in Atlas Building: A Review.Seminars in nephrology · 2024Review
- D-LMBmap: a fully automated deep-learning pipeline for whole-brain profiling of neural circuitry.Nature methods · 2023Article
- DeepSlice: rapid fully automatic registration of mouse brain imaging to a volumetric atlas.Nature communications · 2023Article
- SMDB: a Spatial Multimodal Data Browser.Nucleic acids research · 2023Article
- Localization and Registration of 2D Histological Mouse Brain Images in 3D Atlas Space.Neuroinformatics · 2023Article
- giRAff: an automated atlas segmentation tool adapted to single histological slices.Frontiers in neuroscience · 2023Article
- Review
- 3D Dynamic Spatiotemporal Atlas of the Vocal Tract during Consonant-Vowel Production from 2D Real Time MRI.Journal of imaging · 2022Article
- BoutonNet: an automatic method to detect anterogradely labeled presynaptic boutons in brain tissue sections.Brain structure & function · 2022Article
- A diffusion MRI-based spatiotemporal continuum of the embryonic mouse brain for probing gene-neuroanatomy connections.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Article
- Macroscopic Structural and Connectome Mapping of the Mouse Brain Using Diffusion Magnetic Resonance Imaging.Bio-protocol · 2021Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Histological brain slices are widely used in neuroscience to study the anatomical organization of neural circuits. Systematic and accurate comparisons of anatomical data from multiple brains, especially from different studies, can benefit tremendously from registering histological slices onto a common reference atlas. Most existing methods rely on an initial reconstruction of the volume before registering it to a reference atlas. Because these slices are prone to distortions during the sectioning process and often sectioned with non-standard angles, reconstruction is challenging and often inaccurate. Here we describe a framework that maps each slice to its corresponding plane in the Allen Mouse Brain Atlas (2015) to build a plane-wise mapping and then perform 2D nonrigid registration to build a pixel-wise mapping. We use the L2 norm of the histogram of oriented gradients difference of two patches as the similarity metric for both steps and a Markov random field formulation that incorporates tissue coherency to compute the nonrigid registration. To fix significantly distorted regions that are misshaped or much smaller than the control grids, we train a context-aggregation network to segment and warp them to their corresponding regions with thin plate spline. We have shown that our method generates results comparable to an expert neuroscientist and is significantly better than reconstruction-first approaches. Code and sample dataset are available at sites.google.com/view/brain-mapping.
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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.