Evidence map›Paper›PMID 41040372›Full record

ArticlebioRxiv : the preprint server for biology2025

Fast segmentation with the NextBrain histological atlas.

Oula Puonti, Jackson Nolan, Robert Dicamillo, Yael Balbastre, Adria Casamitjana, Matteo Mancini, Eleanor Robinson, Loic Peter, Roberto Annunziata, Juri Althonayan and 16 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

26 authors.

Oula PuontiDanish Research Centre for Magnetic Resonance, Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital - Amager and Hvidovre, Copenhagen, Denmark.
Jackson NolanAthinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States.
Robert DicamilloAthinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States.
Yael BalbastreAthinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States.
Adria CasamitjanaDepartment of Medical Physics and Biomedical Engineering, University College London, London, United Kingdom.
Matteo ManciniDepartment of Medical Physics and Biomedical Engineering, University College London, London, United Kingdom.
Eleanor RobinsonDepartment of Medical Physics and Biomedical Engineering, University College London, London, United Kingdom.
Loic PeterDepartment of Medical Physics and Biomedical Engineering, University College London, London, United Kingdom.
Roberto AnnunziataDepartment of Medical Physics and Biomedical Engineering, University College London, London, United Kingdom.
Juri AlthonayanDepartment of Medical Physics and Biomedical Engineering, University College London, London, United Kingdom.
Shauna CrampsieDepartment of Medical Physics and Biomedical Engineering, University College London, London, United Kingdom.
Emily BlackburnDepartment of Medical Physics and Biomedical Engineering, University College London, London, United Kingdom.
Benjamin BillotDepartment of Medical Physics and Biomedical Engineering, University College London, London, United Kingdom.
Alessia AtzeniDepartment of Medical Physics and Biomedical Engineering, University College London, London, United Kingdom.
Peter SchmidtAdvanced Research Computing Centre, University College London, London, United Kingdom.
James HughesAdvanced Research Computing Centre, University College London, London, United Kingdom.
Jean AugustinackAthinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States.
Brian EdlowAthinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States.ORCID 0000-0001-7235-8456
Lilla ZölleiAthinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States.
David L ThomasDementia Research Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom.
Dorit KliemannDepartment of Psychological and Brain Sciences, University of Iowa, Iowa City, IA, United States.
Martina BocchettaDementia Research Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom.
Catherine StrandQueen Square Brain Bank for Neurological Disorders, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom.
Janice HoltonQueen Square Brain Bank for Neurological Disorders, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom.
Zane JaunmuktaneQueen Square Brain Bank for Neurological Disorders, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom.
Juan Eugenio IglesiasAthinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States.

Funding

Functionally guided adult whole brain cell atlas in human and NHPUM1MH130981 · NIMH · ALLEN INSTITUTE · PI Ed Lein, Hongkui Zeng · 2022 to 2026
$91.9M
Acquisition-independent machine learning for morphometric analysis of underrepresented aging populations with clinical and low-field brain MRIRF1AG080371 · NIA · MASSACHUSETTS GENERAL HOSPITAL · PI Juan Eugenio Iglesias Gonzalez · 2023 to 2026
$4.0M
Diagnosing the undiagnosable: studies of Alzheimer disease mimics and confounders via "neuropathometry" of dissection photos with 3D scanningR01AG070988 · NIA · MASSACHUSETTS GENERAL HOSPITAL · PI IGLESIAS GONZALEZ, JUAN EUGENIO · 2021 to 2025
$2.7M
Open-source software for multi-scale mapping of the human brainRF1MH123195 · NIMH · MASSACHUSETTS GENERAL HOSPITAL · PI FISCHL, BRUCE, IGLESIAS GONZALEZ, JUAN EUGENIO · 2020 to 2020
$2.0M
Measuring Brain Health Using Low-Field Portable MRIR21NS138995 · NINDS · YALE UNIVERSITY · PI DE HAVENON, ADAM H. · 2024 to 2024
$477k
NIA NIH HHS R01 AG070988NIA NIH HHS RF1 AG080371NIMH NIH HHS RF1 MH123195NIMH NIH HHS UM1 MH130981NINDS NIH HHS R21 NS138995Wellcome Trust
6 · The paper itself

Abstract

Structural brain analysis at the subregion level offers critical insights into healthy aging and neurodegenerative diseases. The NextBrain histological atlas was recently introduced to support such fine-grained investigations, but its existing Bayesian segmentation framework remains computationally prohibitive, particularly for large-scale studies. We present a new, open-source tool that dramatically accelerates segmentation using a hybrid approach combining: machine learning, contrast-adaptive segmentation; target-specific image synthesis; and fast diffeomorphic registration (all three with GPU support). Our method enables highly granular segmentation of brain MRI scans of any resolution and contrast (

Indexed as

Brain MRI segmentationDomain-agnostic neuroimagingHistological atlas

Identifiers

PMID41040372
PMCPMC12485876

What OpenQuestion holds

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Registered trials

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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.