ArticleeLife2024
Machine learning of dissection photographs and surface scanning for quantitative 3D neuropathology.
Abstract read
In one paragraph
Article in eLife, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
0numbers the graph read from it
0cells of the map it votes in
8citing papers in PubMed
–field-weighted citation impact
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
8 citing papers in PubMed.
- Improving Neuropathological Reconstruction Fidelity via AI Slice Imputation.Research square · 2026Article
- A public generalizable AI tool for automated segmentation of coronal brain tissue slabs for 3D neuropathology.PloS one · 2026Article
- UC Irvine's Brain Initiative Cell Atlas Network (BICAN) Brain Procurement Program for the Center for Multiomic Human Brain Cell Atlas Project.bioRxiv : the preprint server for biology · 2025Article
- Celebrating neuropathology's contributions to Alzheimer's Disease Research Centers.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2025Article
- Pseudo-Rendering for Resolution and Topology-Invariant Cortical Parcellation.Machine learning in medical imaging. MLMI (Workshop) · 2025Article
- Synthetic data in generalizable, learning-based neuroimaging.Imaging neuroscience (Cambridge, Mass.) · 2024Article
- Inferotemporal face patches are histo-architectonically distinct.Cell reports · 2024Article
- An Australian brain bank and the future of alcohol and major neuropsychiatric disorders research.Frontiers in neurologyReview
Corrections and comments
- Update of
Authors and funding
26 authors.
Harshvardhan GazulaMartinos Center for Biomedical Imaging, MGH and Harvard Medical School, Charlestown, United States.
Henry F J TregidgoCentre for Medical Image Computing, University College London, London, United Kingdom.ORCID https://orcid.org/0000-0002-3509-8154
Benjamin BillotComputer Science and Artificial Intelligence Laboratory, MIT, Cambridge, United States.
Yael BalbastreMartinos Center for Biomedical Imaging, MGH and Harvard Medical School, Charlestown, United States.
Jonathan Williams-RamirezMartinos Center for Biomedical Imaging, MGH and Harvard Medical School, Charlestown, United States.
Rogeny HerisseMartinos Center for Biomedical Imaging, MGH and Harvard Medical School, Charlestown, United States.
Lucas J Deden-BinderMartinos Center for Biomedical Imaging, MGH and Harvard Medical School, Charlestown, United States.
Adria CasamitjanaCentre for Medical Image Computing, University College London, London, United Kingdom.
Erica J MeliefBioRepository and Integrated Neuropathology (BRaIN) Laboratory and Precision Neuropathology Core, UW School of Medicine, Seattle, United States.
Caitlin S LatimerBioRepository and Integrated Neuropathology (BRaIN) Laboratory and Precision Neuropathology Core, UW School of Medicine, Seattle, United States.
Mitchell D KilgoreBioRepository and Integrated Neuropathology (BRaIN) Laboratory and Precision Neuropathology Core, UW School of Medicine, Seattle, United States.ORCID https://orcid.org/0000-0003-1101-6924
Mark MontineBioRepository and Integrated Neuropathology (BRaIN) Laboratory and Precision Neuropathology Core, UW School of Medicine, Seattle, United States.
Eleanor RobinsonCentre for Medical Image Computing, University College London, London, United Kingdom.
Emily BlackburnCentre for Medical Image Computing, University College London, London, United Kingdom.
Michael S MarshallMassachusetts Alzheimer Disease Research Center, MGH and Harvard Medical School, Charlestown, United States.
Theresa R ConnorsMassachusetts Alzheimer Disease Research Center, MGH and Harvard Medical School, Charlestown, United States.
Derek H OakleyMassachusetts Alzheimer Disease Research Center, MGH and Harvard Medical School, Charlestown, United States.
Matthew P FroschMassachusetts Alzheimer Disease Research Center, MGH and Harvard Medical School, Charlestown, United States.
Sean I YoungMartinos Center for Biomedical Imaging, MGH and Harvard Medical School, Charlestown, United States.
Koen Van LeemputMartinos Center for Biomedical Imaging, MGH and Harvard Medical School, Charlestown, United States.
Adrian V DalcaMartinos Center for Biomedical Imaging, MGH and Harvard Medical School, Charlestown, United States.
Bruce FischlMartinos Center for Biomedical Imaging, MGH and Harvard Medical School, Charlestown, United States.
Christine L MacDonaldDepartment of Neurological Surgery, UW School of Medicine, Seattle, United States.
C Dirk KeeneBioRepository and Integrated Neuropathology (BRaIN) Laboratory and Precision Neuropathology Core, UW School of Medicine, Seattle, United States.ORCID https://orcid.org/0000-0002-5291-1469
Bradley T HymanMassachusetts Alzheimer Disease Research Center, MGH and Harvard Medical School, Charlestown, United States.ORCID https://orcid.org/0000-0002-7959-9401
Juan E IglesiasMartinos Center for Biomedical Imaging, MGH and Harvard Medical School, Charlestown, United States.ORCID https://orcid.org/0000-0001-7569-173X
Funding
Functionally guided adult whole brain cell atlas in human and NHPUM1MH130981 · NIMH · ALLEN INSTITUTE · PI Ed Lein, Hongkui Zeng · 2022 to 2026
$91.9MTopographic, cell type and molecular pathway characterization ofAlzheimer's disease using single cell transcriptomics and epigenomicsU19AG060909 · NIA · ALLEN INSTITUTE · PI Michael Hawrylycz · 2020 to 2026
$83.6MTranslational pharmacoepidemiology: neuroprotection and neurotoxicity of antihypertensives and strong anticholinergicsU19AG066567 · NIA · KAISER FOUNDATION RESEARCH INSTITUTE · PI Paul K Crane, Andrea Z. LaCroix · 2021 to 2026
$80.4MResearch Education ComponentP30AG062421 · NIA · MASSACHUSETTS GENERAL HOSPITAL · PI Sudeshna Das · 2019 to 2026
$36.5MUniversity of Washington Alzheimer's Disease Research CenterP30AG066509 · NIA · UNIVERSITY OF WASHINGTON · PI SUMAN JAYADEV · 2020 to 2026
$29.0MEPIDEMIOLOGY OF DEMENTIA IN THE FRAMINGHAM STUDYR01AG008122 · NIA · BOSTON UNIVERSITY MEDICAL CAMPUS · PI AU, RHODA, SESHADRI, SUDHA · 1989 to 2015
$14.4MMRI, Genetics &Cognitive Precursors of AD &DementiaR01AG016495 · NIA · BOSTON UNIVERSITY MEDICAL CAMPUS · PI AU, RHODA · 1999 to 2016
$12.5MThe Human Connectome Project (HCP)U01MH093765 · NIMH · MASSACHUSETTS GENERAL HOSPITAL · PI ROSEN, BRUCE R · 2010 to 2014
$12.1MTraining and Dissemination CoreP41EB030006 · NIBIB · MASSACHUSETTS GENERAL HOSPITAL · PI BRUCE R ROSEN · 2020 to 2026
$10.9MImaging and Analysis Techniques to Construct a Cell Census Atlas of the Human Brain Admin SupplementU01MH117023 · NIMH · MASSACHUSETTS GENERAL HOSPITAL · PI BOAS, DAVID A, FISCHL, BRUCE · 2018 to 2022
$7.6MNeuropathology of CTE and Delayed Effects of TBI: Toward In-Vivo DiagnosticsU01NS086625 · NINDS · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI DAMS-O'CONNOR, KRISTEN · 2014 to 2017
$6.1MFreeSurfer Development, Maintenance, and HardeningR01EB023281 · NIBIB · MASSACHUSETTS GENERAL HOSPITAL · PI Bruce Fischl, Douglas Nowlin Greve · 2016 to 2026
$5.6MAlzheimer's Research UK ARUK-IRG2019A-003European Union ERC Starting Grant 677697NCRR NIH HHS S10 RR019307NCRR NIH HHS S10 RR023043NCRR NIH HHS S10 RR023401NIA NIH HHS K08 AG065426NIA NIH HHS P30 AG062421NIA NIH HHS P30AG062421NIA NIH HHS P30 AG066509NIA NIH HHS R01 AG008122NIA NIH HHS R01 AG016495NIA NIH HHS R01 AG064027NIA NIH HHS R01 AG070988NIA NIH HHS R01AG070988NIA NIH HHS R56 AG064027NIA NIH HHS U19 AG060909NIA NIH HHS U19 AG066567NIBIB NIH HHS P41 EB030006NIBIB NIH HHS R01 EB006758NIBIB NIH HHS R01 EB019956NIBIB NIH HHS R01 EB023281NIBIB NIH HHS R01 EB031114NIBIB NIH HHS R21 EB018907NIH HHS 1R01AG064027NIH HHS 1R01AG070988NIH HHS 1R01EB023281NIH HHS 1R56AG064027NIH HHS 1RF1MH123195NIH HHS 1S10RR019307NIH HHS 1S10RR023043NIH HHS 1S10RR023401NIH HHS 5R01AG008122NIH HHS 5U01MH093765NIH HHS 5U01NS086625NIH HHS 5U24NS10059103NIH HHS K08AG065426NIH HHS P30AG066509 (UW ADRC)NIH HHS P41EB030006NIH HHS R01AG016495NIH HHS R01EB006758NIH HHS R01EB019956NIH HHS R01EB031114NIH HHS R01 MH121885NIH HHS R01 MH123195NIH HHS R01NS0525851NIH HHS R01NS070963NIH HHS R01NS083534NIH HHS R01NS105820NIH HHS R01NS112161NIH HHS R21EB018907NIH HHS R21NS072652NIH HHS RF1MH123195NIH HHS U01MH117023NIH HHS U19AG060909NIH HHS U19AG066567NIH HHS UM1MH130981NIMH NIH HHS RF1 MH121885NIMH NIH HHS RF1 MH123195NIMH NIH HHS U01 MH093765NIMH NIH HHS U01 MH117023NIMH NIH HHS UM1 MH130981NINDS NIH HHS R01 NS070963NINDS NIH HHS R01 NS083534NINDS NIH HHS R01 NS105820NINDS NIH HHS R01 NS112161NINDS NIH HHS R21 NS072652NINDS NIH HHS U01 NS086625Politècnica de Catalunya Grant Ref 2021UPC-MS-67573
Abstract
We present open-source tools for three-dimensional (3D) analysis of photographs of dissected slices of human brains, which are routinely acquired in brain banks but seldom used for quantitative analysis. Our tools can: (1) 3D reconstruct a volume from the photographs and, optionally, a surface scan; and (2) produce a high-resolution 3D segmentation into 11 brain regions per hemisphere (22 in total), independently of the slice thickness. Our tools can be used as a substitute for ex vivo magnetic resonance imaging (MRI), which requires access to an MRI scanner, ex vivo scanning expertise, and considerable financial resources. We tested our tools on synthetic and real data from two NIH Alzheimer's Disease Research Centers. The results show that our methodology yields accurate 3D reconstructions, segmentations, and volumetric measurements that are highly correlated to those from MRI. Our method also detects expected differences between
Indexed as
Alzheimer DiseaseBrainImaging, Three-DimensionalMachine LearningDissectionHumansMagnetic Resonance ImagingNeuroimagingNeuropathologyPhotographydissection photographyhumanmachine learningneurosciencesurface scanningvolumetry
Identifiers
What OpenQuestion holds
Textmetadata
LicenceCC BY
Read underepoch 390
Registered trials
None linked
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.