Twitter Email Top

BigBrain References

Posters, Publications, and News involving the BigBrain

  • Publications

    Schiffer C, Amunts K, Harmeling S, Dickscheid T (2021) Contrastive Representation Learning for Whole Brain Cytoarchitectonic Mapping in Histological Human Brain Sections,. International Symposium on Biomedical Imaging (ISBI 2021), link
    Schiffer C, Spitzer H, Kiwitz K, Unger N, Wagstyl K, Evans AC, Harmeling S, Amunts K, Dickscheid T (2021) Convolutional Neural Networks for cytoarchitectonic brain mapping at large scale. NeuroImage, 2021, 118327, ISSN 1053-8119, doi
    Valdés-Sosa PA, Galan L, Bosch-Bayard J, Bringas-Vega ML, Aubert-Vazquez E, Rodriguez-Gil I, Das S, Madjar C, Virues-Alba T, Mohades Z, MacIntyre LC, Rogers C, Brown S, Valdes-Urrutia L, Evans AC, Valdés-Sosa MJ (2021) The Cuban Human Brain Mapping Project, a young and middle age population-based EEG, MRI, and cognition dataset. Nature Scientific Data, accepted Jan/2021.
    Zachlod D, Rüttgers B, Bludau S, Mohlberg H, Langner R, Zilles K, Amunts K (2020) Four new cytoarchitectonic areas surrounding the primary and early auditory cortex in human brains. DCortex, 128:1-21 doi: link
    Royer J, Paquola C, Larivière S, Vos de Wael R, Tavakol S, Lowe AJ, Benkarim O, Evans AC, Bzdok D, Smallwood J, Frauscher B, Bernhardt BC (2020) Myeloarchitecture gradients in the human insula: Histological underpinnings and association to intrinsic functional connectivity. NeuroImage, 216:116859 doi: link
    Bosch-Bayard J, Galan L, Aubert E, Virues T, Valdés-Sosa PA (2020) Resting state healthy EEG: the first wave of the Cuban normative database. Data Report, Front. Neurosci. - Brain Imaging Methods, 14:555119. doi: link
    Paquola C, Seidlitz J, Benkarim O, Royer J, Klimes P, Bethlehem RAI, Larivière S, Vos de Wael R, Rodríguez-Cruces R, Hall JA, Frauscher B, Smallwood J, Bernhardt BC (2020) AA multi-scale cortical wiring space links cellular architecture and functional dynamics in the human brain. PLoS Biology 18(11): e3000979. link
    Kiwitz K, Schiffer C, Spitzer H, Dickscheid T, Amunts K (2020) Deep learning networks reflect cytoarchitectonic features used in brain mapping. Sci Rep 10, 22039. doi: link
    Amunts K, Mohlberg H, Bludau S, Zilles K (2020) Julich-Brain: A 3D probabilistic atlas of the human brain’s cytoarchitecture. Science, 369(6506):988-992 doi:link
    Wagstyl K, Larocque S, Cucurull G, Lepage C, Cohen JP, Bludau S, Palomero-Gallagher N, Lewis LB, Funck T, Spitzer H, Dickscheid T, Fletcher PC, Romero A, Zilles K, Amunts K, Bengio Y, Evans AC (2020) BigBrain 3D atlas of cortical layers: Cortical and laminar thickness gradients diverge in sensory and motor cortices. PlosBiology doi: link
    Seidlitz J, Nadig A, Liu S, Bethlehem RAI, Vértes PE, Morgan SE, Váša F, Romero-Garcia F, Lalonde FM, Clasen LS, Blumenthal JD, Paquola C, Bernhardt B, Wagstyl K, Polioudakis D, de la Torre-Ubieta L, Geschwind DH, Han JC, Lee NR, Murphy DG, Bullmore ET, Raznahan A (2020) Transcriptomic and cellular decoding of regional brain vulnerability to neurogenetic disorders. Nature Communications, 11(3358), doi: link
    DeKraker J, Lau JC, Ferko KM, Khan AR, Kohler S (2019) Hippocampal subfields revealed through unfolding and unsupervised clustering of laminar and morphological features in 3D BigBrain. NeuroImage, 206(116328), doi: link
    Lau JC, Parrent AG, Demarco J, Gupta G, Kai J, Stanley OW, Kuehn T, Park PJ, Ferko K, Khan AR, Peters TM (2019) A framework for evaluating correspondence between brain images using anatomical fiducials. Hum Brain Mapp. 2019; 40: 4163– 4179. doi: link
    Seidlitz J, Nadig A, Liu S, Bethlehem RAI, Vértes PE, Morgan SE, Váša F, Romero-Garcia R, Lalonde FM, Clasen LS, Blumenthal JD, Paquola C, Bernhardt B, Wagstyl K, Polioudakis D, de la Torre-Ubieta L, Geschwind DH, Han JC, Lee NR, Murphy DG, Bullmore ET, Raznahan A (2019) Transcriptomic and Cellular Decoding of Regional Brain Vulnerability to Neurodevelopmental Disorders. bioRxiv, doi: link
    Irmen F, Horn A, Mosley P, Perry A, Petry-Schmelzer JN, Dafsari HS, Barbe M, Visser-Vandewalle V, Schneider GH, Li N, Kübler D, Wenzel G, Kühn A (2019) Left prefrontal connectivity links subthalamic stimulation with depressive symptoms in Parkinson’s disease. bioRxiv 665976; doi: link
    Horn A, Wenzel G, Irmen F, Huebl J, Li N, Neumann WJ, Krause P, Bohner G, Scheel M, Kühn AA (2019) Deep brain stimulation induced normalization of the human functional connectome in Parkinson’s disease. Brain , awz239, doi: link
    Horn A, Li N, Dembek TA, Kappel A, Boulay C, Ewert S, Tietze A, Husch A, Perera T, Neumann WJ, Reisert M, Si H, Oostenveld R, Rorden C, Yeh FC, Fang Q, Herrington TM, Vorwerk J, Kühn AA (2019) Lead-DBS v2: Towards a comprehensive pipeline for deep brain stimulation imaging. NeuroImage, 184:293-316 doi: link
    Dugré M, Hayot-Sasson M, Glatard T (2019) A performance comparison of Dask and Apache Spark for data-intensive neuroimaging pipelines. arxiv, link
    Hayot-Sasson V, Brown ST, Glatard T (2019) Performance Evaluation of Big Data Processing Strategies for Neuroimaging. arxiv, link
    Xiao Y, Lau JC, Anderson T, DeKraker J, Collins DL, Peters T, Khan AR (2019) Bridging micro and macro: accurate registration of the BigBrain dataset with the MNI PD25 and ICBM152 atlases. bioRxiv 561118; doi: link
    Sitek KR, Gulban OF, Calabrese E, Johnson GA, Lage-Castellanos A, Moerel M, Ghosh SS, De Martino F (2019) Mapping the human subcortical auditory system using histology, postmortem MRI and in vivo MRI at 7T. eLife 2019;8:e48932. doi: link
    Wagstyl K, Larocque S, Cucurull G, Lepage C, Cohen JP, Bludau S, Palomero-Gallagher N, Funck T, Spitzer H, Dicksheid T, Fletcher PC, Romero A, Zilles K, Amunts K, Bengio Y, Evans AC (2019) Automated segmentation of cortical layers in BigBrain reveals divergent cortical and laminar thickness gradients in sensory and motor cortices. bioRxiv, doi: link
    DeKraker J, Lau JC, Ferko KM, Khan AR, Köhler S (2019) Hippocampal morphology and cytoarchitecture in the 3D BigBrain. bioRxiv, doi: link
    Paquola C, Vos De Wael R, Wagstyl K,Bethlehem RAI, Hong S-J, Seidlitz J, Bullmore ET, Evans AC, Misic B, Margulies DS, Smallwood J, Bernhardt BC (2019) Microstructural and functional gradients are increasingly dissociated in transmodal cortices. PLoSBiol 17(5):e3000284. doi: link
    Wei Y, Scholtens LH,Turk E, van den Heuvel MP (2019) Multiscale examination of cytoarchitectonic similarity and human brain connectivity, NetworkNeuroscience,3(1), 124–137. doi: link
    Oden L, Schiffer C, Spitzer H, Dickscheid T, Pleiter D (2019) IO Challenges for Human Brain Atlasing Using Deep Learning Methods - An In-Depth Analysis. 27th Euromicro International Conference on Parallel, Distributed and Network-Based Processing (PDP), Pavia, Italy, 2019, pp. 291-298. doi: link
    Iglesias JE, Modat M, Peter L, Stevens A, Annunziata R, Vercauteren T, Lein E, Fischl B, Ourselin S, for the ADNI (2018) Joint registration and synthesis using a probabilistic model for alignment of MRI and histological sections. Med Image Analysis, 50:127-144. doi: link
    Maia PD, Pandya S, Torok J, Gupta A, Zeighami Y, Raj A (2018) Heterogeneity of Incipient Atrophy Patterns in Parkinson’s Disease. bioRxiv, doi: link
    Yu Y, Herman P, Rothman D L, Agarwal D, Hyder F (2018) Evaluating the gray and white matter energy budgets of human brain function. ournal of Cerebral Blood Flow & Metabolism, 38(8), 1339–1353. doi: link
    Wagstyl K, Lepage C, Bludau S, Zilles K, Fletcher P, Amunts K, Evans AC (2018) Mapping Cortical Laminar Structure in the 3D BigBrain. Cerebral Cortex (New York, N.Y. : 1991), 28 (7), 2551-2562. doi: link
    Spitzer H, Amunts K, Harmeling S, Dickscheid T (2018) Compact feature representations for human brain cytoarchitecture using self-supervised learning. Medical Imaging with Deep Learning (MIDL 2018, Amsterdam). link
    Spitzer H, Kiwitz K, Amunts K, Harmeling S, Dickscheid T (2018) Improving Cytoarchitectonic Segmentation of Human Brain Areas with Self-supervised Siamese Networks. MICCAI 2018 link
    Gulban OF, Schneider M, Marquardt I, Haast RAM, De Martino F (2018) A scalable method to improve gray matter segmentation at ultra high field MRI. PLoS ONE 13(6): e0198335. doi: link
    Yeh FC, Panesar S, Fernandes D, Meola A, Yoshino M, Fernandez-Miranda JC, Vettel JM, Verstynen T (2018) Population-averaged atlas of the macroscale human structural connectome and its network topology. NeuroImage 178 (2018):57-68 doi: link. Epub 2018 May 24.
    Fournier M, Lewis LB, Evans AC (2017) BigBrain: Automated cortical parcellation and comparison with existing brain atlases. Springer Lecture Notes in Computer Science, Vol. 10081, No. 1, 2017, 14-25. link
    Lambert C, Simon H, Colman J, Barrick TR (2017) Defining thalamic nuclei and topographic connectivity gradients in vivo. NeuroImage 158:466-479. doi: link
    Spitzer H, Amunts K, Harmeling S, Dickscheid T (2017) Parcellation of visual cortex on high-resolution histological brain sections using convolutional neural networks. IEEE 14th International Symposium on Biomedical Imaging (ISBI 2017), Melbourne, VIC, 2017, pp. 920-923. doi: link
    Neuro Cloud Consortium: Vogelstein JT, Mensh B, Häusser M, Spruston N, Evans AC, Kording K, Amunts K, Ebell C, Muller J, Telefont M, Hill S, Koushika SP, Calì C, Valdés-Sosa PA, Littlewood PB, Koch C, Saalfeld S, Kepecs A, Peng H, Halchenko YO, Kiar G, Poo MM, Poline JB, Milham MP, Schaffer AP, Gidron R, Okano H, Calhoun VD, Chun M, Kleissas DM, Vogelstein RJ, Perlman E, Burns R, Huganir R, Miller MI (2016) To the Cloud! A Grassroots Proposal to Accelerate Brain Science Discovery. Neuron. 92(3):622-627. doi: link Beukema P, Yeh FC, Verstynen T (2015) In vivo characterization of the connectivity and subcomponents of the human globus pallidus. NeuroImage 120(2015):382-393 doi: link
    Amunts K, Hawrylycz M, Van Essen D, Van Horn JD, Harel N, Poline JB, De Martino F, Bjaalie JG, Dehaene-Lambertz G, Dehaene S, Valdes-Sosa P, Thirion B, Zilles K, Hill SL, Abrams MB, Tass PA, Vanduffel W, Evans AC, Eickhoff SB (2014) Interoperable atlases of the human brain. Neuroimage, 99: 525-532. doi: link
    Amunts K, Lepage C, Borgeat L, Mohlberg H, Dickscheid T, Rousseau ME, Bludau S, Bazin PL, Lewis LB, Oros-Peusquens AM, Shah NJ, Lippert T, Zilles K, Evans AC (2013) BigBrain: An ultrahigh-resolution 3D human brain model. Science, 340(6139): 1472-1475. link

  • Dissertations

    Jordan DeKraker, PhD, U. of Western Ontario, 2020. link,
    Hannah Spitzer, PhD Thesis, Forschungszentrum Jülich GmbH, 2020. link
    Thomas Funck, PhD, McGill University, 2020. link
    Konrad Wagstyl, PhD, Cambridge, 2018. doi
    Jordan DeKraker, MSc, U. of Western Ontario, 2016. link,

  • Conference Materials

    Areces-Gonzalez A, Paz-Linares D, Huang S, Wang Y, Riaz U, González-Mitjans A, Ahmed Z, Wang Q, Gonzalez-Moreira E, Bosch-Bayard J, Valdés-Sosa P (2020) MRI-DWI-EEG pipeline for individualized insilico BigBrain like preparation. OHBM 2020 Montreal. Poster
    Bezgin G, McIntosh AR, Rosa-Neto P, Evans AC (2020) Mapping cross-scale brain data using inter-atlas connectivity transformation (IntACT). OHBM 2020 Montreal. Poster
    Christidis N, DeKraker J, Xiao Y, Köhler S, Steven DA, Khan AR (2020) Piriform cortex parcellation through unfolding and clustering of laminar features in the 3D BigBrain. OHBM 2020 Montreal. Poster
    Funck T, Palomero-Gallagher N, Wagstyl K, Omidyeganeh M, Lepage C, Toussaint PJ, Thiel A, Zilles K, Evans AC (2020) Towards a dataset of 20 ultra-high resolution 3D atlases of human neurotransmitter receptor binding sites. OHBM 2020 Montreal. Poster
    Lewis LB, Lepage CY, Glasser MF, Coalson TS, Van Essen DC, Evans AC (2020) A multimodal surface matching (MSM) surface registration pipeline to bridge atlases across the MNI and FreeSurfer / Human Connectome Project worlds. OHBM 2020 Montreal. Poster
    Jones SL, Lepage C, Omidyeganeh M, Toussaint PJ, Lewis LB, Borgeat L, Massicotte P, Altinkaya A, Nguyen TV, Sadikot A, Evans AC, Pruessner JC (2020) An atlas of the human hypothalamus at ultra-high resolution using the BigBrain. OHBM 2020 Montreal. Poster
    Omidyeganeh M, Lepage C, Wagstyl K, Spitzer H, Dickscheid T, Amunts K, Evans A (2020) Non-linear registration of 1µm histology sections into 3D 20µm BigBrain space. OHBM 2020 Montreal. Poster
    Toussaint PJ, Lo D, Wenzel S, Dickscheid T, Adalat R, Amunts K, Evans AC (2020) The BigBrain Project web platform as a pedagogical tool. OHBM 2020 Montreal. Poster
    Zeighami Y, Bakken T, Hawrylycz M, Evans A (2020) Brain disorders taxonomy: A transcriptomics point of view. OHBM 2020 Montreal. Poster
    Wagstyl, K. et al.: BigBrain: Automated identification of cortical layers in the primary visual cortex, HBM 2017. link
    Lepage, C. et al.: BigBrain: From Artifact Corrections, Alignment, and Optical-Balancing to Segmentation and Surface Extraction, RBIQ/QBIN Toward a super-big brain: promises and pitfalls of microstructural imaging, Montreal, August 2016. link
    Wagstyl, K. et al.: Automated Analysis of Laminar Structure in the Cerebral Cortex, HBM 2016. link
    Lewis, L.B. et al.: BigBrain: Initial Tissue Classification and Surface Extraction, HBM 2014 link
    Bludau, S. et al.: "Two new Cytoarchitectonic Areas of the Human Frontal Pole", OHBM 2012 link
    Lepage, C. et al.: "Automatic Repair of Acquisition Defects in Reconstruction of Histology Sections of a Human Brain", HBM 2010 link

  • Press

    German Interview with Katrin Amunts Dem Gehirn auf der Spur, link
    Interview with Katrin Amunts at France24's Tech24 about Julich-Brain, the world's first 3D atlas of the human brain, Inside the human brain, video 2:45 - 8:02 link
    German Interview with Katrin Amunts 'WIE SIEHT DIE HIRNFORSCHUNG DER ZUKUNFT AUS?' link
    New EBRAINS-enabled tool to help guide surgery in drug-resistant epilepsy patients, Scaling up the potential for personalised brain representation with the help of large brain data sets from the EBRAINS Brain Atlas, including the most detailed 3D representation of the brain’s anatomy, the BigBrain, at a resolution of 20 micrometers. link
    Katrin Amunts talking about building a digital model of the brain at NewsTalk 'Futureproof with Jonathan McCrea', a podcast. 00:13:59 to 00:33:58 link
    Deep learning networks reflect cytoarchitectonic features used in brain mapping, Kai Kiwitz, Christian Schiffer, Hannah Spitzer, Timo Dickscheid & Katrin Amunts, Dec 2020, link
    Mikrometer um Mikrometer: Dem Gehirn auf der Spur, PR of FZJ about the launch of HIBALL, July 2020, link
    The human brain built by AI: A transatlantic collaboration, HIBALL at Laboratory News UK, July 2020, link
    A centerpiece of EBRAINS’ human brain atlas is presented in “Science”, Véronique Morin, July 2020, link
    Six découvertes et contributions québécoises marquantes de la dernière décennie, Forschungszentrum Jülich, Dec 2019, link
    Interview with AC Evans for McGill Reporter, Jennifer Morrow, June 26 2019, link
    Interview with K Amunts at PASC17 conference - section on BB, Simone Ulmer, July 26 2019, link
    BRAIN Research: They Wish It Was Only Rocket Science, Geralyn Miller, June 25 2015, link
    Huron Technologies and the BigBrain, Huron Digital Pathology, May 11 2015, link
    Jülich Supercomputing Centre and the BigBrain project, Lenovo Blog, Feb 02 2015, link
    Human Brain in 3-D Detail, Kate McGowan, Jan 2014, link
    Significant Science of 2013: Brain Mapping Gets a Big Boost, Allison Eck, Dec 27 2013, link
    Prof. Evans's Lecture-BigBrain: An ultra-high resolution 3D model of human neuroanatomy, Brainnetome, July 4 2013, link
    An Ultra-High-Resolution, 3D View of the Human Brain, Alzforum, June 21 2013, link
    BigBrain: Ultra-high resolution 3D map of human brain, Kristen Butler, June 21 2013, link
    BigBrain: an ultra-high-resolution 3D roadmap of the human brain, Kurzweil, June 21 2013, link
    Whole human brain mapped in 3D, Helen Shen, June 20 2013, link
    Groundbreaking Brain Atlas Maps Whole Brain at Cellular Level, Becky Lang, June 20 2013, link
    “BigBrain” Project Makes Terabyte Map of a Human Brain, Mia Feldman, June 20 2013, link
    BigBrain: The Best Gray Matter Map Ever Made, William Herkewitz, June 20 2013, link
    Bigbrain: An ultra-high resolution 3-D roadmap of the human brain, American Association for the Advancement of Science, June 20 2013 2013, link
    The 'Google Earth' of 3D Brain Maps is Here, Abby Ohlheiser, June 20 2013, link
    El mapa Big Brain, Memeroteca, June 20 2013, link
    “BigBrain” Model Offers Microscopic Views of Human Brain, Rebecca Voelker, June 20 2013, link
    The Human Brain in Exquisite Detail, Ruth Williams, June 20 2013, link
    A Detailed 3-D Atlas of a Human Brain, Courtney Humphries, June 20 2013, link
    3D map of human brain is the most detailed ever, Sara Reardon, June 20 2013, link
    Scientists create detailed 3-D model of human brain, Melissa Healy, June 20 2013, link
    The Brain: Now in Ultra High-Res 3D, Jesse Emspak, June 20 2013, link
    Ultra-high resolution 3D map of a human brain, The Guarduab, June 20 2013, link

  • Related Publications

    Glatard T, Kiar G, Aumentado-Armstrong T, Beck N, Bellec P, Bernard R, Bonnet A, Brown ST, Camarasu-Pop S, Cervenansky F, Das D, Ferreira da Silva R, Flandin G, Girard P, Gorgolewski KJ, Guttmann CRG, Hayot-Sasson V, Quirion PO, Rioux P, Rousseau ME, Evans AC. Boutiques: a flexible framework to integrate command-line applications in computing platforms. GigaScience, Volume 7, Issue 5, May 2018, doi: link
    Sherif T, Rioux P, Rousseau ME, Kassis N, Beck N, Adalat R, Das S, Glatard T, Evans AC. CBRAIN: a web-based, distributed computing platform for collaborative neuroimaging research. Front Neuroinform. 8:54, 2014, doi: link
    Sanz Leon P, Knock S, Woodman M, Domide L, Mersmann J, McIntosh A, Jirsa V. The Virtual Brain: a simulator of primate brain network dynamics. Front Neuroinform. 7:10, 2013, doi: link
    Das S, Zijdenbos AP, Harlap J, Vins D, Evans AC. LORIS: a web-based data management system for multi-center studies. Front Neuroinform. 5:37, 2012, doi: link
    Massicotte P, Blais F, Godin G, Beraldin J, Borgeat L, Poirier G. Visualizing and Analyzing the Mona Lisa. IEEE Computer Graphics and Applications. 27(6):1558-1756, 2007, doi: link