{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,28]],"date-time":"2026-07-28T20:03:28Z","timestamp":1785269008496,"version":"3.55.0"},"reference-count":72,"publisher":"MIT Press","license":[{"start":{"date-parts":[[2026,7,2]],"date-time":"2026-07-02T00:00:00Z","timestamp":1782950400000},"content-version":"vor","delay-in-days":182,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000156","name":"Fonds de Recherche du Qu\u00e9bec - Sant\u00e9","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000156","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000024","name":"Canadian Institutes of Health Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Healthy Brains Healthy Lives Initiative"},{"name":"Translational Initiative in De-Risking Neurotherapeutics"},{"name":"New Frontiers in Research Fund","award":["NFRFT-2022-00051"],"award-info":[{"award-number":["NFRFT-2022-00051"]}]},{"name":"Fonds de Recherche Quebec Sant\u00e9 Junior Investigator Award"},{"name":"Natural Sciences and Engineering Research Council of Canada, Discovery Grant"},{"DOI":"10.13039\/501100000024","name":"Canadian Institutes of Health Research","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Douglas Research Centre"},{"DOI":"10.13039\/100008100","name":"Douglas Foundation","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100008100","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["direct.mit.edu"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2026,7,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The Allen Mouse Brain Connectivity Atlas (AMBCA) is widely used to represent structural connectivity in the mouse brain. The AMBCA consists of tracer injection experiments where neuronal projections axonally connected to the initial injection site are labeled. The resulting whole-brain structural connectomes, derived from a subset of these experiments in C57BL\/6 mice, have been used in several studies of connectomic architectures. However, through close inspection of n = 437 distinct experiments used in a publicly-available connectome (Knox et al., 2018), we observed experiments with off-target injections, diffuse projections, unrealistically small injections and projections, and anatomical misalignments, affecting the accuracy and applicability of these connectivity experiments. We applied a combined automated and manual quality control (QC) and identified n = 56 (~13% of the original n = 437) experiments representing a wide variety of injection and projection failures across the brain. Automated QC was used to detect extreme injection and projection sizes and misalignments, while manual QC was used to detect subtle off-target tracer spreading. Using the remaining n = 381 experiments, we rebuilt two different connectomes using previously-published methods; specifically: the regionalized voxel model from Knox et al. (2018), and the homogeneous model from Oh et al. (2014). Our rebuilt connectomes show strong losses in connectivity between regions with limited evidence of structural connectivity by other methods (e.g., hippocampus-medulla, cerebellum-isocortex) and gains in connectivity between regions with strong connectivity evidence (hypothalamus-cerebellum, hypothalamus-isocortex). Finally, we analyzed the rich club and community organization to demonstrate the potential downstream impacts on the representation of the overall structural connectome architectures of our QC\u2019d connectomes and observed subtle whole-brain organizational changes. We present our rebuilt connectomes, and particularly highlight the regionalized voxel model, as more accurate representations of structural connectivity derived from the AMBCA.<\/jats:p>","DOI":"10.1162\/imag.a.1310","type":"journal-article","created":{"date-parts":[[2026,7,2]],"date-time":"2026-07-02T20:02:24Z","timestamp":1783022544000},"update-policy":"https:\/\/doi.org\/10.1162\/mitpressjournals.corrections.policy","source":"Crossref","is-referenced-by-count":0,"title":["Experimental quality control induces changes in Allen mouse brain connectomes"],"prefix":"10.1162","volume":"4","author":[{"ORCID":"https:\/\/orcid.org\/0009-0002-0845-3461","authenticated-orcid":false,"given":"Vikram","family":"Nathan","sequence":"first","affiliation":[{"name":"Cerebral Imaging Center, Douglas Mental Health University Institute, Montr\u00e9al, QC, Canada"},{"name":"Integrated Program in Neuroscience, McGill University, Montr\u00e9al, QC, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephanie","family":"Tullo","sequence":"additional","affiliation":[{"name":"Cerebral Imaging Center, Douglas Mental Health University Institute, Montr\u00e9al, QC, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lizette","family":"Herrera-Portillo","sequence":"additional","affiliation":[{"name":"Cerebral Imaging Center, Douglas Mental Health University Institute, Montr\u00e9al, QC, Canada"},{"name":"Integrated Program in Neuroscience, McGill University, Montr\u00e9al, QC, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gabriel A.","family":"Devenyi","sequence":"additional","affiliation":[{"name":"Cerebral Imaging Center, Douglas Mental Health University Institute, Montr\u00e9al, QC, Canada"},{"name":"Department of Psychiatry, McGill University, Montr\u00e9al, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yohan","family":"Yee","sequence":"additional","affiliation":[{"name":"Department of Radiology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada"},{"name":"Experimental Imaging Centre, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M. Mallar","family":"Chakravarty","sequence":"additional","affiliation":[{"name":"Cerebral Imaging Center, Douglas Mental Health University Institute, Montr\u00e9al, QC, Canada"},{"name":"Department of Psychiatry, McGill University, Montr\u00e9al, Canada"},{"name":"Department of Biological & Biomedical Engineering, McGill University, Montr\u00e9al, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"281","published-online":{"date-parts":[[2026,7,28]]},"reference":[{"issue":"22","key":"2026072815553611700_IMAG.a.1310-b1","doi-asserted-by":"crossref","first-page":"e4221","DOI":"10.21769\/BioProtoc.4221","article-title":"Macroscopic structural and connectome mapping of the mouse brain using diffusion magnetic resonance imaging","volume":"11","author":"Arefin","year":"2021","journal-title":"Bio-Protocol"},{"issue":"5","key":"2026072815553611700_IMAG.a.1310-b2","doi-asserted-by":"crossref","first-page":"e0215520","DOI":"10.1371\/journal.pone.0215520","article-title":"Multi-scale detection of hierarchical community architecture in structural and functional brain networks","volume":"14","author":"Ashourvan","year":"2019","journal-title":"PLoS One"},{"issue":"1","key":"2026072815553611700_IMAG.a.1310-b3","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1016\/j.conb.2011.08.005","article-title":"Human connectomics","volume":"22","author":"Behrens","year":"2012","journal-title":"Current Opinion in Neurobiology"},{"issue":"e80379","key":"2026072815553611700_IMAG.a.1310-b4","doi-asserted-by":"crossref","first-page":"e80379","DOI":"10.7554\/eLife.80379","article-title":"Individual behavioral trajectories shape whole-brain connectivity in mice","volume":"12","author":"Bogado Lopes","year":"2023","journal-title":"eLife"},{"issue":"5","key":"2026072815553611700_IMAG.a.1310-b5","doi-asserted-by":"crossref","first-page":"e26669","DOI":"10.1002\/hbm.26669","article-title":"Community detection in the human connectome: Method types, differences and their impact on inference","volume":"45","author":"Brooks","year":"2024","journal-title":"Human Brain Mapping"},{"issue":"2","key":"2026072815553611700_IMAG.a.1310-b6","doi-asserted-by":"crossref","first-page":"1033","DOI":"10.1007\/s00429-014-0954-y","article-title":"Afferent projections to the different medial amygdala subdivisions: A retrograde tracing study in the mouse","volume":"221","author":"C\u00e1diz-Moretti","year":"2016","journal-title":"Brain Structure & Function"},{"issue":"5","key":"2026072815553611700_IMAG.a.1310-b7","doi-asserted-by":"crossref","first-page":"1280","DOI":"10.1016\/j.cell.2018.03.031","article-title":"Dissociable structural and functional hippocampal outputs via distinct subiculum cell classes","volume":"173","author":"Cembrowski","year":"2018","journal-title":"Cell"},{"issue":"51","key":"2026072815553611700_IMAG.a.1310-b8","doi-asserted-by":"crossref","first-page":"eabb7187","DOI":"10.1126\/sciadv.abb7187","article-title":"Network structure of the mouse brain connectome with voxel resolution","volume":"6","author":"Coletta","year":"2020","journal-title":"Science Advances"},{"issue":"24","key":"2026072815553611700_IMAG.a.1310-b9","doi-asserted-by":"crossref","first-page":"eabg6677","DOI":"10.1126\/sciadv.abg6677","article-title":"Computational modeling of tau pathology spread reveals patterns of regional vulnerability and the impact of a genetic risk factor","volume":"7","author":"Cornblath","year":"2021","journal-title":"Science Advances"},{"issue":"119199","key":"2026072815553611700_IMAG.a.1310-b10","doi-asserted-by":"crossref","first-page":"119199","DOI":"10.1016\/j.neuroimage.2022.119199","article-title":"Resolution and b value dependent structural connectome in ex vivo mouse brain","volume":"255","author":"Crater","year":"2022","journal-title":"NeuroImage"},{"issue":"1","key":"2026072815553611700_IMAG.a.1310-b11","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1007\/s00429-016-1204-2","article-title":"A role for the anteromedial thalamic nucleus in the acquisition of contextual fear memory to predatory threats","volume":"222","author":"de Lima","year":"2017","journal-title":"Brain Structure & Function"},{"issue":"1","key":"2026072815553611700_IMAG.a.1310-b12","doi-asserted-by":"crossref","first-page":"6708","DOI":"10.1038\/s41467-024-50826-8","article-title":"A standardized image processing and data quality platform for rodent fMRI","volume":"15","author":"Desrosiers-Gr\u00e9goire","year":"2024","journal-title":"Nature Communications"},{"issue":"4636","key":"2026072815553611700_IMAG.a.1310-b13","doi-asserted-by":"crossref","first-page":"591","DOI":"10.1126\/science.6198719","article-title":"Cerebellar autonomic function: Direct hypothalamocerebellar pathway","volume":"223","author":"Dietrichs","year":"1984","journal-title":"Science (New York, N.Y.)"},{"issue":"1","key":"2026072815553611700_IMAG.a.1310-b14","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1016\/j.neuroimage.2008.03.037","article-title":"High resolution three-dimensional brain atlas using an average magnetic resonance image of 40 adult C57Bl\/6J mice","volume":"42","author":"Dorr","year":"2008","journal-title":"NeuroImage"},{"issue":"e82376","key":"2026072815553611700_IMAG.a.1310-b15","doi-asserted-by":"crossref","first-page":"e82376","DOI":"10.7554\/eLife.82376","article-title":"Sex, strain, and lateral differences in brain cytoarchitecture across a large mouse population","volume":"12","author":"Elkind","year":"2023","journal-title":"eLife"},{"key":"2026072815553611700_IMAG.a.1310-b16","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1016\/j.ymeth.2015.01.009","article-title":"Exploration and visualization of connectivity in the adult mouse brain","volume":"73","author":"Feng","year":"2015","journal-title":"Methods (San Diego, Calif.)"},{"key":"2026072815553611700_IMAG.a.1310-b17","doi-asserted-by":"crossref","first-page":"426","DOI":"10.1016\/j.neuroimage.2013.04.087","article-title":"Graph analysis of the human connectome: Promise, progress, and pitfalls","volume":"80","author":"Fornito","year":"2013","journal-title":"NeuroImage"},{"key":"2026072815553611700_IMAG.a.1310-b18","doi-asserted-by":"crossref","DOI":"10.52294\/001c.133510","article-title":"Longitudinal deformation-based morphometry pipeline to study neuroanatomical differences in structural MRI based on SyN unbiased templates","volume":"5","author":"Germann","year":"2025","journal-title":"Aperture Neuro"},{"issue":"1668","key":"2026072815553611700_IMAG.a.1310-b19","doi-asserted-by":"crossref","first-page":"20140165","DOI":"10.1098\/rstb.2014.0165","article-title":"Dwelling quietly in the rich club: Brain network determinants of slow cortical fluctuations","volume":"370","author":"Gollo","year":"2015","journal-title":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences"},{"issue":"7781","key":"2026072815553611700_IMAG.a.1310-b20","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1038\/s41586-019-1716-z","article-title":"Hierarchical organization of cortical and thalamic connectivity","volume":"575","author":"Harris","year":"2019","journal-title":"Nature"},{"issue":"1","key":"2026072815553611700_IMAG.a.1310-b21","doi-asserted-by":"crossref","DOI":"10.1002\/0471142301.ns0120s59","article-title":"Adeno-associated viral vectors for anterograde axonal tracing with fluorescent proteins in nontransgenic and cre driver mice","volume":"Chapter 1","author":"Harris","year":"2012","journal-title":"Current Protocols in Neuroscience"},{"issue":"8","key":"2026072815553611700_IMAG.a.1310-b22","doi-asserted-by":"crossref","first-page":"1248","DOI":"10.1038\/s41593-019-0457-5","article-title":"Spread of \u03b1-synuclein pathology through the brain connectome is modulated by selective vulnerability and predicted by network analysis","volume":"22","author":"Henderson","year":"2019","journal-title":"Nature Neuroscience"},{"key":"2026072815553611700_IMAG.a.1310-b23","article-title":"Whole brain dimensional approach identifies shared and sex-specific networks of stress susceptibility in male and female mice. In","author":"Herrera Portillo","year":"2025","journal-title":"bioRxiv"},{"issue":"1","key":"2026072815553611700_IMAG.a.1310-b24","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1186\/s13293-024-00611-5","article-title":"Whole-brain connections of glutamatergic neurons in the mouse lateral habenula in both sexes","volume":"15","author":"Huang","year":"2024","journal-title":"Biology of Sex Differences"},{"issue":"12","key":"2026072815553611700_IMAG.a.1310-b25","doi-asserted-by":"crossref","first-page":"5186","DOI":"10.1016\/j.csda.2007.11.008","article-title":"An adjusted boxplot for skewed distributions","volume":"52","author":"Hubert","year":"2008","journal-title":"Computational Statistics & Data Analysis"},{"key":"2026072815553611700_IMAG.a.1310-b26","doi-asserted-by":"crossref","first-page":"561822","DOI":"10.3389\/fncir.2020.561822","article-title":"Subpopulations of projection neurons in the olfactory bulb","volume":"14","author":"Imamura","year":"2020","journal-title":"Frontiers in Neural Circuits"},{"issue":"5","key":"2026072815553611700_IMAG.a.1310-b28","doi-asserted-by":"crossref","first-page":"1073","DOI":"10.1038\/s41593-025-01919-0","article-title":"Projectome-based characterization of hypothalamic peptidergic neurons in male mice","volume":"28","author":"Jiao","year":"2025","journal-title":"Nature Neuroscience"},{"issue":"17","key":"2026072815553611700_IMAG.a.1310-b29","doi-asserted-by":"crossref","first-page":"e2218617120","DOI":"10.1073\/pnas.2218617120","article-title":"Merged magnetic resonance and light sheet microscopy of the whole mouse brain","volume":"120","author":"Johnson","year":"2023","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"2026072815553611700_IMAG.a.1310-b30","doi-asserted-by":"crossref","first-page":"759948","DOI":"10.3389\/fnana.2021.759948","article-title":"Recent advances in the understanding of specific efferent pathways emerging from the cerebellum","volume":"15","author":"Kang","year":"2021","journal-title":"Frontiers in Neuroanatomy"},{"issue":"3","key":"2026072815553611700_IMAG.a.1310-b31","doi-asserted-by":"crossref","first-page":"647","DOI":"10.1007\/s00429-020-02190-8","article-title":"Mapping the living mouse brain neural architecture: Strain-specific patterns of brain structural and functional connectivity","volume":"226","author":"Karatas","year":"2021","journal-title":"Brain Structure & Function"},{"issue":"6523","key":"2026072815553611700_IMAG.a.1310-b32","doi-asserted-by":"crossref","DOI":"10.1126\/science.abd5059","article-title":"Cerebellar nuclei evolved by repeatedly duplicating a conserved cell-type set","volume":"370","author":"Kebschull","year":"2020","journal-title":"Science (New York, N.Y.)"},{"issue":"1","key":"2026072815553611700_IMAG.a.1310-b33","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1038\/s41467-022-35181-w","article-title":"Finding shortest and nearly shortest path nodes in large substantially incomplete networks by hyperbolic mapping","volume":"14","author":"Kitsak","year":"2023","journal-title":"Nature Communications"},{"issue":"1","key":"2026072815553611700_IMAG.a.1310-b34","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1162\/netn_a_00066","article-title":"High-resolution data-driven model of the mouse connectome","volume":"3","author":"Knox","year":"2018","journal-title":"Network Neuroscience (Cambridge, Mass.)"},{"key":"2026072815553611700_IMAG.a.1310-b35","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1016\/j.ymeth.2014.12.013","article-title":"Neuroinformatics of the allen mouse brain connectivity atlas","volume":"73","author":"Kuan","year":"2015","journal-title":"Methods (San Diego, Calif.)"},{"issue":"1","key":"2026072815553611700_IMAG.a.1310-b36","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1186\/s40035-024-00403-2","article-title":"LRRK2 kinase inhibition reverses G2019S mutation-dependent effects on tau pathology progression","volume":"13","author":"Lubben","year":"2024","journal-title":"Translational Neurodegeneration"},{"key":"2026072815553611700_IMAG.a.1310-b37","volume":"99","author":"Maechler","year":"2025","journal-title":"robustbase: Basic robust statistics. R package version 0"},{"issue":"13","key":"2026072815553611700_IMAG.a.1310-b38","doi-asserted-by":"crossref","first-page":"4320","DOI":"10.1016\/j.celrep.2019.11.096","article-title":"A spatiomolecular map of the striatum","volume":"29","author":"M\u00e4rtin","year":"2019","journal-title":"Cell Reports"},{"issue":"1","key":"2026072815553611700_IMAG.a.1310-b39","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1186\/s40478-017-0459-z","article-title":"Connectivity, not region-intrinsic properties, predicts regional vulnerability to progressive tau pathology in mouse models of disease","volume":"5","author":"Mezias","year":"2017","journal-title":"Acta Neuropathologica Communications"},{"key":"2026072815553611700_IMAG.a.1310-b40","doi-asserted-by":"crossref","first-page":"104623","DOI":"10.1016\/j.nbd.2019.104623","article-title":"Neural connectivity predicts spreading of alpha-synuclein pathology in fibril-injected mouse models: Involvement of retrograde and anterograde axonal propagation","volume":"134","author":"Mezias","year":"2020","journal-title":"Neurobiology of Disease"},{"issue":"Suppl 5","key":"2026072815553611700_IMAG.a.1310-b41","doi-asserted-by":"crossref","first-page":"V1","DOI":"10.1007\/PL00007778","article-title":"Neural circuits and functional organization of the striatum","volume":"247","author":"Nakano","year":"2000","journal-title":"Journal of Neurology"},{"issue":"7495","key":"2026072815553611700_IMAG.a.1310-b42","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1038\/nature13186","article-title":"A mesoscale connectome of the mouse brain","volume":"508","author":"Oh","year":"2014","journal-title":"Nature"},{"issue":"4","key":"2026072815553611700_IMAG.a.1310-b43","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1080\/14734220310016187","article-title":"Cerebellar connections: Hypothalamus","volume":"2","author":"Onat","year":"2003","journal-title":"Cerebellum (London, England)"},{"key":"2026072815553611700_IMAG.a.1310-b44","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1007\/978-3-319-24551-5_31","article-title":"Serotonin in the cerebellum","volume-title":"Essentials of cerebellum and cerebellar disorders","author":"Oostland","year":"2016"},{"issue":"2","key":"2026072815553611700_IMAG.a.1310-b45","doi-asserted-by":"crossref","first-page":"626","DOI":"10.1523\/JNEUROSCI.4254-11.2012","article-title":"Why do axons differ in caliber?","volume":"32","author":"Perge","year":"2012","journal-title":"The Journal of Neuroscience: The Official Journal of the Society for Neuroscience"},{"issue":"1","key":"2026072815553611700_IMAG.a.1310-b46","doi-asserted-by":"crossref","first-page":"2615","DOI":"10.1038\/s41467-018-04921-2","article-title":"Mouse MRI shows brain areas relatively larger in males emerge before those larger in females","volume":"9","author":"Qiu","year":"2018","journal-title":"Nature Communications"},{"issue":"6682","key":"2026072815553611700_IMAG.a.1310-b47","doi-asserted-by":"crossref","first-page":"eadj9198","DOI":"10.1126\/science.adj9198","article-title":"Whole-brain spatial organization of hippocampal single-neuron projectomes","volume":"383","author":"Qiu","year":"2024","journal-title":"Science (New York, N.Y.)"},{"issue":"5","key":"2026072815553611700_IMAG.a.1310-b48","doi-asserted-by":"crossref","first-page":"1743","DOI":"10.1093\/brain\/awab440","article-title":"Differentially targeted seeding reveals unique pathological alpha-synuclein propagation patterns","volume":"145","author":"Rahayel","year":"2022","journal-title":"Brain: A Journal of Neurology"},{"key":"2026072815553611700_IMAG.a.1310-b49","article-title":"Endogenous pathology in tauopathy mice progresses via brain networks. In","author":"Ramirez","year":"2023","journal-title":"bioRxivorg"},{"issue":"3","key":"2026072815553611700_IMAG.a.1310-b50","doi-asserted-by":"crossref","first-page":"732","DOI":"10.1016\/j.neuroimage.2011.06.025","article-title":"Segmentation of the mouse hippocampal formation in magnetic resonance images","volume":"58","author":"Richards","year":"2011","journal-title":"NeuroImage"},{"issue":"2\u20133","key":"2026072815553611700_IMAG.a.1310-b51","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1016\/S0165-0173(97)00007-6","article-title":"The structural organization of connections between hypothalamus and cerebral cortex","volume":"24","author":"Risold","year":"1997","journal-title":"Brain Research. Brain Research Reviews"},{"key":"2026072815553611700_IMAG.a.1310-b52","doi-asserted-by":"crossref","DOI":"10.1016\/S1053-8119(09)71504-6","article-title":"Structural connectivity and nonperiodic synchronization in large-scale networks of spiking neurons","author":"Rubinov","year":"2009","journal-title":"NeuroImage"},{"key":"2026072815553611700_IMAG.a.1310-b53","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1007\/978-3-030-19898-5_7","article-title":"The mouse cerebellum","volume-title":"Neuroanatomy of the mouse","author":"Schr\u00f6der","year":"2020"},{"key":"2026072815553611700_IMAG.a.1310-b54","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1007\/978-3-030-19898-5_11","article-title":"The mouse hippocampus","volume-title":"Neuroanatomy of the mouse","author":"Schr\u00f6der","year":"2020"},{"key":"2026072815553611700_IMAG.a.1310-b200","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1007\/978-3-030-19898-5_14","article-title":"The mouse olfactory system","volume-title":"Neuroanatomy of the mouse","author":"Schr\u00f6der","year":"2020"},{"issue":"25","key":"2026072815553611700_IMAG.a.1310-b55","doi-asserted-by":"crossref","first-page":"5021","DOI":"10.1523\/JNEUROSCI.0307-22.2022","article-title":"Whole-brain wiring diagram of Oxytocin system in adult mice","volume":"42","author":"Son","year":"2022","journal-title":"The Journal of Neuroscience: The Official Journal of the Society for Neuroscience"},{"issue":"1","key":"2026072815553611700_IMAG.a.1310-b56","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1002\/aur.1344","article-title":"Genetic effects on cerebellar structure across mouse models of autism using a magnetic resonance imaging atlas","volume":"7","author":"Steadman","year":"2014","journal-title":"Autism Research: Official Journal of the International Society for Autism Research"},{"issue":"45","key":"2026072815553611700_IMAG.a.1310-b57","first-page":"E9692","article-title":"Organizing principles for the cerebral cortex network of commissural and association connections","volume":"114","author":"Swanson","year":"2017","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"2026072815553611700_IMAG.a.1310-b58","first-page":"1","article-title":"Combining multimodal connectivity information improves modelling of pathology spread in Alzheimer\u2019s disease","volume":"2","author":"Thompson","year":"2024","journal-title":"Imaging Neuroscience (Cambridge, Mass.)"},{"issue":"5","key":"2026072815553611700_IMAG.a.1310-b59","doi-asserted-by":"crossref","first-page":"e70092","DOI":"10.1002\/alz.70092","article-title":"Directionality bias underpins divergent spatiotemporal progression of Alzheimer-related tauopathy in mouse models","volume":"21","author":"Torok","year":"2025","journal-title":"Alzheimer\u2019s & Dementia: The Journal of the Alzheimer\u2019s Association"},{"key":"2026072815553611700_IMAG.a.1310-b60","article-title":"In vivo and in silico alpha-synuclein propagation dynamics: The role of genotype, epicentre, and connectivity","author":"Tullo","year":"2025","journal-title":"Neuroscience"},{"key":"2026072815553611700_IMAG.a.1310-b61","doi-asserted-by":"crossref","first-page":"196","DOI":"10.1016\/j.neuroimage.2013.04.008","article-title":"A segmentation protocol and MRI atlas of the C57BL\/6J mouse neocortex","volume":"78","author":"Ullmann","year":"2013","journal-title":"NeuroImage"},{"issue":"44","key":"2026072815553611700_IMAG.a.1310-b62","doi-asserted-by":"crossref","first-page":"15775","DOI":"10.1523\/JNEUROSCI.3539-11.2011","article-title":"Rich-club organization of the human connectome","volume":"31","author":"van den Heuvel","year":"2011","journal-title":"The Journal of Neuroscience: The Official Journal of the Society for Neuroscience"},{"issue":"2","key":"2026072815553611700_IMAG.a.1310-b63","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1016\/j.neuron.2017.03.037","article-title":"Chemogenetic interrogation of a brain-wide fear memory network in mice","volume":"94","author":"Vetere","year":"2017","journal-title":"Neuron"},{"issue":"4","key":"2026072815553611700_IMAG.a.1310-b64","doi-asserted-by":"crossref","first-page":"936","DOI":"10.1016\/j.cell.2020.04.007","article-title":"The Allen mouse brain common coordinate framework: A 3D reference atlas","volume":"181","author":"Wang","year":"2020","journal-title":"Cell"},{"issue":"4","key":"2026072815553611700_IMAG.a.1310-b65","doi-asserted-by":"crossref","first-page":"460","DOI":"10.1002\/cne.902490403","article-title":"Topographical distribution of dorsal and median raphe neurons projecting to motor, sensorimotor, and visual cortical areas in the rat","volume":"249","author":"Waterhouse","year":"1986","journal-title":"The Journal of Comparative Neurology"},{"issue":"1","key":"2026072815553611700_IMAG.a.1310-b66","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1016\/j.cell.2019.07.042","article-title":"Reconstruction of 1,000 projection neurons reveals new cell types and organization of long-range connectivity in the mouse brain","volume":"179","author":"Winnubst","year":"2019","journal-title":"Cell"},{"issue":"12","key":"2026072815553611700_IMAG.a.1310-b67","doi-asserted-by":"crossref","first-page":"2670","DOI":"10.1038\/s41592-025-02784-2","article-title":"Reconstruction of a connectome of single neurons in mouse brains by cross-validating multi-scale multi-modality data","volume":"22","author":"Xiong","year":"2025","journal-title":"Nature Methods"},{"issue":"120453","key":"2026072815553611700_IMAG.a.1310-b68","doi-asserted-by":"crossref","first-page":"120453","DOI":"10.1016\/j.neuroimage.2023.120453","article-title":"Organization of thalamocortical structural covariance and a corresponding 3D atlas of the mouse thalamus","volume":"285","author":"Yee","year":"2024","journal-title":"NeuroImage"},{"key":"2026072815553611700_IMAG.a.1310-b69","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1016\/j.neuroimage.2018.05.028","article-title":"Structural covariance of brain region volumes is associated with both structural connectivity and transcriptomic similarity","volume":"179","author":"Yee","year":"2018","journal-title":"NeuroImage"},{"key":"2026072815553611700_IMAG.a.1310-b70","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1016\/j.neuroimage.2016.06.035","article-title":"Connectome sensitivity or specificity: Which is more important?","volume":"142","author":"Zalesky","year":"2016","journal-title":"NeuroImage"},{"key":"2026072815553611700_IMAG.a.1310-b71","doi-asserted-by":"crossref","first-page":"4302","DOI":"10.1109\/TNSRE.2025.3616957","article-title":"Controlling epileptic seizures through hippocampal regulation: A complex network analysis in the mouse brain","volume":"33","author":"Zhou","year":"2025","journal-title":"IEEE Transactions on Neural Systems and Rehabilitation Engineering"},{"issue":"1","key":"2026072815553611700_IMAG.a.1310-b72","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1016\/j.brainresrev.2006.01.003","article-title":"The cerebellar-hypothalamic circuits: Potential pathways underlying cerebellar involvement in somatic-visceral integration","volume":"52","author":"Zhu","year":"2006","journal-title":"Brain Research Reviews"}],"container-title":["Imaging Neuroscience"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/direct.mit.edu\/imag\/article-pdf\/doi\/10.1162\/IMAG.a.1310\/2611111\/imag.a.1310.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/direct.mit.edu\/imag\/article-pdf\/doi\/10.1162\/IMAG.a.1310\/2611111\/imag.a.1310.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,28]],"date-time":"2026-07-28T19:55:49Z","timestamp":1785268549000},"score":1,"resource":{"primary":{"URL":"https:\/\/direct.mit.edu\/imag\/article\/doi\/10.1162\/IMAG.a.1310\/137531\/Experimental-quality-control-induces-changes-in"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026]]},"references-count":72,"URL":"https:\/\/doi.org\/10.1162\/imag.a.1310","relation":{},"ISSN":["2837-6056"],"issn-type":[{"value":"2837-6056","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026]]},"published":{"date-parts":[[2026]]},"article-number":"IMAG.a.1310"}}