{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,29]],"date-time":"2026-03-29T08:08:18Z","timestamp":1774771698350,"version":"3.50.1"},"reference-count":72,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2024,2,9]],"date-time":"2024-02-09T00:00:00Z","timestamp":1707436800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Neuroinform."],"abstract":"<jats:p>Neuroscientists employ a range of methods and generate increasing amounts of data describing brain structure and function. The anatomical locations from which observations or measurements originate represent a common context for data interpretation, and a starting point for identifying data of interest. However, the multimodality and abundance of brain data pose a challenge for efforts to organize, integrate, and analyze data based on anatomical locations. While structured metadata allow faceted data queries, different types of data are not easily represented in a standardized and machine-readable way that allow comparison, analysis, and queries related to anatomical relevance. To this end, three-dimensional (3D) digital brain atlases provide frameworks in which disparate multimodal and multilevel neuroscience data can be spatially represented. We propose to represent the locations of different neuroscience data as geometric objects in 3D brain atlases. Such geometric objects can be specified in a standardized file format and stored as location metadata for use with different computational tools. We here present the Locare workflow developed for defining the anatomical location of data elements from rodent brains as geometric objects. We demonstrate how the workflow can be used to define geometric objects representing multimodal and multilevel experimental neuroscience in rat or mouse brain atlases. We further propose a collection of JSON schemas (LocareJSON) for specifying geometric objects by atlas coordinates, suitable as a starting point for co-visualization of different data in an anatomical context and for enabling spatial data queries.<\/jats:p>","DOI":"10.3389\/fninf.2024.1284107","type":"journal-article","created":{"date-parts":[[2024,2,9]],"date-time":"2024-02-09T04:37:41Z","timestamp":1707453461000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":5,"title":["The Locare workflow: representing neuroscience data locations as geometric objects in 3D brain atlases"],"prefix":"10.3389","volume":"18","author":[{"given":"Camilla H.","family":"Blixhavn","sequence":"first","affiliation":[]},{"given":"Ingrid","family":"Reiten","sequence":"additional","affiliation":[]},{"given":"Heidi","family":"Kleven","sequence":"additional","affiliation":[]},{"given":"Martin","family":"\u00d8vsthus","sequence":"additional","affiliation":[]},{"given":"Sharon C.","family":"Yates","sequence":"additional","affiliation":[]},{"given":"Ulrike","family":"Schlegel","sequence":"additional","affiliation":[]},{"given":"Maja A.","family":"Puchades","sequence":"additional","affiliation":[]},{"given":"Oliver","family":"Schmid","sequence":"additional","affiliation":[]},{"given":"Jan G.","family":"Bjaalie","sequence":"additional","affiliation":[]},{"given":"Ingvild E.","family":"Bjerke","sequence":"additional","affiliation":[]},{"given":"Trygve B.","family":"Leergaard","sequence":"additional","affiliation":[]}],"member":"1965","published-online":{"date-parts":[[2024,2,9]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1007\/s12021-020-09509-0","article-title":"A standards Organization for Open and FAIR neuroscience: the international Neuroinformatics coordinating facility","volume":"20","author":"Abrams","year":"2022","journal-title":"Neuroinformatics"},{"key":"ref2","doi-asserted-by":"publisher","first-page":"e3000344","DOI":"10.1371\/journal.pbio.3000344","article-title":"The human brain project\u2014synergy between neuroscience, computing, informatics, and brain-inspired technologies","volume":"17","author":"Amunts","year":"2019","journal-title":"PLoS Biol."},{"key":"ref3","doi-asserted-by":"publisher","first-page":"988","DOI":"10.1126\/science.abb4588","article-title":"Julich-brain: a 3D probabilistic atlas of the human brain\u2019s cytoarchitecture","volume":"369","author":"Amunts","year":"2020","journal-title":"Science"},{"key":"ref4","author":"Arena","year":"2020"},{"key":"ref5","author":"Arena","year":"2018"},{"key":"ref6","author":"Arena","year":""},{"key":"ref7","author":"Arena","year":""},{"key":"ref8","doi-asserted-by":"publisher","first-page":"112","DOI":"10.1038\/nmeth.4152","article-title":"Win\u2013win data sharing in neuroscience","volume":"14","author":"Ascoli","year":"2017","journal-title":"Nat. Methods"},{"key":"ref9001","doi-asserted-by":"publisher","first-page":"353","DOI":"10.1007\/s12021-014-9258-x","article-title":"The scalable brain atlas: instant web-based access to public brain atlases and related content","volume":"13","author":"Bakker","year":"2015","journal-title":"Neuroinform"},{"key":"ref9","doi-asserted-by":"publisher","DOI":"10.1162\/imag_a_00077","article-title":"MEBRAINS 1.0: a new population-based macaque atlas. Imaging","author":"Balan","year":"2024","journal-title":"Neuroscience"},{"key":"ref10","doi-asserted-by":"publisher","first-page":"353","DOI":"10.1038\/nn.4502","article-title":"Network neuroscience","volume":"20","author":"Bassett","year":"2017","journal-title":"Nat. Neurosci."},{"key":"ref9002","author":"Bjerke","year":"2021"},{"key":"ref11","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3389\/fnana.2018.00082","article-title":"Navigating the murine brain: toward best practices for determining and documenting neuroanatomical locations in experimental studies","volume":"12","author":"Bjerke","year":"","journal-title":"Front. Neuroanat."},{"key":"ref12","doi-asserted-by":"publisher","first-page":"70","DOI":"10.1016\/j.eurpsy.2018.02.004","article-title":"Data integration through brain atlasing: human brain project tools and strategies","volume":"50","author":"Bjerke","year":"","journal-title":"Eur. Psychiatry"},{"key":"ref13","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1038\/s41597-020-0550-3","article-title":"Database of literature derived cellular measurements from the murine basal ganglia","volume":"7","author":"Bjerke","year":"","journal-title":"Sci. Data"},{"key":"ref14","author":"Bjerke","year":""},{"key":"ref15","author":"Bjerke","year":""},{"key":"ref16","doi-asserted-by":"publisher","first-page":"107562","DOI":"10.1016\/j.isci.2023.107562","article-title":"Scaling up cell-counting efforts in neuroscience through semi-automated methods","volume":"26","author":"Bjerke","year":"2023","journal-title":"iScience"},{"key":"ref17","author":"Bjerke","year":""},{"key":"ref18","author":"Blixhavn","year":""},{"key":"ref19","author":"Blixhavn","year":"2022"},{"key":"ref20","author":"Blixhavn","year":""},{"key":"ref21","author":"Blixhavn","year":""},{"key":"ref22","author":"Blixhavn","year":""},{"key":"ref23","author":"Blixhavn","year":""},{"key":"ref24","author":"Blixhavn","year":""},{"key":"ref25","doi-asserted-by":"publisher","first-page":"W553","DOI":"10.1093\/nar\/gkad413","article-title":"SMDB: a spatial multimodal data browser","volume":"51","author":"Cao","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"5884","DOI":"10.1038\/s41467-023-41645-4","article-title":"DeepSlice: rapid fully automatic registration of mouse brain imaging to a volumetric atlas","volume":"14","author":"Carey","year":"2023","journal-title":"Nat. Commun."},{"key":"ref27","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1186\/s12861-016-0116-y","article-title":"Representation of anatomy in online atlases and databases: a survey and collection of patterns for interface design","volume":"16","author":"Clarkson","year":"2016","journal-title":"BMC Dev. Biol."},{"key":"ref28","author":"Conti","year":"2019"},{"key":"ref29","author":"Feldmeyer","year":"2020"},{"key":"ref30","doi-asserted-by":"publisher","first-page":"1442","DOI":"10.1038\/nn.3838","article-title":"Big data from small data: data-sharing in the \u2018long tail\u2019 of neuroscience","volume":"17","author":"Ferguson","year":"2014","journal-title":"Nat. Neurosci."},{"key":"ref31","author":"Fiorilli","year":"2023"},{"key":"ref32","author":"Fiorilli","year":"2022"},{"key":"ref33","volume-title":"The mouse brain in stereotaxic coordinates","author":"Franklin","year":"2007"},{"key":"ref35","doi-asserted-by":"publisher","first-page":"e83496","DOI":"10.7554\/eLife.83496","article-title":"Histological E-data registration in rodent brain spaces","volume":"12","author":"Fuglstad","year":"2023","journal-title":"Elife"},{"key":"ref36","doi-asserted-by":"publisher","first-page":"895","DOI":"10.1038\/s41593-017-0058-0","article-title":"An interactive framework for whole-brain maps at cellular resolution","volume":"21","author":"F\u00fcrth","year":"2018","journal-title":"Nat. Neurosci."},{"key":"ref37","author":"Garc\u00eda-Amado","year":"2020"},{"key":"ref38","doi-asserted-by":"publisher","first-page":"341ps12","DOI":"10.1126\/scitranslmed.aaf5027","article-title":"What does research reproducibility mean?","volume":"8","author":"Goodman","year":"2016","journal-title":"Sci. Transl. Med."},{"key":"ref39","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3389\/fninf.2020.00037","article-title":"Nutil: a pre- and post-processing toolbox for histological rodent brain section images","volume":"14","author":"Groeneboom","year":"2020","journal-title":"Front. Neuroinform."},{"key":"ref40","author":"Gurdon","year":"2023"},{"key":"ref41","doi-asserted-by":"publisher","first-page":"20140164","DOI":"10.1098\/rstb.2014.0164","article-title":"The BRAIN initiative: developing technology to catalyse neuroscience discovery","volume":"370","author":"Jorgenson","year":"2015","journal-title":"Philos. Trans. R. Soc. B"},{"key":"ref42","doi-asserted-by":"publisher","first-page":"456","DOI":"10.1016\/j.cell.2017.09.020","article-title":"Brain-wide maps reveal stereotyped cell-type-based cortical architecture and subcortical sexual resource brain-wide maps reveal stereotyped cell-type-based cortical architecture and subcortical sexual dimorphism","volume":"171","author":"Kim","year":"2017","journal-title":"Cell"},{"key":"ref43","doi-asserted-by":"publisher","first-page":"441","DOI":"10.1016\/j.neuroimage.2014.12.080","article-title":"Waxholm space atlas of the rat brain hippocampal region: three-dimensional delineations based on magnetic resonance and diffusion tensor imaging","volume":"108","author":"Kjonigsen","year":"2015","journal-title":"Neuroimage"},{"key":"ref44","doi-asserted-by":"publisher","first-page":"196","DOI":"10.1109\/TMI.2009.2035616","article-title":"Elastix: a toolbox for intensity-based medical image registration","volume":"29","author":"Klein","year":"2010","journal-title":"IEEE Trans. Med. Imaging"},{"key":"ref45","doi-asserted-by":"publisher","first-page":"1822","DOI":"10.1038\/s41592-023-02034-3","article-title":"Waxholm space atlas of the rat brain: a 3D atlas supporting data analysis and integration","volume":"20","author":"Kleven","year":"","journal-title":"Nat. Methods"},{"key":"ref46","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3389\/fninf.2023.1154080","article-title":"A neuroscientist\u2019s guide to using murine brain atlases for efficient analysis and transparent reporting","volume":"17","author":"Kleven","year":"","journal-title":"Front. Neuroinform."},{"key":"ref47","author":"Kondo","year":"2022"},{"key":"ref48","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1016\/j.neuron.2019.04.034","article-title":"A cellular-resolution atlas of the larval zebrafish brain","volume":"103","author":"Kunst","year":"2019","journal-title":"Neuron"},{"key":"ref49","doi-asserted-by":"publisher","first-page":"488","DOI":"10.1126\/science.abq2594","article-title":"Atlas-based data integration for mapping the connections and architecture of the brain","volume":"378","author":"Leergaard","year":"2022","journal-title":"Science"},{"key":"ref50","doi-asserted-by":"publisher","first-page":"467","DOI":"10.1038\/nn1229","article-title":"E-neuroscience: challenges and triumphs in integrating distributed data from molecules to brains","volume":"7","author":"Martone","year":"2004","journal-title":"Nat. Neurosci."},{"key":"ref52","doi-asserted-by":"publisher","first-page":"11879","DOI":"10.1038\/ncomms11879","article-title":"AMAP is a validated pipeline for registration and segmentation of high-resolution mouse brain data","volume":"7","author":"Niedworok","year":"2016","journal-title":"Nat. Commun."},{"key":"ref53","doi-asserted-by":"publisher","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"},{"key":"ref54","doi-asserted-by":"publisher","first-page":"38","DOI":"10.1016\/j.neuroimage.2019.05.016","article-title":"Waxholm space atlas of the rat brain auditory system: three-dimensional delineations based on structural and diffusion tensor magnetic resonance imaging","volume":"199","author":"Osen","year":"2019","journal-title":"Neuroimage"},{"key":"ref55","doi-asserted-by":"publisher","first-page":"GRDI19","DOI":"10.2481\/dsj.GRDI-004","article-title":"Data interoperability","volume":"12","author":"Pagano","year":"2013","journal-title":"Data Sci. J."},{"key":"ref56","doi-asserted-by":"publisher","first-page":"374","DOI":"10.1016\/j.neuroimage.2014.04.001","article-title":"Waxholm space atlas of the Sprague Dawley rat brain","volume":"97","author":"Papp","year":"2014","journal-title":"Neuroimage"},{"key":"ref57","volume-title":"Paxinos and Watson\u2019s The rat brain in stereotaxic coordinates compact","author":"Paxinos","year":"2018"},{"key":"ref59","doi-asserted-by":"publisher","first-page":"e0216796","DOI":"10.1371\/journal.pone.0216796","article-title":"Spatial registration of serial microscopic brain images to three-dimensional reference atlases with the QuickNII tool","volume":"14","author":"Puchades","year":"2019","journal-title":"PloS One"},{"key":"ref60","author":"Reiten","year":""},{"key":"ref61","author":"Reiten","year":""},{"key":"ref62","author":"Reiten","year":""},{"key":"ref63","author":"Resta","year":"2021"},{"key":"ref64","author":"Schnabel","year":"2020"},{"key":"ref65","doi-asserted-by":"publisher","first-page":"1440","DOI":"10.1038\/nn.3839","article-title":"Putting big data to good use in neuroscience","volume":"17","author":"Sejnowski","year":"2014","journal-title":"Nat. Neurosci."},{"key":"ref66","doi-asserted-by":"publisher","first-page":"79","DOI":"10.1038\/s41746-019-0079-z","article-title":"The reproducibility crisis in the age of digital medicine","volume":"2","author":"Stupple","year":"2019","journal-title":"NPJ Digit. Med."},{"key":"ref67","doi-asserted-by":"publisher","first-page":"2200","DOI":"10.1002\/cne.24635","article-title":"Automatic navigation system for the mouse brain","volume":"527","author":"Tappan","year":"2019","journal-title":"J. Comp. Neurol."},{"key":"ref68","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1016\/j.pbiomolbio.2021.06.013","article-title":"Mesoscale microscopy and image analysis tools for understanding the brain","volume":"168","author":"Tyson","year":"2022","journal-title":"Prog. Biophys. Mol. Biol."},{"key":"ref69","doi-asserted-by":"publisher","first-page":"867","DOI":"10.1038\/s41598-021-04676-9","article-title":"Accurate determination of marker location within whole-brain microscopy images","volume":"12","author":"Tyson","year":"2022","journal-title":"Sci. Rep."},{"key":"ref70","doi-asserted-by":"publisher","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"},{"key":"ref71","doi-asserted-by":"publisher","first-page":"160018","DOI":"10.1038\/sdata.2016.18","article-title":"The FAIR guiding principles for scientific data management and stewardship","volume":"3","author":"Wilkinson","year":"2016","journal-title":"Sci. Data"},{"key":"ref72","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3389\/fninf.2019.00075","article-title":"QUINT: workflow for quantification and spatial analysis of features in histological images from rodent brain","volume":"13","author":"Yates","year":"2019","journal-title":"Front. Neuroinform."},{"key":"ref73","doi-asserted-by":"publisher","first-page":"74","DOI":"10.3389\/fninf.2014.00074","article-title":"Cyberinfrastructure for the digital brain: spatial standards for integrating rodent brain atlases","volume":"8","author":"Zaslavsky","year":"2014","journal-title":"Front. Neuroinform."}],"container-title":["Frontiers in Neuroinformatics"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fninf.2024.1284107\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,2,28]],"date-time":"2024-02-28T14:14:40Z","timestamp":1709129680000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fninf.2024.1284107\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,2,9]]},"references-count":72,"alternative-id":["10.3389\/fninf.2024.1284107"],"URL":"https:\/\/doi.org\/10.3389\/fninf.2024.1284107","relation":{},"ISSN":["1662-5196"],"issn-type":[{"value":"1662-5196","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,2,9]]},"article-number":"1284107"}}