{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,11]],"date-time":"2026-06-11T05:43:04Z","timestamp":1781156584395,"version":"3.54.1"},"reference-count":98,"publisher":"Institute of Electrical and Electronics Engineers (IEEE)","license":[{"start":{"date-parts":[[2022,1,1]],"date-time":"2022-01-01T00:00:00Z","timestamp":1640995200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/ieeexplore.ieee.org\/Xplorehelp\/downloads\/license-information\/IEEE.html"},{"start":{"date-parts":[[2022,1,1]],"date-time":"2022-01-01T00:00:00Z","timestamp":1640995200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2022,1,1]],"date-time":"2022-01-01T00:00:00Z","timestamp":1640995200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IEEE Trans. Visual. Comput. Graphics"],"published-print":{"date-parts":[[2022]]},"DOI":"10.1109\/tvcg.2022.3209378","type":"journal-article","created":{"date-parts":[[2022,9,28]],"date-time":"2022-09-28T15:54:10Z","timestamp":1664380450000},"page":"1-11","source":"Crossref","is-referenced-by-count":19,"title":["Visinity: Visual Spatial Neighborhood Analysis for Multiplexed Tissue Imaging Data"],"prefix":"10.1109","author":[{"given":"Simon","family":"Warchol","sequence":"first","affiliation":[{"name":"Harvard John A. Paulson School of Engineering and Applied Sciences, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert","family":"Krueger","sequence":"additional","affiliation":[{"name":"Harvard John A. Paulson School of Engineering and Applied Sciences, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ajit Johnson","family":"Nirmal","sequence":"additional","affiliation":[{"name":"Harvard John A. Paulson School of Engineering and Applied Sciences, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Giorgio","family":"Gaglia","sequence":"additional","affiliation":[{"name":"Harvard John A. Paulson School of Engineering and Applied Sciences, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jared","family":"Jessup","sequence":"additional","affiliation":[{"name":"Harvard John A. Paulson School of Engineering and Applied Sciences, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cecily C.","family":"Ritch","sequence":"additional","affiliation":[{"name":"Harvard John A. Paulson School of Engineering and Applied Sciences, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John","family":"Hoffer","sequence":"additional","affiliation":[{"name":"Harvard John A. Paulson School of Engineering and Applied Sciences, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeremy","family":"Muhlich","sequence":"additional","affiliation":[{"name":"Harvard John A. Paulson School of Engineering and Applied Sciences, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Megan L.","family":"Burger","sequence":"additional","affiliation":[{"name":"Harvard John A. Paulson School of Engineering and Applied Sciences, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tyler","family":"Jacks","sequence":"additional","affiliation":[{"name":"Harvard John A. Paulson School of Engineering and Applied Sciences, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sandro","family":"Santagata","sequence":"additional","affiliation":[{"name":"Harvard John A. Paulson School of Engineering and Applied Sciences, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter K.","family":"Sorger","sequence":"additional","affiliation":[{"name":"Harvard John A. Paulson School of Engineering and Applied Sciences, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hanspeter","family":"Pfister","sequence":"additional","affiliation":[{"name":"Harvard John A. Paulson School of Engineering and Applied Sciences, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"263","reference":[{"key":"ref39","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-020-00809-z"},{"key":"ref38","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-13056-x"},{"key":"ref33","doi-asserted-by":"publisher","DOI":"10.1109\/TVCG.2009.153"},{"key":"ref32","first-page":"1","article-title":"Scope2Screen: Focus+Context Techniques for Pathology Tumor Assessment in Multivariate Image Data","author":"jessup","year":"2021","journal-title":"IEEE Transactions on Visualization and Computer Graphics"},{"key":"ref31","doi-asserted-by":"publisher","DOI":"10.1186\/s40064-016-2941-7"},{"key":"ref30","doi-asserted-by":"publisher","DOI":"10.1016\/0169-2607(91)90103-Z"},{"key":"ref37","author":"kingma","year":"2014","journal-title":"Auto-encoding variational bayes"},{"key":"ref36","author":"kakde","year":"2005","journal-title":"Range Searching using Kd Tree"},{"key":"ref35","volume":"9413","author":"moore","year":"2015","journal-title":"OMERO and Bio-Formats 5 flexible access to large bioimaging datasets at scale"},{"key":"ref34","article-title":"Billion-scale similarity search with GPUs","author":"johnson","year":"2017","journal-title":"ArXiv Preprint"},{"key":"ref28","doi-asserted-by":"publisher","DOI":"10.1179\/000870403235002042"},{"key":"ref27","doi-asserted-by":"publisher","DOI":"10.15252\/msb.20177651"},{"key":"ref29","doi-asserted-by":"publisher","DOI":"10.21105\/joss.02579"},{"key":"ref20","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1300136110"},{"key":"ref22","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2018.07.010"},{"key":"ref21","doi-asserted-by":"publisher","DOI":"10.1109\/TPAMI.2015.2437384"},{"key":"ref24","doi-asserted-by":"publisher","DOI":"10.1109\/TVCG.2016.2598918"},{"key":"ref23","doi-asserted-by":"publisher","DOI":"10.1101\/gad.314617.118"},{"key":"ref26","article-title":"Accelerating Large-Scale Inference with Anisotropic Vector Quantization","author":"guo","year":"0","journal-title":"International Conference on Machine Learning"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"1041","DOI":"10.1109\/TVCG.2009.143","article-title":"Flow Mapping and Multivariate Visualization of Large Spatial Interaction Data","volume":"15","author":"guo","year":"2009","journal-title":"IEEE Transactions on Visualization and Computer Graphics"},{"key":"ref50","article-title":"Multiplexed 3D atlas of state transitions and immune interactions in colorectal cancer","author":"lin","year":"2021","journal-title":"BioRxiv"},{"key":"ref51","doi-asserted-by":"publisher","DOI":"10.1109\/TVCG.2013.124"},{"key":"ref59","doi-asserted-by":"publisher","DOI":"10.1609\/aaai.v35i1.16118"},{"key":"ref58","doi-asserted-by":"publisher","DOI":"10.2139\/ssrn.3862021"},{"key":"ref57","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-030-61864-3_29"},{"key":"ref56","doi-asserted-by":"publisher","DOI":"10.2307\/2332142"},{"key":"ref55","author":"miles","year":"2020","journal-title":"zarr-developers\/zarr-python v2 4 0"},{"key":"ref54","author":"mcinnes","year":"2020","journal-title":"Umap Uniform manifold approximation and projection for dimension reduction"},{"key":"ref53","article-title":"Viv: Multiscale Visualization of High-Resolution Multiplexed Bioimaging Data on the Web","author":"manz","year":"2020","journal-title":"OSF Preprints"},{"key":"ref52","doi-asserted-by":"publisher","DOI":"10.1109\/VAST.2012.6400491"},{"key":"ref40","doi-asserted-by":"publisher","DOI":"10.1109\/TVCG.2019.2934547"},{"key":"ref4","year":"0","journal-title":"Visinity codebase"},{"key":"ref3","year":"0","journal-title":"An overview of the Spatial Statistics toolbox&#x2014;Help ? ArcGIS Desktop"},{"key":"ref6","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jproteome.7b00725"},{"key":"ref5","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btaa816"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1177\/1473871615581216","article-title":"Scalable and privacy-respectful interactive discovery of place semantics from human mobility traces","volume":"15","author":"andrienko","year":"2016","journal-title":"Information Visualization"},{"key":"ref49","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.31657"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"12244","DOI":"10.1073\/pnas.1510227113","article-title":"Data-driven identification of prognostic tumor subpopulations using spatially mapped t-SNE of mass spectrometry imaging data","volume":"113","author":"walid","year":"2016","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"ref9","doi-asserted-by":"publisher","DOI":"10.1109\/INFVIS.1998.729559"},{"key":"ref46","doi-asserted-by":"publisher","DOI":"10.1016\/j.ymeth.2015.10.006"},{"key":"ref45","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2015.05.047"},{"key":"ref48","doi-asserted-by":"publisher","DOI":"10.1002\/cpch.14"},{"key":"ref47","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr260"},{"key":"ref42","author":"landesberger","year":"2009","journal-title":"A System for Interactive Visual Analysis of Large Graphs Using Motifs in Graph Editing and Aggregation"},{"key":"ref41","doi-asserted-by":"publisher","DOI":"10.1145\/2833157.2833162"},{"key":"ref44","doi-asserted-by":"publisher","DOI":"10.1111\/cgf.13971"},{"key":"ref43","author":"lekschas","year":"2021","journal-title":"flekschas\/regl-scatterplot"},{"key":"ref73","doi-asserted-by":"publisher","DOI":"10.1109\/CMV.2007.20"},{"key":"ref72","doi-asserted-by":"publisher","DOI":"10.2307\/3212829"},{"key":"ref71","author":"ribeiro","year":"2019","journal-title":"A survey on subgraph counting Concepts algorithms and applications to network motifs and graphlets"},{"key":"ref70","first-page":"2020.03.27.001834","article-title":"Online narrative guides for illuminating tissue atlas data and digital pathology images","author":"rashid","year":"2020","journal-title":"BioRxiv"},{"key":"ref76","author":"russakovsky","year":"2015","journal-title":"Imagenet Large Scale Visual Recognition Challenge"},{"key":"ref77","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4391"},{"key":"ref74","doi-asserted-by":"publisher","DOI":"10.1016\/j.cag.2011.01.011"},{"key":"ref75","doi-asserted-by":"publisher","DOI":"10.1002\/prca.201800057"},{"key":"ref78","article-title":"MCMICRO: A scalable, modular image-processing pipeline for multiplexed tissue imaging","author":"schapiro","year":"2021","journal-title":"BioRxiv"},{"key":"ref79","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-642-03647-7_2"},{"key":"ref60","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-019-2725-5"},{"key":"ref62","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-23807-4"},{"key":"ref61","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-021-01182-1"},{"key":"ref63","first-page":"2825","article-title":"Scikit-learn: Machine learning in Python","volume":"12","author":"pedregosa","year":"2011","journal-title":"Journal of Machine Learning Research"},{"key":"ref64","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-021-01044-w"},{"key":"ref65","doi-asserted-by":"publisher","DOI":"10.1109\/TVCG.2016.2570755"},{"key":"ref66","doi-asserted-by":"publisher","DOI":"10.1109\/TVCG.2019.2934307"},{"key":"ref67","author":"pham","year":"2020","journal-title":"stLearn integrating spatial location tissue morphology and gene expression to find cell types cell-cell interactions and spatial trajectories within undissociated tissues"},{"key":"ref68","doi-asserted-by":"publisher","DOI":"10.1109\/INFVIS.2005.1532150"},{"key":"ref2","year":"0","journal-title":"Halo"},{"key":"ref69","doi-asserted-by":"publisher","DOI":"10.1109\/BDVA.2017.8114626"},{"key":"ref1","year":"0","journal-title":"About ArcGIS ? Mapping & Analytics Software and Services"},{"key":"ref95","doi-asserted-by":"publisher","DOI":"10.1109\/ICCV48922.2021.01037"},{"key":"ref94","doi-asserted-by":"publisher","DOI":"10.3138\/carto.46.4.239"},{"key":"ref93","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbr033"},{"key":"ref92","doi-asserted-by":"crossref","DOI":"10.23915\/distill.00002","article-title":"How to Use t-SNE Effectively","author":"wattenberg","year":"2016","journal-title":"Distillation"},{"key":"ref91","first-page":"8","author":"wang","year":"0","journal-title":"Spatial Latent Dirichlet Allocation"},{"key":"ref90","doi-asserted-by":"publisher","DOI":"10.1109\/TVCG.2015.2468111"},{"key":"ref98","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.4260"},{"key":"ref96","doi-asserted-by":"publisher","DOI":"10.1016\/j.patcog.2012.04.031"},{"key":"ref97","doi-asserted-by":"publisher","DOI":"10.1109\/TVCG.2016.2598885"},{"key":"ref10","author":"borchert","year":"2022","journal-title":"PyCave"},{"key":"ref11","first-page":"1","article-title":"Attraction-Repulsion Spectrum in Neighbor Embeddings","volume":"23","author":"b\u00f6hm","year":"2022","journal-title":"Journal of Machine Learning Research"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1007\/978-3-540-70956-5_2","article-title":"Evaluating Information Visualizations","author":"carpendale","year":"2008","journal-title":"Information Visualization Human-Centered Issues and Perspectives"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"5871","DOI":"10.1021\/acs.analchem.6b00672","article-title":"Spatial Autocorrelation in Mass Spectrometry Imaging","volume":"88","author":"cassese","year":"2016","journal-title":"Analytical Chemistry"},{"key":"ref14","first-page":"1109","article-title":"Large Scale Online Learning of Image Similarity Through Ranking","volume":"11","author":"chechik","year":"2010","journal-title":"J Mach Learn Res"},{"key":"ref15","doi-asserted-by":"publisher","DOI":"10.1214\/21-SS133"},{"key":"ref82","author":"sofroniew","year":"2022","journal-title":"napari\/napari 0 4 15rc1"},{"key":"ref16","doi-asserted-by":"publisher","DOI":"10.1214\/09-STS312"},{"key":"ref81","author":"segaran","year":"2007","journal-title":"Programming Collective Intelligence Building Smart Web 2 0 Applications"},{"key":"ref17","doi-asserted-by":"publisher","DOI":"10.1021\/ac302330a"},{"key":"ref84","doi-asserted-by":"publisher","DOI":"10.1109\/TVCG.2019.2931299"},{"key":"ref18","doi-asserted-by":"publisher","DOI":"10.2307\/2986645"},{"key":"ref83","doi-asserted-by":"publisher","DOI":"10.1109\/TVCG.2020.3030336"},{"key":"ref19","year":"0","journal-title":"Vitessce"},{"key":"ref80","doi-asserted-by":"publisher","DOI":"10.1109\/TVCG.2012.213"},{"key":"ref89","doi-asserted-by":"publisher","DOI":"10.1109\/PacificVis53943.2022.00010"},{"key":"ref85","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2020.107523"},{"key":"ref86","doi-asserted-by":"publisher","DOI":"10.2307\/143141"},{"key":"ref87","first-page":"2579","article-title":"Visualizing data using t-SNE","volume":"9","author":"van der maaten","year":"2008","journal-title":"Journal of Machine Learning Research"},{"key":"ref88","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-017-01689-9"}],"container-title":["IEEE Transactions on Visualization and Computer Graphics"],"original-title":[],"link":[{"URL":"http:\/\/xplorestaging.ieee.org\/ielx7\/2945\/4359476\/09904770.pdf?arnumber=9904770","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,12,19]],"date-time":"2022-12-19T10:51:48Z","timestamp":1671447108000},"score":1,"resource":{"primary":{"URL":"https:\/\/ieeexplore.ieee.org\/document\/9904770\/"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022]]},"references-count":98,"URL":"https:\/\/doi.org\/10.1109\/tvcg.2022.3209378","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2022.05.09.490039","asserted-by":"object"}]},"ISSN":["1077-2626","1941-0506","2160-9306"],"issn-type":[{"value":"1077-2626","type":"print"},{"value":"1941-0506","type":"electronic"},{"value":"2160-9306","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022]]}}}