{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,31]],"date-time":"2025-12-31T11:21:36Z","timestamp":1767180096852,"version":"build-2238731810"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1012504","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2024,10,17]],"date-time":"2024-10-17T00:00:00Z","timestamp":1729123200000}}],"reference-count":14,"publisher":"Public Library of Science (PLoS)","issue":"10","license":[{"start":{"date-parts":[[2024,10,7]],"date-time":"2024-10-07T00:00:00Z","timestamp":1728259200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003042","name":"Else Kr\u00f6ner-Fresenius-Stiftung","doi-asserted-by":"publisher","award":["2019_A70"],"award-info":[{"award-number":["2019_A70"]}],"id":[{"id":"10.13039\/501100003042","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>\n                    Spatio-molecular data and microscopy images provide complementary information, essential to study structure and function of spatially organised multicellular systems such as healthy or diseased tissues. However, aligning these two types of data can be challenging due to distortions and differences in resolution, orientation, and position. Manual registration is tedious but may be necessary for challenging samples as well as for the generation of ground-truth data sets that enable benchmarking of existing and emerging automated alignment tools. To make the process of manual registration more convenient, efficient, and integrated, we created\n                    <jats:italic>BoReMi<\/jats:italic>\n                    , a python-based, Jupyter-integrated, visual tool that offers all the relevant functionalities for aligning and registering spatio-molecular data and associated microscopy images. We showcase\n                    <jats:italic>BoReMi\u2019s<\/jats:italic>\n                    utility using publicly available data and images and make\n                    <jats:italic>BoReMi<\/jats:italic>\n                    as well as an interactive demo available on GitHub.\n                  <\/jats:p>","DOI":"10.1371\/journal.pcbi.1012504","type":"journal-article","created":{"date-parts":[[2024,10,7]],"date-time":"2024-10-07T13:36:41Z","timestamp":1728308201000},"page":"e1012504","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["BoReMi: Bokeh-based jupyter-interface for registering spatio-molecular data to related microscopy images"],"prefix":"10.1371","volume":"20","author":[{"given":"Jaspreet","family":"Ishar","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0009-0008-8269-3619","authenticated-orcid":true,"given":"Yee Man","family":"Tam","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1447-6811","authenticated-orcid":true,"given":"Simon","family":"Mages","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3628-9278","authenticated-orcid":true,"given":"Johanna","family":"Klughammer","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2024,10,7]]},"reference":[{"key":"pcbi.1012504.ref001","doi-asserted-by":"crossref","first-page":"236","DOI":"10.1016\/j.cell.2020.03.053","article-title":"The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution","volume":"181","author":"O Rozenblatt-Rosen","year":"2020","journal-title":"Cell"},{"key":"pcbi.1012504.ref002","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41592-020-01042-x","article-title":"Method of the Year 2020: spatially resolved transcriptomics","volume":"18","year":"2021","journal-title":"Nat Methods"},{"key":"pcbi.1012504.ref003","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1126\/science.aaf2403","article-title":"Visualization and analysis of gene expression in tissue sections by spatial transcriptomics","volume":"353","author":"PL St\u00e5hl","year":"2016","journal-title":"Science"},{"key":"pcbi.1012504.ref004","doi-asserted-by":"crossref","first-page":"11046","DOI":"10.1073\/pnas.1612826113","article-title":"High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization","volume":"113","author":"JR Moffitt","year":"2016","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi.1012504.ref005","doi-asserted-by":"crossref","first-page":"1463","DOI":"10.1126\/science.aaw1219","article-title":"Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution","volume":"363","author":"SG Rodriques","year":"2019","journal-title":"Science"},{"key":"pcbi.1012504.ref006","doi-asserted-by":"crossref","first-page":"968","DOI":"10.1016\/j.cell.2018.07.010","article-title":"Deep Profiling of Mouse Splenic Architecture with CODEX Multiplexed Imaging","volume":"174","author":"Y Goltsev","year":"2018","journal-title":"Cell"},{"key":"pcbi.1012504.ref007","doi-asserted-by":"crossref","first-page":"168","DOI":"10.1038\/nature05453","article-title":"Genome-wide atlas of gene expression in the adult mouse brain","volume":"445","author":"ES Lein","year":"2007","journal-title":"Nature"},{"key":"pcbi.1012504.ref008","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1038\/s41592-022-01459-6","article-title":"Alignment and integration of spatial transcriptomics data.","volume":"19","author":"R Zeira","year":"2022","journal-title":"Nat Methods"},{"key":"pcbi.1012504.ref009","first-page":"2023","article-title":"Spatial-linked alignment tool (SLAT) for aligning heterogenous slices properly.","author":"C-R Xia","year":"2023","journal-title":"bioRxiv"},{"key":"pcbi.1012504.ref010","article-title":"A landmark-based common coordinate framework for spatial transcriptomics data.","author":"A Andersson","year":"2021","journal-title":"bioRxiv"},{"key":"pcbi.1012504.ref011","doi-asserted-by":"crossref","first-page":"8123","DOI":"10.1038\/s41467-023-43915-7","article-title":"STalign: Alignment of spatial transcriptomics data using diffeomorphic metric mapping.","volume":"14","author":"K. Clifton","year":"2023","journal-title":"Nat Commun"},{"key":"pcbi.1012504.ref012","doi-asserted-by":"crossref","first-page":"1373","DOI":"10.1016\/j.cell.2018.08.039","article-title":"A Structured Tumor-Immune Microenvironment in Triple Negative Breast Cancer Revealed by Multiplexed Ion Beam Imaging","volume":"174","author":"L Keren","year":"2018","journal-title":"Cell"},{"key":"pcbi.1012504.ref013","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1186\/s12859-018-2375-z","article-title":"A deep learning-based algorithm for 2-D cell segmentation in microscopy images","volume":"19","author":"Y Al-Kofahi","year":"2018","journal-title":"BMC Bioinformatics"},{"key":"pcbi.1012504.ref014","author":"B. 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