{"id":"https://openalex.org/W4403183614","doi":"https://doi.org/10.1371/journal.pcbi.1012504","title":"BoReMi: Bokeh-based jupyter-interface for registering spatio-molecular data to related microscopy images","display_name":"BoReMi: Bokeh-based jupyter-interface for registering spatio-molecular data to related microscopy images","publication_year":2024,"publication_date":"2024-10-07","ids":{"openalex":"https://openalex.org/W4403183614","doi":"https://doi.org/10.1371/journal.pcbi.1012504","pmid":"https://pubmed.ncbi.nlm.nih.gov/39374301"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1012504","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012504","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1012504","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5107806731","display_name":"Jaspreet Ishar","orcid":null},"institutions":[{"id":"https://openalex.org/I16391192","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49","country_code":"IL","type":"education","lineage":["https://openalex.org/I16391192"]}],"countries":["IL"],"is_corresponding":true,"raw_author_name":"Jaspreet Ishar","raw_affiliation_strings":["School of Neurobiology, Biochemistry and Biophysics, Tel Aviv University, Tel Aviv, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Neurobiology, Biochemistry and Biophysics, Tel Aviv University, Tel Aviv, Israel","institution_ids":["https://openalex.org/I16391192"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006166420","display_name":"Yee Man Tam","orcid":"https://orcid.org/0009-0008-8269-3619"},"institutions":[{"id":"https://openalex.org/I8204097","display_name":"Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen","ror":"https://ror.org/05591te55","country_code":"DE","type":"education","lineage":["https://openalex.org/I8204097"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Yee Man Tam","raw_affiliation_strings":["Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universit\u00e4t, Munich, Germany"],"raw_orcid":"https://orcid.org/0009-0008-8269-3619","affiliations":[{"raw_affiliation_string":"Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universit\u00e4t, Munich, Germany","institution_ids":["https://openalex.org/I8204097"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012103892","display_name":"Simon Mages","orcid":"https://orcid.org/0000-0003-1447-6811"},"institutions":[{"id":"https://openalex.org/I8204097","display_name":"Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen","ror":"https://ror.org/05591te55","country_code":"DE","type":"education","lineage":["https://openalex.org/I8204097"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Simon Mages","raw_affiliation_strings":["Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universit\u00e4t, Munich, Germany"],"raw_orcid":"https://orcid.org/0000-0003-1447-6811","affiliations":[{"raw_affiliation_string":"Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universit\u00e4t, Munich, Germany","institution_ids":["https://openalex.org/I8204097"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5091889636","display_name":"Johanna Klughammer","orcid":"https://orcid.org/0000-0002-3628-9278"},"institutions":[{"id":"https://openalex.org/I8204097","display_name":"Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen","ror":"https://ror.org/05591te55","country_code":"DE","type":"education","lineage":["https://openalex.org/I8204097"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Johanna Klughammer","raw_affiliation_strings":["Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universit\u00e4t, Munich, Germany"],"raw_orcid":"https://orcid.org/0000-0002-3628-9278","affiliations":[{"raw_affiliation_string":"Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universit\u00e4t, Munich, Germany","institution_ids":["https://openalex.org/I8204097"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5006166420","https://openalex.org/A5012103892","https://openalex.org/A5091889636","https://openalex.org/A5107806731"],"corresponding_institution_ids":["https://openalex.org/I16391192","https://openalex.org/I8204097"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.15476242,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"20","issue":"10","first_page":"e1012504","last_page":"e1012504"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.987500011920929,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.7546588182449341},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7258796095848083},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.5374031662940979},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.5094009041786194},{"id":"https://openalex.org/keywords/orientation","display_name":"Orientation (vector space)","score":0.4935077428817749},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4879283607006073},{"id":"https://openalex.org/keywords/ground-truth","display_name":"Ground truth","score":0.4339580535888672},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.37751805782318115},{"id":"https://openalex.org/keywords/computer-vision","display_name":"Computer vision","score":0.3600512146949768}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.7546588182449341},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7258796095848083},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.5374031662940979},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.5094009041786194},{"id":"https://openalex.org/C16345878","wikidata":"https://www.wikidata.org/wiki/Q107472979","display_name":"Orientation (vector space)","level":2,"score":0.4935077428817749},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4879283607006073},{"id":"https://openalex.org/C146849305","wikidata":"https://www.wikidata.org/wiki/Q370766","display_name":"Ground truth","level":2,"score":0.4339580535888672},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.37751805782318115},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.3600512146949768},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":true},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":true},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":true},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":true},{"descriptor_ui":"D008853","descriptor_name":"Microscopy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D008853","descriptor_name":"Microscopy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D008853","descriptor_name":"Microscopy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D008853","descriptor_name":"Microscopy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1371/journal.pcbi.1012504","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012504","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:39374301","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39374301","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11486395","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11486395","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11486395/pdf/pcbi.1012504.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1012504","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012504","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G727481207","display_name":null,"funder_award_id":"CRC237","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G7469652280","display_name":null,"funder_award_id":"2019_A70","funder_id":"https://openalex.org/F4320321672","funder_display_name":"Else Kr\u00f6ner-Fresenius-Stiftung"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320321672","display_name":"Else Kr\u00f6ner-Fresenius-Stiftung","ror":"https://ror.org/03zcxha54"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":14,"referenced_works":["https://openalex.org/W2123491442","https://openalex.org/W2471536144","https://openalex.org/W2520858613","https://openalex.org/W2890156321","https://openalex.org/W2895303488","https://openalex.org/W2915848182","https://openalex.org/W2949238013","https://openalex.org/W3016787828","https://openalex.org/W3213559550","https://openalex.org/W4233578221","https://openalex.org/W4280494993","https://openalex.org/W4362735969","https://openalex.org/W4388530027","https://openalex.org/W4389481214"],"related_works":["https://openalex.org/W4238897586","https://openalex.org/W435179959","https://openalex.org/W2619091065","https://openalex.org/W2059640416","https://openalex.org/W1490753184","https://openalex.org/W2284465472","https://openalex.org/W2291782699","https://openalex.org/W1993948687","https://openalex.org/W2000169967","https://openalex.org/W2112883198"],"abstract_inverted_index":{"Spatio-molecular":[0],"data":[1,31,64,107,119],"and":[2,12,38,43,71,86,104,108,120,122],"microscopy":[3,110],"images":[4,121],"provide":[5],"complementary":[6],"information,":[7],"essential":[8],"to":[9,36],"study":[10],"structure":[11],"function":[13],"of":[14,30,62,69,80],"spatially":[15],"organised":[16],"multicellular":[17],"systems":[18],"such":[19],"as":[20,56,58,125,127],"healthy":[21],"or":[22],"diseased":[23],"tissues.":[24],"However,":[25],"aligning":[26,103],"these":[27],"two":[28],"types":[29],"can":[32],"be":[33,51],"challenging":[34,54],"due":[35],"distortions":[37],"differences":[39],"in":[40],"resolution,":[41],"orientation,":[42],"position.":[44],"Manual":[45],"registration":[46,82],"is":[47],"tedious":[48],"but":[49],"may":[50],"necessary":[52],"for":[53,59,102],"samples":[55],"well":[57,126],"the":[60,78,99],"generation":[61],"ground-truth":[63],"sets":[65],"that":[66,96],"enable":[67],"benchmarking":[68],"existing":[70],"emerging":[72],"automated":[73],"alignment":[74],"tools.":[75],"To":[76],"make":[77,123],"process":[79],"manual":[81],"more":[83],"convenient,":[84],"efficient,":[85],"integrated,":[87],"we":[88],"created":[89],"BoReMi,":[90],"a":[91],"python-based,":[92],"Jupyter-integrated,":[93],"visual":[94],"tool":[95],"offers":[97],"all":[98],"relevant":[100],"functionalities":[101],"registering":[105],"spatio-molecular":[106],"associated":[109],"images.":[111],"We":[112],"showcase":[113],"BoReMi's":[114],"utility":[115],"using":[116],"publicly":[117],"available":[118,131],"BoReMi":[124],"an":[128],"interactive":[129],"demo":[130],"on":[132],"GitHub.":[133]},"counts_by_year":[],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}
