{"id":"https://openalex.org/W2994957847","doi":"https://doi.org/10.1093/bioinformatics/btz945","title":"LOBSTER: an environment to design bioimage analysis workflows for large and complex fluorescence microscopy data","display_name":"LOBSTER: an environment to design bioimage analysis workflows for large and complex fluorescence microscopy data","publication_year":2019,"publication_date":"2019-12-17","ids":{"openalex":"https://openalex.org/W2994957847","doi":"https://doi.org/10.1093/bioinformatics/btz945","mag":"2994957847","pmid":"https://pubmed.ncbi.nlm.nih.gov/31860062"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz945","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz945","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5039459359","display_name":"S\u00e9bastien Tosi","orcid":"https://orcid.org/0000-0001-8348-2778"},"institutions":[{"id":"https://openalex.org/I4210132884","display_name":"Barcelona Institute of Science and Technology","ror":"https://ror.org/03kpps236","country_code":"ES","type":"education","lineage":["https://openalex.org/I4210132884"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"S\u00e9bastien Tosi","raw_affiliation_strings":["Institute for Research in Biomedicine\u2013\u2013IRB Barcelona , The Barcelona Institute for Science and Technology\u2013BIST"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Research in Biomedicine\u2013\u2013IRB Barcelona , The Barcelona Institute for Science and Technology\u2013BIST","institution_ids":["https://openalex.org/I4210132884"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036258959","display_name":"L\u00eddia Bardia","orcid":"https://orcid.org/0000-0003-2232-683X"},"institutions":[{"id":"https://openalex.org/I4210132884","display_name":"Barcelona Institute of Science and Technology","ror":"https://ror.org/03kpps236","country_code":"ES","type":"education","lineage":["https://openalex.org/I4210132884"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"L\u00eddia Bardia","raw_affiliation_strings":["Institute for Research in Biomedicine\u2013\u2013IRB Barcelona , The Barcelona Institute for Science and Technology\u2013BIST"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Research in Biomedicine\u2013\u2013IRB Barcelona , The Barcelona Institute for Science and Technology\u2013BIST","institution_ids":["https://openalex.org/I4210132884"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064211121","display_name":"Maria Jose Filgueira","orcid":null},"institutions":[{"id":"https://openalex.org/I4210111366","display_name":"Centre for Biomedical Network Research on Rare Diseases","ror":"https://ror.org/01ygm5w19","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210111366"]},{"id":"https://openalex.org/I4210115082","display_name":"Centro de Investigaci\u00f3n Biom\u00e9dica en Red","ror":"https://ror.org/02g87qh62","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2801357902","https://openalex.org/I4210115082","https://openalex.org/I4387152914"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Maria Jose Filgueira","raw_affiliation_strings":["Department of Developmental Biology, Instituto de Biolog\u00eda Molecular de Barcelona , CSIC, and Centro de Investigaci\u00f3n Biom\u00e9dica en Red de Enfermedades Raras (CIBERER), 08028 Barcelona, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Developmental Biology, Instituto de Biolog\u00eda Molecular de Barcelona , CSIC, and Centro de Investigaci\u00f3n Biom\u00e9dica en Red de Enfermedades Raras (CIBERER), 08028 Barcelona, Spain","institution_ids":["https://openalex.org/I4210111366","https://openalex.org/I4210115082"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025233783","display_name":"Alexandre Calon","orcid":"https://orcid.org/0000-0002-3398-6131"},"institutions":[{"id":"https://openalex.org/I4210130874","display_name":"Hospital Del Mar","ror":"https://ror.org/03a8gac78","country_code":"ES","type":"healthcare","lineage":["https://openalex.org/I4210130874"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Alexandre Calon","raw_affiliation_strings":["Cancer Research Programme, Hospital del Mar Research Institute (IMIM) , 08003 Barcelona, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cancer Research Programme, Hospital del Mar Research Institute (IMIM) , 08003 Barcelona, Spain","institution_ids":["https://openalex.org/I4210130874"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5011037748","display_name":"Julien Colombelli","orcid":"https://orcid.org/0000-0002-2784-4276"},"institutions":[{"id":"https://openalex.org/I4210132884","display_name":"Barcelona Institute of Science and Technology","ror":"https://ror.org/03kpps236","country_code":"ES","type":"education","lineage":["https://openalex.org/I4210132884"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Julien Colombelli","raw_affiliation_strings":["Institute for Research in Biomedicine\u2013\u2013IRB Barcelona , The Barcelona Institute for Science and Technology\u2013BIST"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Research in Biomedicine\u2013\u2013IRB Barcelona , The Barcelona Institute for Science and Technology\u2013BIST","institution_ids":["https://openalex.org/I4210132884"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5039459359"],"corresponding_institution_ids":["https://openalex.org/I4210132884"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.7548,"has_fulltext":false,"cited_by_count":11,"citation_normalized_percentile":{"value":0.86922392,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"36","issue":"8","first_page":"2634","last_page":"2635"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9961000084877014,"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"}},"topics":[{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9961000084877014,"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/T10540","display_name":"Advanced Fluorescence Microscopy Techniques","score":0.00139999995008111,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.0007999999797903001,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/toolbox","display_name":"Toolbox","score":0.8094582557678223},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8009411692619324},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.6844578981399536},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.6812404990196228},{"id":"https://openalex.org/keywords/matlab","display_name":"MATLAB","score":0.5495530366897583},{"id":"https://openalex.org/keywords/bottleneck","display_name":"Bottleneck","score":0.5020205974578857},{"id":"https://openalex.org/keywords/image-processing","display_name":"Image processing","score":0.4938738942146301},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4885216951370239},{"id":"https://openalex.org/keywords/workstation","display_name":"Workstation","score":0.4853619337081909},{"id":"https://openalex.org/keywords/sample","display_name":"Sample (material)","score":0.46723419427871704},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.4455844461917877},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4373684227466583},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.43722736835479736},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.42408493161201477},{"id":"https://openalex.org/keywords/image-segmentation","display_name":"Image segmentation","score":0.41522741317749023},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.39525726437568665},{"id":"https://openalex.org/keywords/segmentation","display_name":"Segmentation","score":0.3597467243671417},{"id":"https://openalex.org/keywords/image","display_name":"Image (mathematics)","score":0.28215622901916504},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.20881003141403198},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.14656290411949158},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.09660303592681885},{"id":"https://openalex.org/keywords/embedded-system","display_name":"Embedded system","score":0.09243157505989075}],"concepts":[{"id":"https://openalex.org/C2777655017","wikidata":"https://www.wikidata.org/wiki/Q1501161","display_name":"Toolbox","level":2,"score":0.8094582557678223},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8009411692619324},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.6844578981399536},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6812404990196228},{"id":"https://openalex.org/C2780365114","wikidata":"https://www.wikidata.org/wiki/Q169478","display_name":"MATLAB","level":2,"score":0.5495530366897583},{"id":"https://openalex.org/C2780513914","wikidata":"https://www.wikidata.org/wiki/Q18210350","display_name":"Bottleneck","level":2,"score":0.5020205974578857},{"id":"https://openalex.org/C9417928","wikidata":"https://www.wikidata.org/wiki/Q1070689","display_name":"Image processing","level":3,"score":0.4938738942146301},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4885216951370239},{"id":"https://openalex.org/C67953723","wikidata":"https://www.wikidata.org/wiki/Q192525","display_name":"Workstation","level":2,"score":0.4853619337081909},{"id":"https://openalex.org/C198531522","wikidata":"https://www.wikidata.org/wiki/Q485146","display_name":"Sample (material)","level":2,"score":0.46723419427871704},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.4455844461917877},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4373684227466583},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.43722736835479736},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.42408493161201477},{"id":"https://openalex.org/C124504099","wikidata":"https://www.wikidata.org/wiki/Q56933","display_name":"Image segmentation","level":3,"score":0.41522741317749023},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.39525726437568665},{"id":"https://openalex.org/C89600930","wikidata":"https://www.wikidata.org/wiki/Q1423946","display_name":"Segmentation","level":2,"score":0.3597467243671417},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.28215622901916504},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.20881003141403198},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.14656290411949158},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.09660303592681885},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.09243157505989075},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0}],"mesh":[{"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":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008121","descriptor_name":"Nephropidae","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008121","descriptor_name":"Nephropidae","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008121","descriptor_name":"Nephropidae","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008856","descriptor_name":"Microscopy, Fluorescence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008856","descriptor_name":"Microscopy, Fluorescence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008856","descriptor_name":"Microscopy, Fluorescence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btz945","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz945","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31860062","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31860062","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:digital.csic.es:10261/223109","is_oa":false,"landing_page_url":"http://hdl.handle.net/10261/223109","pdf_url":null,"source":{"id":"https://openalex.org/S4306400616","display_name":"DIGITAL.CSIC (Spanish National Research Council (CSIC))","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I134820265","host_organization_name":"Consejo Superior de Investigaciones Cient\u00edficas","host_organization_lineage":["https://openalex.org/I134820265"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"art\u00edculo"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Responsible consumption and production","id":"https://metadata.un.org/sdg/12","score":0.4699999988079071}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":6,"referenced_works":["https://openalex.org/W2037586865","https://openalex.org/W2037947871","https://openalex.org/W2099540110","https://openalex.org/W2529052661","https://openalex.org/W2745296509","https://openalex.org/W6728710511"],"related_works":["https://openalex.org/W2496284459","https://openalex.org/W2384199595","https://openalex.org/W1603231086","https://openalex.org/W2353433747","https://openalex.org/W3154136120","https://openalex.org/W2370158852","https://openalex.org/W2390627398","https://openalex.org/W2103285227","https://openalex.org/W2370031282","https://openalex.org/W2095148239"],"abstract_inverted_index":{"SUMMARY:":[0],"Open":[1],"source":[2],"software":[3,35],"such":[4],"as":[5],"ImageJ":[6],"and":[7,26,57,86,96,134,156,159,170],"CellProfiler":[8],"greatly":[9],"simplified":[10],"the":[11,23,29,38,63],"quantitative":[12],"analysis":[13,64,99,132],"of":[14,28,40,65,110,127],"microscopy":[15,68,112],"images":[16,30,69,116,136,172],"but":[17,48],"their":[18],"applicability":[19],"is":[20,70],"limited":[21],"by":[22],"size,":[24],"dimensionality":[25],"complexity":[27],"under":[31],"study.":[32],"In":[33],"contrast,":[34],"optimized":[36],"for":[37,76],"needs":[39],"specific":[41],"research":[42,141],"projects":[43],"can":[44],"overcome":[45],"these":[46],"limitations,":[47],"they":[49],"may":[50],"be":[51],"harder":[52],"to":[53,59,92,101],"find,":[54],"set":[55,126],"up":[56],"customize":[58,97],"different":[60],"needs.":[61],"Overall,":[62],"large,":[66],"complex,":[67],"hence":[71],"still":[72],"a":[73,107,124],"critical":[74],"bottleneck":[75],"many":[77],"Life":[78],"Scientists.":[79],"We":[80],"introduce":[81],"LOBSTER":[82,121,146],"(Little":[83],"Objects":[84],"Segmentation":[85],"Tracking":[87],"Environment),":[88],"an":[89],"environment":[90],"designed":[91],"help":[93],"scientists":[94],"design":[95],"image":[98,131],"workflows":[100,133],"accurately":[102],"characterize":[103],"biological":[104],"objects":[105],"from":[106,138],"broad":[108],"range":[109],"fluorescence":[111],"images,":[113],"including":[114],"large":[115],"exceeding":[117],"workstation":[118],"main":[119],"memory.":[120],"comes":[122],"with":[123],"starting":[125],"over":[128],"75":[129],"sample":[130,171],"associated":[135],"stemming":[137],"state-of-the-art":[139],"image-based":[140],"projects.":[142],"AVAILABILITY":[143],"AND":[144],"IMPLEMENTATION:":[145],"requires":[147],"MATLAB":[148,152,157],"(version":[149],"\u2265":[150],"2015a),":[151],"Image":[153],"processing":[154],"toolbox,":[155],"statistics":[158],"machine":[160],"learning":[161],"toolbox.":[162],"Code":[163],"source,":[164],"online":[165],"tutorials,":[166],"video":[167],"demonstrations,":[168],"documentation":[169],"are":[173,182],"freely":[174],"available":[175,183],"from:":[176],"https://sebastients.github.io.":[177],"SUPPLEMENTARY":[178],"INFORMATION:":[179],"Supplementary":[180],"data":[181],"at":[184],"Bioinformatics":[185],"online.":[186]},"counts_by_year":[{"year":2024,"cited_by_count":3},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":2}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
