{"id":"https://openalex.org/W7133220229","doi":"https://doi.org/10.1093/bioinformatics/btag105","title":"FishFeats: streamlined quantification of multimodal labeling at the single-cell level in 3D tissues","display_name":"FishFeats: streamlined quantification of multimodal labeling at the single-cell level in 3D tissues","publication_year":2026,"publication_date":"2026-02-28","ids":{"openalex":"https://openalex.org/W7133220229","doi":"https://doi.org/10.1093/bioinformatics/btag105","pmid":"https://pubmed.ncbi.nlm.nih.gov/41769836"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btag105","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag105","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bioinformatics/btag105","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5017317489","display_name":"Ga\u00eblle Letort","orcid":"https://orcid.org/0000-0002-5866-0322"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I157536573","display_name":"Institut Pasteur","ror":"https://ror.org/0495fxg12","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I157536573"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Ga\u00eblle Letort","raw_affiliation_strings":["Dynamics of Developmental Decisions Unit, Institut Pasteur\u2014Universit\u00e9 Paris Cit\u00e9, UMR3738, CNRS , Paris 75015,"],"affiliations":[{"raw_affiliation_string":"Dynamics of Developmental Decisions Unit, Institut Pasteur\u2014Universit\u00e9 Paris Cit\u00e9, UMR3738, CNRS , Paris 75015,","institution_ids":["https://openalex.org/I204730241","https://openalex.org/I157536573","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038175587","display_name":"Tanya Foley","orcid":"https://orcid.org/0000-0003-3029-1905"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I157536573","display_name":"Institut Pasteur","ror":"https://ror.org/0495fxg12","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I157536573"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Tanya Foley","raw_affiliation_strings":["Zebrafish Neurogenetics Unit, Institut Pasteur\u2014Universit\u00e9 Paris Cit\u00e9, UMR3738, CNRS , Paris 75015,"],"affiliations":[{"raw_affiliation_string":"Zebrafish Neurogenetics Unit, Institut Pasteur\u2014Universit\u00e9 Paris Cit\u00e9, UMR3738, CNRS , Paris 75015,","institution_ids":["https://openalex.org/I204730241","https://openalex.org/I157536573","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5119450807","display_name":"Ilona Mignerey","orcid":null},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I157536573","display_name":"Institut Pasteur","ror":"https://ror.org/0495fxg12","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I157536573"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Ilona Mignerey","raw_affiliation_strings":["Zebrafish Neurogenetics Unit, Institut Pasteur\u2014Universit\u00e9 Paris Cit\u00e9, UMR3738, CNRS , Paris 75015,"],"affiliations":[{"raw_affiliation_string":"Zebrafish Neurogenetics Unit, Institut Pasteur\u2014Universit\u00e9 Paris Cit\u00e9, UMR3738, CNRS , Paris 75015,","institution_ids":["https://openalex.org/I204730241","https://openalex.org/I157536573","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056514536","display_name":"Laure Bally\u2010Cuif","orcid":"https://orcid.org/0000-0001-6611-6274"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I157536573","display_name":"Institut Pasteur","ror":"https://ror.org/0495fxg12","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I157536573"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Laure Bally-Cuif","raw_affiliation_strings":["Zebrafish Neurogenetics Unit, Institut Pasteur\u2014Universit\u00e9 Paris Cit\u00e9, UMR3738, CNRS , Paris 75015,"],"affiliations":[{"raw_affiliation_string":"Zebrafish Neurogenetics Unit, Institut Pasteur\u2014Universit\u00e9 Paris Cit\u00e9, UMR3738, CNRS , Paris 75015,","institution_ids":["https://openalex.org/I204730241","https://openalex.org/I157536573","https://openalex.org/I1294671590"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5030908322","display_name":"Nicolas Dray","orcid":"https://orcid.org/0000-0002-2632-6004"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I157536573","display_name":"Institut Pasteur","ror":"https://ror.org/0495fxg12","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I157536573"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Nicolas Dray","raw_affiliation_strings":["Zebrafish Neurogenetics Unit, Institut Pasteur\u2014Universit\u00e9 Paris Cit\u00e9, UMR3738, CNRS , Paris 75015,"],"affiliations":[{"raw_affiliation_string":"Zebrafish Neurogenetics Unit, Institut Pasteur\u2014Universit\u00e9 Paris Cit\u00e9, UMR3738, CNRS , Paris 75015,","institution_ids":["https://openalex.org/I204730241","https://openalex.org/I157536573","https://openalex.org/I1294671590"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5017317489"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I157536573","https://openalex.org/I204730241"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.52911631,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"42","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9363999962806702,"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":0.9363999962806702,"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/T10336","display_name":"Cancer Cells and Metastasis","score":0.009100000374019146,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10971","display_name":"Olfactory and Sensory Function Studies","score":0.006099999882280827,"subfield":{"id":"https://openalex.org/subfields/2809","display_name":"Sensory Systems"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.41110000014305115},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.391400009393692},{"id":"https://openalex.org/keywords/automated-method","display_name":"Automated method","score":0.24719999730587006},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.2078000009059906}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6636999845504761},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4587000012397766},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.41110000014305115},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.391400009393692},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.359499990940094},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.30059999227523804},{"id":"https://openalex.org/C3019060180","wikidata":"https://www.wikidata.org/wiki/Q184199","display_name":"Automated method","level":2,"score":0.24719999730587006},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.21549999713897705},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.2078000009059906},{"id":"https://openalex.org/C2781170535","wikidata":"https://www.wikidata.org/wiki/Q30587856","display_name":"Noisy data","level":2,"score":0.20589999854564667}],"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":"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":"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":"D008856","descriptor_name":"Microscopy, Fluorescence","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D008856","descriptor_name":"Microscopy, Fluorescence","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"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":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btag105","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag105","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41769836","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41769836","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:pubmedcentral.nih.gov:13003315","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13003315/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btag105","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag105","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.6170246601104736,"id":"https://metadata.un.org/sdg/2","display_name":"Zero hunger"}],"awards":[{"id":"https://openalex.org/G5268079395","display_name":null,"funder_award_id":"AAPG2021","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G5549440890","display_name":null,"funder_award_id":"ANR-10-LAB","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G7240651115","display_name":null,"funder_award_id":"ANR-10","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G8292747610","display_name":null,"funder_award_id":"EQU202203014636","funder_id":"https://openalex.org/F4320321589","funder_display_name":"Fondation pour la Recherche M\u00e9dicale"},{"id":"https://openalex.org/G8987543086","display_name":null,"funder_award_id":"ANR-10-LABX-0073","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"}],"funders":[{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"},{"id":"https://openalex.org/F4320321589","display_name":"Fondation pour la Recherche M\u00e9dicale","ror":"https://ror.org/04w6kn183"},{"id":"https://openalex.org/F4320322892","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73"},{"id":"https://openalex.org/F4320333359","display_name":"College of Natural Resources and Sciences, Humboldt State University","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W2006302594","https://openalex.org/W2222512263","https://openalex.org/W2950501364","https://openalex.org/W3021714323","https://openalex.org/W3107480794","https://openalex.org/W3111521801","https://openalex.org/W3173392742","https://openalex.org/W3212726233","https://openalex.org/W4223945485","https://openalex.org/W4377010744","https://openalex.org/W4383904262","https://openalex.org/W4383956887","https://openalex.org/W4402163497","https://openalex.org/W4407353336","https://openalex.org/W4408500917","https://openalex.org/W4409988818","https://openalex.org/W4416179695"],"related_works":[],"abstract_inverted_index":{"FishFeats":[0,15,41],"is":[1,16,29],"open":[2],"source":[3],"under":[4],"the":[5,25,32,51],"BSD-3":[6],"license,":[7],"freely":[8],"available":[9,30],"on":[10],"github:":[11],"https://github.com/gletort/FishFeats":[12],"(DOI":[13],"10.5281/zenodo.17701225).":[14],"developed":[17],"in":[18,31,50],"python,":[19],"as":[20],"a":[21],"napari":[22],"plugin":[23],"for":[24],"user":[26],"interface.":[27],"Documentation":[28],"github":[33,52],"pages:":[34],"https://gletort.github.io/FishFeats/.":[35],"To":[36],"report":[37],"an":[38,48],"issue":[39,49],"using":[40],"or":[42],"contributing":[43],"to":[44],"it":[45],"please":[46],"file":[47],"repository":[53],"https://github.com/gletort/FishFeats/issues.":[54]},"counts_by_year":[],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2026-03-03T00:00:00"}
