{"id":"https://openalex.org/W4397292782","doi":"https://doi.org/10.1080/15548627.2024.2353458","title":"Accurate automated segmentation of autophagic bodies in yeast vacuoles using cellpose 2.0","display_name":"Accurate automated segmentation of autophagic bodies in yeast vacuoles using cellpose 2.0","publication_year":2024,"publication_date":"2024-05-18","ids":{"openalex":"https://openalex.org/W4397292782","doi":"https://doi.org/10.1080/15548627.2024.2353458","pmid":"https://pubmed.ncbi.nlm.nih.gov/38762750","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/11346527"},"language":"en","primary_location":{"id":"doi:10.1080/15548627.2024.2353458","doi":"https://doi.org/10.1080/15548627.2024.2353458","is_oa":true,"landing_page_url":"https://doi.org/10.1080/15548627.2024.2353458","pdf_url":"https://www.tandfonline.com/doi/pdf/10.1080/15548627.2024.2353458","source":{"id":"https://openalex.org/S102544370","display_name":"Autophagy","issn_l":"1554-8627","issn":["1554-8627","1554-8635"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-a","doyens","jufo-2","ki-jl-2","medline","norway-2","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320547","host_organization_name":"Taylor & Francis","host_organization_lineage":["https://openalex.org/P4310320547","https://openalex.org/P4310320449"],"host_organization_lineage_names":["Taylor & Francis","Informa"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Autophagy","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://www.tandfonline.com/doi/pdf/10.1080/15548627.2024.2353458","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5098695221","display_name":"Emily C. Marron","orcid":"https://orcid.org/0009-0007-0584-9758","observed_orcids":["https://orcid.org/0009-0007-0584-9758"]},"institutions":[{"id":"https://openalex.org/I138216421","display_name":"Eastern Michigan University","ror":"https://ror.org/02ehshm78","country_code":"US","type":"education","lineage":["https://openalex.org/I138216421"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Emily C. Marron","raw_affiliation_strings":["Eastern Michigan University","Department of Mathematic and Statistics, Eastern Michigan University, Ypsilanti, MI, USA"],"raw_orcid":"https://orcid.org/0009-0007-0584-9758","affiliations":[{"raw_affiliation_string":"Eastern Michigan University","institution_ids":["https://openalex.org/I138216421"]},{"raw_affiliation_string":"Department of Mathematic and Statistics, Eastern Michigan University, Ypsilanti, MI, USA","institution_ids":["https://openalex.org/I138216421"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5098695222","display_name":"Jonathan Backues","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jonathan Backues","raw_affiliation_strings":["Euler Scientific","Euler Scientific, San Diego, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Euler Scientific","institution_ids":[]},{"raw_affiliation_string":"Euler Scientific, San Diego, CA, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064943570","display_name":"Andrew M. Ross","orcid":"https://orcid.org/0000-0002-8607-0469","observed_orcids":["https://orcid.org/0000-0002-8607-0469"]},"institutions":[{"id":"https://openalex.org/I138216421","display_name":"Eastern Michigan University","ror":"https://ror.org/02ehshm78","country_code":"US","type":"education","lineage":["https://openalex.org/I138216421"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Andrew M. Ross","raw_affiliation_strings":["Eastern Michigan University","Department of Mathematic and Statistics, Eastern Michigan University, Ypsilanti, MI, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Eastern Michigan University","institution_ids":["https://openalex.org/I138216421"]},{"raw_affiliation_string":"Department of Mathematic and Statistics, Eastern Michigan University, Ypsilanti, MI, USA","institution_ids":["https://openalex.org/I138216421"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5069406918","display_name":"Steven K. Backues","orcid":"https://orcid.org/0000-0002-7346-1428","observed_orcids":["https://orcid.org/0000-0002-7346-1428"]},"institutions":[{"id":"https://openalex.org/I138216421","display_name":"Eastern Michigan University","ror":"https://ror.org/02ehshm78","country_code":"US","type":"education","lineage":["https://openalex.org/I138216421"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Steven K. Backues","raw_affiliation_strings":["Eastern Michigan University","Department of Chemistry, Eastern Michigan University, Ypsilanti, MI, USA"],"raw_orcid":"https://orcid.org/0000-0002-7346-1428","affiliations":[{"raw_affiliation_string":"Eastern Michigan University","institution_ids":["https://openalex.org/I138216421"]},{"raw_affiliation_string":"Department of Chemistry, Eastern Michigan University, Ypsilanti, MI, USA","institution_ids":["https://openalex.org/I138216421"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5064943570","https://openalex.org/A5069406918"],"corresponding_institution_ids":["https://openalex.org/I138216421"],"apc_list":null,"apc_paid":null,"fwci":0.3832,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.50374532,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"20","issue":"9","first_page":"2092","last_page":"2099"},"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/T10587","display_name":"Autophagy in Disease and Therapy","score":0.0012000000569969416,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"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/T10036","display_name":"Advanced Neural Network Applications","score":0.0008999999845400453,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/autophagic-bodies","display_name":"autophagic bodies","score":0.9089999794960022},{"id":"https://openalex.org/keywords/autophagosomes","display_name":"autophagosomes","score":0.8450000286102295},{"id":"https://openalex.org/keywords/automatic-image-segmentation","display_name":"automated image segmentation","score":0.9089999794960022},{"id":"https://openalex.org/keywords/yeast-vacuole","display_name":"yeast vacuole","score":0.8320000171661377},{"id":"https://openalex.org/keywords/transmission-electron-microscopy","display_name":"transmission electron microscopy","score":0.7770000100135803},{"id":"https://openalex.org/keywords/macroautophagy","display_name":"macroautophagy","score":0.8299999833106995},{"id":"https://openalex.org/keywords/multivesicular-bodies","display_name":"multivesicular bodies","score":0.6909999847412109}],"concepts":[{"id":"https://openalex.org/C89600930","wikidata":"https://www.wikidata.org/wiki/Q1423946","display_name":"Segmentation","level":2,"score":0.873345136642456},{"id":"https://openalex.org/C203522944","wikidata":"https://www.wikidata.org/wiki/Q288322","display_name":"Autophagy","level":3,"score":0.8148287534713745},{"id":"https://openalex.org/C102568950","wikidata":"https://www.wikidata.org/wiki/Q127702","display_name":"Vacuole","level":3,"score":0.627981960773468},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6126308441162109},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.5599213242530823},{"id":"https://openalex.org/C125308379","wikidata":"https://www.wikidata.org/wiki/Q363057","display_name":"Market segmentation","level":2,"score":0.5244148969650269},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5107526779174805},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.48494794964790344},{"id":"https://openalex.org/C124504099","wikidata":"https://www.wikidata.org/wiki/Q56933","display_name":"Image segmentation","level":3,"score":0.4539496898651123},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.4438970386981964},{"id":"https://openalex.org/C2779222958","wikidata":"https://www.wikidata.org/wiki/Q45422","display_name":"Yeast","level":2,"score":0.412606418132782},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.26877760887145996},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.08693450689315796},{"id":"https://openalex.org/C190283241","wikidata":"https://www.wikidata.org/wiki/Q14599311","display_name":"Apoptosis","level":2,"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/C190062978","wikidata":"https://www.wikidata.org/wiki/Q79899","display_name":"Cytoplasm","level":2,"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}],"mesh":[{"descriptor_ui":"D000071182","descriptor_name":"Autophagosomes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000071182","descriptor_name":"Autophagosomes","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D001331","descriptor_name":"Automation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001343","descriptor_name":"Autophagy","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"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":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":true},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014617","descriptor_name":"Vacuoles","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014617","descriptor_name":"Vacuoles","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":true},{"descriptor_ui":"D046529","descriptor_name":"Microscopy, Electron, Transmission","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1080/15548627.2024.2353458","doi":"https://doi.org/10.1080/15548627.2024.2353458","is_oa":true,"landing_page_url":"https://doi.org/10.1080/15548627.2024.2353458","pdf_url":"https://www.tandfonline.com/doi/pdf/10.1080/15548627.2024.2353458","source":{"id":"https://openalex.org/S102544370","display_name":"Autophagy","issn_l":"1554-8627","issn":["1554-8627","1554-8635"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-a","doyens","jufo-2","ki-jl-2","medline","norway-2","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320547","host_organization_name":"Taylor & Francis","host_organization_lineage":["https://openalex.org/P4310320547","https://openalex.org/P4310320449"],"host_organization_lineage_names":["Taylor & Francis","Informa"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Autophagy","raw_type":"journal-article"},{"id":"doi:10.1101/2023.10.23.563617","doi":"https://doi.org/10.1101/2023.10.23.563617","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2023.10.23.563617","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2023/10/25/2023.10.23.563617.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmh:oai:pubmedcentral.nih.gov:11346527","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11346527","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11346527/pdf/KAUP_20_2353458.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,"listed_in":[],"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":"Autophagy","raw_type":"Text"},{"id":"pmid:38762750","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38762750","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,"listed_in":[],"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":"Autophagy","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1080/15548627.2024.2353458","doi":"https://doi.org/10.1080/15548627.2024.2353458","is_oa":true,"landing_page_url":"https://doi.org/10.1080/15548627.2024.2353458","pdf_url":"https://www.tandfonline.com/doi/pdf/10.1080/15548627.2024.2353458","source":{"id":"https://openalex.org/S102544370","display_name":"Autophagy","issn_l":"1554-8627","issn":["1554-8627","1554-8635"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-a","doyens","jufo-2","ki-jl-2","medline","norway-2","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320547","host_organization_name":"Taylor & Francis","host_organization_lineage":["https://openalex.org/P4310320547","https://openalex.org/P4310320449"],"host_organization_lineage_names":["Taylor & Francis","Informa"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Autophagy","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G2577596421","display_name":"RUI: Tools and Approaches for Investigating the Basic Mechanisms of Autophagy","funder_award_id":"2243163","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7990772921","display_name":null,"funder_award_id":"2243163","funder_id":"https://openalex.org/F4320332167","funder_display_name":"Directorate for Biological Sciences"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320317542","display_name":"Eastern Michigan University","ror":"https://ror.org/02ehshm78"},{"id":"https://openalex.org/F4320332167","display_name":"Directorate for Biological Sciences","ror":"https://ror.org/001xhss06"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4397292782.pdf","grobid_xml":"https://content.openalex.org/works/W4397292782.grobid-xml"},"referenced_works_count":20,"referenced_works":["https://openalex.org/W2024099469","https://openalex.org/W2055064168","https://openalex.org/W2099540110","https://openalex.org/W2100605768","https://openalex.org/W2111423166","https://openalex.org/W2121469024","https://openalex.org/W2126801593","https://openalex.org/W2150038290","https://openalex.org/W2163508965","https://openalex.org/W2167088833","https://openalex.org/W2170678054","https://openalex.org/W2467628122","https://openalex.org/W2601810315","https://openalex.org/W2806530968","https://openalex.org/W2809299334","https://openalex.org/W2975634117","https://openalex.org/W3083883345","https://openalex.org/W3111521801","https://openalex.org/W4238269746","https://openalex.org/W4308361273"],"related_works":["https://openalex.org/W7132986913","https://openalex.org/W4411257378","https://openalex.org/W1496299506","https://openalex.org/W2592723117","https://openalex.org/W2951482883","https://openalex.org/W4308361273","https://openalex.org/W2946813309","https://openalex.org/W1975150215","https://openalex.org/W6908543834","https://openalex.org/W4308469795"],"abstract_inverted_index":{"Abstract":[0],"Segmenting":[1],"autophagic":[2],"bodies":[3],"in":[4,15,20],"yeast":[5],"TEM":[6],"images":[7,30,40,58],"is":[8,92],"a":[9,49],"key":[10],"technique":[11],"for":[12,43,72,79,84,107,113],"measuring":[13],"changes":[14],"autophagosome":[16],"size":[17],"and":[18,105],"number":[19],"order":[21],"to":[22,62],"better":[23],"understand":[24],"autophagy.":[25],"Manual":[26],"segmentation":[27],"of":[28,39,64],"these":[29,57],"can":[31,55,69],"be":[32,70],"very":[33],"time":[34],"consuming,":[35],"particularly":[36],"since":[37],"hundreds":[38],"are":[41,110],"needed":[42],"accurate":[44],"measurements.":[45],"Here":[46],"we":[47],"describe":[48],"validated":[50],"Cellpose":[51],"2.0":[52],"model":[53,68,104],"that":[54,63],"segment":[56],"with":[59],"accuracy":[60],"comparable":[61],"human":[65,89],"experts.":[66],"This":[67],"used":[71],"fully":[73],"automated":[74],"segmentation,":[75,86],"eliminating":[76],"the":[77,99,114],"need":[78],"manual":[80,101],"body":[81],"outlining,":[82],"or":[83],"model-assisted":[85],"which":[87],"allows":[88],"oversight":[90],"but":[91],"still":[93],"five":[94],"times":[95],"as":[96,98],"fast":[97],"current":[100],"method.":[102],"The":[103],"instructions":[106],"its":[108],"use":[109],"presented":[111],"here":[112],"autophagy":[115],"community.":[116]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2024-05-20T00:00:00"}