{"id":"https://openalex.org/W3194988201","doi":"https://doi.org/10.1093/bioinformatics/btab589","title":"PyJAMAS: open-source, multimodal segmentation and analysis of microscopy images","display_name":"PyJAMAS: open-source, multimodal segmentation and analysis of microscopy images","publication_year":2021,"publication_date":"2021-08-12","ids":{"openalex":"https://openalex.org/W3194988201","doi":"https://doi.org/10.1093/bioinformatics/btab589","mag":"3194988201","pmid":"https://pubmed.ncbi.nlm.nih.gov/34390579"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab589","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab589","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":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8722751","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5078934880","display_name":"Rodrigo Fern\u00e1ndez\u2010Gonz\u00e1lez","orcid":"https://orcid.org/0000-0003-0770-744X"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]},{"id":"https://openalex.org/I2801317318","display_name":"Hospital for Sick Children","ror":"https://ror.org/057q4rt57","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I2801317318"]},{"id":"https://openalex.org/I4210091032","display_name":"Ted Rogers Centre for Heart Research","ror":"https://ror.org/00cgnj660","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1325899441","https://openalex.org/I185261750","https://openalex.org/I4210091032","https://openalex.org/I4210141030"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Rodrigo Fernandez-Gonzalez","raw_affiliation_strings":["Department of Cell and Systems Biology, University of Toronto , Toronto, ON M5S 3G5, Canada","Developmental and Stem Cell Biology Program, The Hospital for Sick Children , Toronto, ON M5G 1X8, Canada","Institute of Biomedical Engineering, University of Toronto , Toronto, ON M5S 3G9, Canada","Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, University of Toronto , Toronto, ON M5G 1M1, Canada"],"raw_orcid":"https://orcid.org/0000-0003-0770-744X","affiliations":[{"raw_affiliation_string":"Department of Cell and Systems Biology, University of Toronto , Toronto, ON M5S 3G5, Canada","institution_ids":["https://openalex.org/I185261750"]},{"raw_affiliation_string":"Developmental and Stem Cell Biology Program, The Hospital for Sick Children , Toronto, ON M5G 1X8, Canada","institution_ids":["https://openalex.org/I2801317318"]},{"raw_affiliation_string":"Institute of Biomedical Engineering, University of Toronto , Toronto, ON M5S 3G9, Canada","institution_ids":["https://openalex.org/I185261750"]},{"raw_affiliation_string":"Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, University of Toronto , Toronto, ON M5G 1M1, Canada","institution_ids":["https://openalex.org/I185261750","https://openalex.org/I4210091032"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077115003","display_name":"Negar Balaghi","orcid":"https://orcid.org/0000-0002-5204-3227"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]},{"id":"https://openalex.org/I4210091032","display_name":"Ted Rogers Centre for Heart Research","ror":"https://ror.org/00cgnj660","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1325899441","https://openalex.org/I185261750","https://openalex.org/I4210091032","https://openalex.org/I4210141030"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Negar Balaghi","raw_affiliation_strings":["Institute of Biomedical Engineering, University of Toronto , Toronto, ON M5S 3G9, Canada","Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, University of Toronto , Toronto, ON M5G 1M1, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biomedical Engineering, University of Toronto , Toronto, ON M5S 3G9, Canada","institution_ids":["https://openalex.org/I185261750"]},{"raw_affiliation_string":"Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, University of Toronto , Toronto, ON M5G 1M1, Canada","institution_ids":["https://openalex.org/I185261750","https://openalex.org/I4210091032"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011507959","display_name":"Kelly Wang","orcid":"https://orcid.org/0000-0002-7803-1005"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]},{"id":"https://openalex.org/I4210091032","display_name":"Ted Rogers Centre for Heart Research","ror":"https://ror.org/00cgnj660","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1325899441","https://openalex.org/I185261750","https://openalex.org/I4210091032","https://openalex.org/I4210141030"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Kelly Wang","raw_affiliation_strings":["Institute of Biomedical Engineering, University of Toronto , Toronto, ON M5S 3G9, Canada","Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, University of Toronto , Toronto, ON M5G 1M1, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biomedical Engineering, University of Toronto , Toronto, ON M5S 3G9, Canada","institution_ids":["https://openalex.org/I185261750"]},{"raw_affiliation_string":"Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, University of Toronto , Toronto, ON M5G 1M1, Canada","institution_ids":["https://openalex.org/I185261750","https://openalex.org/I4210091032"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009851021","display_name":"Ray Hawkins","orcid":null},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]},{"id":"https://openalex.org/I4210091032","display_name":"Ted Rogers Centre for Heart Research","ror":"https://ror.org/00cgnj660","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1325899441","https://openalex.org/I185261750","https://openalex.org/I4210091032","https://openalex.org/I4210141030"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Ray Hawkins","raw_affiliation_strings":["Institute of Biomedical Engineering, University of Toronto , Toronto, ON M5S 3G9, Canada","Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, University of Toronto , Toronto, ON M5G 1M1, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biomedical Engineering, University of Toronto , Toronto, ON M5S 3G9, Canada","institution_ids":["https://openalex.org/I185261750"]},{"raw_affiliation_string":"Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, University of Toronto , Toronto, ON M5G 1M1, Canada","institution_ids":["https://openalex.org/I185261750","https://openalex.org/I4210091032"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075949337","display_name":"Katheryn E. Rothenberg","orcid":"https://orcid.org/0000-0002-8191-7528"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]},{"id":"https://openalex.org/I4210091032","display_name":"Ted Rogers Centre for Heart Research","ror":"https://ror.org/00cgnj660","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1325899441","https://openalex.org/I185261750","https://openalex.org/I4210091032","https://openalex.org/I4210141030"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Katheryn Rothenberg","raw_affiliation_strings":["Institute of Biomedical Engineering, University of Toronto , Toronto, ON M5S 3G9, Canada","Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, University of Toronto , Toronto, ON M5G 1M1, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biomedical Engineering, University of Toronto , Toronto, ON M5S 3G9, Canada","institution_ids":["https://openalex.org/I185261750"]},{"raw_affiliation_string":"Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, University of Toronto , Toronto, ON M5G 1M1, Canada","institution_ids":["https://openalex.org/I185261750","https://openalex.org/I4210091032"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027203855","display_name":"Christopher McFaul","orcid":null},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]},{"id":"https://openalex.org/I4210091032","display_name":"Ted Rogers Centre for Heart Research","ror":"https://ror.org/00cgnj660","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1325899441","https://openalex.org/I185261750","https://openalex.org/I4210091032","https://openalex.org/I4210141030"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Christopher McFaul","raw_affiliation_strings":["Institute of Biomedical Engineering, University of Toronto , Toronto, ON M5S 3G9, Canada","Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, University of Toronto , Toronto, ON M5G 1M1, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biomedical Engineering, University of Toronto , Toronto, ON M5S 3G9, Canada","institution_ids":["https://openalex.org/I185261750"]},{"raw_affiliation_string":"Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, University of Toronto , Toronto, ON M5G 1M1, Canada","institution_ids":["https://openalex.org/I185261750","https://openalex.org/I4210091032"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008596468","display_name":"Clara Schimmer","orcid":"https://orcid.org/0000-0002-8941-1740"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]},{"id":"https://openalex.org/I4210091032","display_name":"Ted Rogers Centre for Heart Research","ror":"https://ror.org/00cgnj660","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1325899441","https://openalex.org/I185261750","https://openalex.org/I4210091032","https://openalex.org/I4210141030"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Clara Schimmer","raw_affiliation_strings":["Institute of Biomedical Engineering, University of Toronto , Toronto, ON M5S 3G9, Canada","Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, University of Toronto , Toronto, ON M5G 1M1, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biomedical Engineering, University of Toronto , Toronto, ON M5S 3G9, Canada","institution_ids":["https://openalex.org/I185261750"]},{"raw_affiliation_string":"Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, University of Toronto , Toronto, ON M5G 1M1, Canada","institution_ids":["https://openalex.org/I185261750","https://openalex.org/I4210091032"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011873877","display_name":"Michelle Ly","orcid":"https://orcid.org/0000-0002-6495-8598"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]},{"id":"https://openalex.org/I4210091032","display_name":"Ted Rogers Centre for Heart Research","ror":"https://ror.org/00cgnj660","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1325899441","https://openalex.org/I185261750","https://openalex.org/I4210091032","https://openalex.org/I4210141030"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Michelle Ly","raw_affiliation_strings":["Institute of Biomedical Engineering, University of Toronto , Toronto, ON M5S 3G9, Canada","Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, University of Toronto , Toronto, ON M5G 1M1, Canada"],"raw_orcid":"https://orcid.org/0000-0002-6495-8598","affiliations":[{"raw_affiliation_string":"Institute of Biomedical Engineering, University of Toronto , Toronto, ON M5S 3G9, Canada","institution_ids":["https://openalex.org/I185261750"]},{"raw_affiliation_string":"Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, University of Toronto , Toronto, ON M5G 1M1, Canada","institution_ids":["https://openalex.org/I185261750","https://openalex.org/I4210091032"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042326305","display_name":"Ana Maria Pican\u00e7o do Carmo","orcid":null},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]},{"id":"https://openalex.org/I4210091032","display_name":"Ted Rogers Centre for Heart Research","ror":"https://ror.org/00cgnj660","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1325899441","https://openalex.org/I185261750","https://openalex.org/I4210091032","https://openalex.org/I4210141030"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Ana Maria do Carmo","raw_affiliation_strings":["Institute of Biomedical Engineering, University of Toronto , Toronto, ON M5S 3G9, Canada","Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, University of Toronto , Toronto, ON M5G 1M1, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biomedical Engineering, University of Toronto , Toronto, ON M5S 3G9, Canada","institution_ids":["https://openalex.org/I185261750"]},{"raw_affiliation_string":"Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, University of Toronto , Toronto, ON M5G 1M1, Canada","institution_ids":["https://openalex.org/I185261750","https://openalex.org/I4210091032"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033142958","display_name":"Gordana Scepanovic","orcid":"https://orcid.org/0000-0001-5762-6838"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]},{"id":"https://openalex.org/I4210091032","display_name":"Ted Rogers Centre for Heart Research","ror":"https://ror.org/00cgnj660","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1325899441","https://openalex.org/I185261750","https://openalex.org/I4210091032","https://openalex.org/I4210141030"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Gordana Scepanovic","raw_affiliation_strings":["Department of Cell and Systems Biology, University of Toronto , Toronto, ON M5S 3G5, Canada","Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, University of Toronto , Toronto, ON M5G 1M1, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Cell and Systems Biology, University of Toronto , Toronto, ON M5S 3G5, Canada","institution_ids":["https://openalex.org/I185261750"]},{"raw_affiliation_string":"Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, University of Toronto , Toronto, ON M5G 1M1, Canada","institution_ids":["https://openalex.org/I185261750","https://openalex.org/I4210091032"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033058601","display_name":"Gonca Erdemci-Tandogan","orcid":"https://orcid.org/0000-0001-6955-8692"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]},{"id":"https://openalex.org/I4210091032","display_name":"Ted Rogers Centre for Heart Research","ror":"https://ror.org/00cgnj660","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1325899441","https://openalex.org/I185261750","https://openalex.org/I4210091032","https://openalex.org/I4210141030"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Gonca Erdemci-Tandogan","raw_affiliation_strings":["Institute of Biomedical Engineering, University of Toronto , Toronto, ON M5S 3G9, Canada","Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, University of Toronto , Toronto, ON M5G 1M1, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biomedical Engineering, University of Toronto , Toronto, ON M5S 3G9, Canada","institution_ids":["https://openalex.org/I185261750"]},{"raw_affiliation_string":"Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, University of Toronto , Toronto, ON M5G 1M1, Canada","institution_ids":["https://openalex.org/I185261750","https://openalex.org/I4210091032"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5070804679","display_name":"Veronica Castle","orcid":null},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]},{"id":"https://openalex.org/I4210091032","display_name":"Ted Rogers Centre for Heart Research","ror":"https://ror.org/00cgnj660","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1325899441","https://openalex.org/I185261750","https://openalex.org/I4210091032","https://openalex.org/I4210141030"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Veronica Castle","raw_affiliation_strings":["Institute of Biomedical Engineering, University of Toronto , Toronto, ON M5S 3G9, Canada","Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, University of Toronto , Toronto, ON M5G 1M1, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biomedical Engineering, University of Toronto , Toronto, ON M5S 3G9, Canada","institution_ids":["https://openalex.org/I185261750"]},{"raw_affiliation_string":"Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, University of Toronto , Toronto, ON M5G 1M1, Canada","institution_ids":["https://openalex.org/I185261750","https://openalex.org/I4210091032"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5078934880"],"corresponding_institution_ids":["https://openalex.org/I185261750","https://openalex.org/I2801317318","https://openalex.org/I4210091032"],"apc_list":{"value":3478,"currency":"USD","value_usd":3478},"apc_paid":null,"fwci":4.4844,"has_fulltext":false,"cited_by_count":28,"citation_normalized_percentile":{"value":0.94486941,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"38","issue":"2","first_page":"594","last_page":"596"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9562000036239624,"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":0.9562000036239624,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.005799999926239252,"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/T10862","display_name":"AI in cancer detection","score":0.005100000184029341,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/python","display_name":"Python (programming language)","score":0.9360928535461426},{"id":"https://openalex.org/keywords/scripting-language","display_name":"Scripting language","score":0.8421576023101807},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7669234275817871},{"id":"https://openalex.org/keywords/graphical-user-interface","display_name":"Graphical user interface","score":0.7510387897491455},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.6315472722053528},{"id":"https://openalex.org/keywords/segmentation","display_name":"Segmentation","score":0.6276581287384033},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.620027482509613},{"id":"https://openalex.org/keywords/extensibility","display_name":"Extensibility","score":0.5770894885063171},{"id":"https://openalex.org/keywords/mac-os","display_name":"Mac OS","score":0.5070903301239014},{"id":"https://openalex.org/keywords/image-segmentation","display_name":"Image segmentation","score":0.4606618285179138},{"id":"https://openalex.org/keywords/open-source-software","display_name":"Open source software","score":0.44697272777557373},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.43595054745674133},{"id":"https://openalex.org/keywords/image-processing","display_name":"Image processing","score":0.4303811192512512},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.42940694093704224},{"id":"https://openalex.org/keywords/user-interface","display_name":"User interface","score":0.41886916756629944},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3867553174495697},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.33548396825790405},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.32659101486206055},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.18997150659561157},{"id":"https://openalex.org/keywords/image","display_name":"Image (mathematics)","score":0.1569455862045288}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.9360928535461426},{"id":"https://openalex.org/C61423126","wikidata":"https://www.wikidata.org/wiki/Q187432","display_name":"Scripting language","level":2,"score":0.8421576023101807},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7669234275817871},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.7510387897491455},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.6315472722053528},{"id":"https://openalex.org/C89600930","wikidata":"https://www.wikidata.org/wiki/Q1423946","display_name":"Segmentation","level":2,"score":0.6276581287384033},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.620027482509613},{"id":"https://openalex.org/C32833848","wikidata":"https://www.wikidata.org/wiki/Q4115054","display_name":"Extensibility","level":2,"score":0.5770894885063171},{"id":"https://openalex.org/C522133331","wikidata":"https://www.wikidata.org/wiki/Q43627","display_name":"Mac OS","level":3,"score":0.5070903301239014},{"id":"https://openalex.org/C124504099","wikidata":"https://www.wikidata.org/wiki/Q56933","display_name":"Image segmentation","level":3,"score":0.4606618285179138},{"id":"https://openalex.org/C2988343187","wikidata":"https://www.wikidata.org/wiki/Q1130645","display_name":"Open source software","level":3,"score":0.44697272777557373},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.43595054745674133},{"id":"https://openalex.org/C9417928","wikidata":"https://www.wikidata.org/wiki/Q1070689","display_name":"Image processing","level":3,"score":0.4303811192512512},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.42940694093704224},{"id":"https://openalex.org/C89505385","wikidata":"https://www.wikidata.org/wiki/Q47146","display_name":"User interface","level":2,"score":0.41886916756629944},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3867553174495697},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33548396825790405},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.32659101486206055},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.18997150659561157},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.1569455862045288},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"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}],"mesh":[{"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":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008853","descriptor_name":"Microscopy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008853","descriptor_name":"Microscopy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008853","descriptor_name":"Microscopy","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":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btab589","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab589","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:34390579","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34390579","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":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8722751","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8722751","pdf_url":null,"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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:8722751","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8722751","pdf_url":null,"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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G533725811","display_name":null,"funder_award_id":"30279","funder_id":"https://openalex.org/F4320319952","funder_display_name":"Canada Foundation for Innovation"},{"id":"https://openalex.org/G7771916705","display_name":null,"funder_award_id":"418438-13","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G7819825814","display_name":null,"funder_award_id":"156279","funder_id":"https://openalex.org/F4320334506","funder_display_name":"Canadian Institutes of Health Research"},{"id":"https://openalex.org/G7825209431","display_name":null,"funder_award_id":"ER14-10-170","funder_id":"https://openalex.org/F4320314607","funder_display_name":"Government of Ontario"}],"funders":[{"id":"https://openalex.org/F4320314607","display_name":"Government of Ontario","ror":"https://ror.org/015pzp858"},{"id":"https://openalex.org/F4320319952","display_name":"Canada Foundation for Innovation","ror":"https://ror.org/000az4664"},{"id":"https://openalex.org/F4320334506","display_name":"Canadian Institutes of Health Research","ror":"https://ror.org/01gavpb45"},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":22,"referenced_works":["https://openalex.org/W1585431621","https://openalex.org/W1974210089","https://openalex.org/W2016539608","https://openalex.org/W2037947871","https://openalex.org/W2099540110","https://openalex.org/W2107554012","https://openalex.org/W2115758207","https://openalex.org/W2167279371","https://openalex.org/W2405708533","https://openalex.org/W2588959863","https://openalex.org/W2601810315","https://openalex.org/W2610675381","https://openalex.org/W2758694956","https://openalex.org/W2760514866","https://openalex.org/W2900936384","https://openalex.org/W3015600294","https://openalex.org/W3035965352","https://openalex.org/W3099878876","https://openalex.org/W3107480794","https://openalex.org/W3134482516","https://openalex.org/W3156859314","https://openalex.org/W6634966438"],"related_works":["https://openalex.org/W4376877853","https://openalex.org/W2048180534","https://openalex.org/W1493891899","https://openalex.org/W4250928611","https://openalex.org/W166480398","https://openalex.org/W1612808768","https://openalex.org/W167327709","https://openalex.org/W1977393088","https://openalex.org/W4387839566","https://openalex.org/W4210922265"],"abstract_inverted_index":{"SUMMARY:":[0],"Our":[1],"increasing":[2,15],"ability":[3],"to":[4,17,22],"resolve":[5],"fine":[6],"details":[7],"using":[8],"light":[9],"microscopy":[10],"is":[11,134],"matched":[12],"by":[13],"an":[14,71],"need":[16],"quantify":[18],"images":[19],"in":[20,31,50,80],"order":[21],"detect":[23],"and":[24,56,77,91,103,108,136],"measure":[25],"phenotypes.":[26],"Despite":[27],"their":[28],"central":[29],"role":[30],"cell":[32],"biology,":[33],"many":[34],"image":[35,75],"analysis":[36,78],"tools":[37],"require":[38],"a":[39,84,113,125],"financial":[40],"investment,":[41],"are":[42,48,58,144],"released":[43],"as":[44,60,119],"proprietary":[45],"software,":[46],"or":[47,118],"implemented":[49],"languages":[51],"not":[52],"friendly":[53],"for":[54,74,100],"beginners,":[55],"thus":[57],"used":[59,111],"black":[61],"boxes.":[62],"To":[63],"overcome":[64],"these":[65],"limitations,":[66],"we":[67],"have":[68],"developed":[69],"PyJAMAS,":[70],"open-source":[72,135],"tool":[73],"processing":[76],"written":[79],"Python.":[81],"PyJAMAS":[82,133],"provides":[83],"variety":[85],"of":[86,97,105,121],"segmentation":[87],"tools,":[88],"including":[89],"watershed":[90],"machine":[92],"learning-based":[93],"methods;":[94],"takes":[95],"advantage":[96],"Jupyter":[98],"notebooks":[99],"the":[101],"display":[102],"reproducibility":[104],"data":[106,143],"analyses;":[107],"can":[109],"be":[110],"through":[112],"cross-platform":[114],"graphical":[115],"user":[116],"interface":[117],"part":[120],"Python":[122],"scripts":[123],"via":[124],"comprehensive":[126],"application":[127],"programming":[128],"interface.":[129],"AVAILABILITY":[130],"AND":[131],"IMPLEMENTATION:":[132],"available":[137,145],"at":[138,146],"https://bitbucket.org/rfg_lab/pyjamas.":[139],"SUPPLEMENTARY":[140],"INFORMATION:":[141],"Supplementary":[142],"Bioinformatics":[147],"online.":[148]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":9}],"updated_date":"2026-08-28T12:50:07.497085","created_date":"2025-10-10T00:00:00"}
