{"id":"https://openalex.org/W3003737728","doi":"https://doi.org/10.1101/2020.01.30.927459","title":"Novel software for automated morphometric analysis of stented arteries","display_name":"Novel software for automated morphometric analysis of stented arteries","publication_year":2020,"publication_date":"2020-01-31","ids":{"openalex":"https://openalex.org/W3003737728","doi":"https://doi.org/10.1101/2020.01.30.927459","mag":"3003737728"},"language":"en","primary_location":{"id":"doi:10.1101/2020.01.30.927459","doi":"https://doi.org/10.1101/2020.01.30.927459","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2020.01.30.927459","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2020/01/31/2020.01.30.927459.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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2020/01/31/2020.01.30.927459.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5022501041","display_name":"Aviel Resnick","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I1335321130","display_name":"Children's Hospital of Philadelphia","ror":"https://ror.org/01z7r7q48","country_code":"US","type":"funder","lineage":["https://openalex.org/I1335321130"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aviel Resnick","raw_affiliation_strings":["The Children\u2019s Hospital of Philadelphia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Children\u2019s Hospital of Philadelphia","institution_ids":["https://openalex.org/I1335321130"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071356913","display_name":"Bahman Hooshdaran","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I1335321130","display_name":"Children's Hospital of Philadelphia","ror":"https://ror.org/01z7r7q48","country_code":"US","type":"funder","lineage":["https://openalex.org/I1335321130"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bahman Hooshdaran","raw_affiliation_strings":["The Children\u2019s Hospital of Philadelphia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Children\u2019s Hospital of Philadelphia","institution_ids":["https://openalex.org/I1335321130"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081453997","display_name":"Benjamin B. Pressly","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I1335321130","display_name":"Children's Hospital of Philadelphia","ror":"https://ror.org/01z7r7q48","country_code":"US","type":"funder","lineage":["https://openalex.org/I1335321130"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Benjamin B. Pressly","raw_affiliation_strings":["The Children\u2019s Hospital of Philadelphia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Children\u2019s Hospital of Philadelphia","institution_ids":["https://openalex.org/I1335321130"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050305140","display_name":"David T. Guerrero","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I1335321130","display_name":"Children's Hospital of Philadelphia","ror":"https://ror.org/01z7r7q48","country_code":"US","type":"funder","lineage":["https://openalex.org/I1335321130"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David T. Guerrero","raw_affiliation_strings":["The Children\u2019s Hospital of Philadelphia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Children\u2019s Hospital of Philadelphia","institution_ids":["https://openalex.org/I1335321130"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009569107","display_name":"Ivan S. Alferiev","orcid":"https://orcid.org/0000-0002-7849-750X","observed_orcids":["https://orcid.org/0000-0002-7849-750X"]},"institutions":[{"id":"https://openalex.org/I1335321130","display_name":"Children's Hospital of Philadelphia","ror":"https://ror.org/01z7r7q48","country_code":"US","type":"funder","lineage":["https://openalex.org/I1335321130"]},{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ivan S. Alferiev","raw_affiliation_strings":["The Children\u2019s Hospital of Philadelphia","University of Pennsylvania Perelman School of Medicine, Department of pediatrics"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Children\u2019s Hospital of Philadelphia","institution_ids":["https://openalex.org/I1335321130"]},{"raw_affiliation_string":"University of Pennsylvania Perelman School of Medicine, Department of pediatrics","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055602430","display_name":"Michael Chorny","orcid":"https://orcid.org/0000-0002-8243-9089","observed_orcids":["https://orcid.org/0000-0002-8243-9089"]},"institutions":[{"id":"https://openalex.org/I1335321130","display_name":"Children's Hospital of Philadelphia","ror":"https://ror.org/01z7r7q48","country_code":"US","type":"funder","lineage":["https://openalex.org/I1335321130"]},{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael Chorny","raw_affiliation_strings":["The Children\u2019s Hospital of Philadelphia","University of Pennsylvania Perelman School of Medicine, Department of pediatrics"],"raw_orcid":"https://orcid.org/0000-0002-8243-9089","affiliations":[{"raw_affiliation_string":"The Children\u2019s Hospital of Philadelphia","institution_ids":["https://openalex.org/I1335321130"]},{"raw_affiliation_string":"University of Pennsylvania Perelman School of Medicine, Department of pediatrics","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102969096","display_name":"Robert J. Levy","orcid":"https://orcid.org/0000-0002-0076-2780","observed_orcids":["https://orcid.org/0000-0002-0076-2780"]},"institutions":[{"id":"https://openalex.org/I1335321130","display_name":"Children's Hospital of Philadelphia","ror":"https://ror.org/01z7r7q48","country_code":"US","type":"funder","lineage":["https://openalex.org/I1335321130"]},{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert J. Levy","raw_affiliation_strings":["The Children\u2019s Hospital of Philadelphia","University of Pennsylvania Perelman School of Medicine, Department of pediatrics"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Children\u2019s Hospital of Philadelphia","institution_ids":["https://openalex.org/I1335321130"]},{"raw_affiliation_string":"University of Pennsylvania Perelman School of Medicine, Department of pediatrics","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5077830846","display_name":"Ilia Fishbein","orcid":"https://orcid.org/0000-0003-4971-1754","observed_orcids":["https://orcid.org/0000-0003-4971-1754"]},"institutions":[{"id":"https://openalex.org/I1335321130","display_name":"Children's Hospital of Philadelphia","ror":"https://ror.org/01z7r7q48","country_code":"US","type":"funder","lineage":["https://openalex.org/I1335321130"]},{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ilia Fishbein","raw_affiliation_strings":["The Children\u2019s Hospital of Philadelphia","University of Pennsylvania Perelman School of Medicine, Department of pediatrics"],"raw_orcid":"https://orcid.org/0000-0003-4971-1754","affiliations":[{"raw_affiliation_string":"The Children\u2019s Hospital of Philadelphia","institution_ids":["https://openalex.org/I1335321130"]},{"raw_affiliation_string":"University of Pennsylvania Perelman School of Medicine, Department of pediatrics","institution_ids":["https://openalex.org/I79576946"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5077830846"],"corresponding_institution_ids":["https://openalex.org/I1335321130","https://openalex.org/I79576946"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10052","display_name":"Medical Image Segmentation Techniques","score":0.9125999808311462,"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"}},"topics":[{"id":"https://openalex.org/T10052","display_name":"Medical Image Segmentation Techniques","score":0.9125999808311462,"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"}},{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.07540000230073929,"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/T12923","display_name":"Digital Image Processing Techniques","score":0.004000000189989805,"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/morphometrics","display_name":"morphometrics","score":0.8420000076293945},{"id":"https://openalex.org/keywords/semiautomatic-segmentation","display_name":"semi-automatic segmentation","score":0.8399999737739563},{"id":"https://openalex.org/keywords/flood-fill-algorithm","display_name":"flood fill algorithm","score":0.9909999966621399},{"id":"https://openalex.org/keywords/convex-hull-algorithm","display_name":"convex hull algorithm","score":0.7599999904632568},{"id":"https://openalex.org/keywords/contour-correction","display_name":"contour correction","score":0.7360000014305115},{"id":"https://openalex.org/keywords/seed-point-selection","display_name":"seed point selection","score":0.6499999761581421},{"id":"https://openalex.org/keywords/arterial-disease","display_name":"arterial disease","score":0.46399998664855957},{"id":"https://openalex.org/keywords/rat-arteries","display_name":"rat arteries","score":0.5619999766349792},{"id":"https://openalex.org/keywords/image-analysis-software","display_name":"image analysis software","score":0.5490000247955322},{"id":"https://openalex.org/keywords/manual-measurement-comparison","display_name":"manual measurement comparison","score":0.44200000166893005}],"concepts":[{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6922540664672852},{"id":"https://openalex.org/C89600930","wikidata":"https://www.wikidata.org/wiki/Q1423946","display_name":"Segmentation","level":2,"score":0.6491397619247437},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6137042045593262},{"id":"https://openalex.org/C206194317","wikidata":"https://www.wikidata.org/wiki/Q1138624","display_name":"Convex hull","level":3,"score":0.4919250011444092},{"id":"https://openalex.org/C138673069","wikidata":"https://www.wikidata.org/wiki/Q322229","display_name":"Tracing","level":2,"score":0.4793161153793335},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.4685578942298889},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4588012099266052},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4485895037651062},{"id":"https://openalex.org/C28719098","wikidata":"https://www.wikidata.org/wiki/Q44946","display_name":"Point (geometry)","level":2,"score":0.4337291717529297},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.4181550145149231},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.24914920330047607},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.21666669845581055},{"id":"https://openalex.org/C112680207","wikidata":"https://www.wikidata.org/wiki/Q714886","display_name":"Regular polygon","level":2,"score":0.14510634541511536},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"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/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1101/2020.01.30.927459","doi":"https://doi.org/10.1101/2020.01.30.927459","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2020.01.30.927459","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2020/01/31/2020.01.30.927459.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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.1101/2020.01.30.927459","doi":"https://doi.org/10.1101/2020.01.30.927459","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2020.01.30.927459","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2020/01/31/2020.01.30.927459.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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.504800021648407,"display_name":"Good health and well-being"}],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3003737728.pdf","grobid_xml":"https://content.openalex.org/works/W3003737728.grobid-xml"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W1905883306","https://openalex.org/W1906495479","https://openalex.org/W2002882918","https://openalex.org/W2014252132","https://openalex.org/W2067179638","https://openalex.org/W2074949023","https://openalex.org/W2076617429","https://openalex.org/W2120194944","https://openalex.org/W2157018249","https://openalex.org/W2282425217","https://openalex.org/W2326671595","https://openalex.org/W2514615007","https://openalex.org/W2901953250"],"related_works":["https://openalex.org/W7160198492","https://openalex.org/W2067179638","https://openalex.org/W4317621310","https://openalex.org/W2065251632","https://openalex.org/W1976153996","https://openalex.org/W2139161977","https://openalex.org/W2903966656","https://openalex.org/W2048207106","https://openalex.org/W7027120396","https://openalex.org/W7008250378"],"abstract_inverted_index":{"Abstract":[0],"Morphometric":[1],"analysis":[2,28,88],"of":[3,14,20,35,38,54,120,164,169,178,192,228,257,259],"explanted":[4],"arteries":[5],"remains":[6],"the":[7,18,41,69,74,118,148,170,193,198,207,217,229],"gold":[8],"standard":[9],"in":[10,254],"assessing":[11],"pathological":[12],"mechanisms":[13],"arterial":[15,59],"disease,":[16],"and":[17,46,63,96,108,123,167,184,210],"efficacy":[19],"therapeutic":[21],"interventions.":[22],"Software":[23],"currently":[24],"used":[25,136,247],"for":[26,50,103,127,219,232,252],"morphometric":[27,82],"(ImageJ,":[29],"ImagePro,":[30],"etc.)":[31],"requires":[32],"manual":[33,159,204,233],"tracing":[34],"each":[36,128],"region":[37],"interest":[39],"by":[40,93,142,206,235],"user":[42],"to":[43,65,73,137,146],"obtain":[44,147],"direct":[45],"derived":[47],"data":[48,97,220],"needed":[49],"analysis.":[51],"Manual":[52],"segmentation":[53,115],"borders":[55],"between":[56],"differently":[57],"stained":[58,180],"compartments":[60],"is":[61,71,135,242],"time-consuming":[62],"prone":[64],"bias,":[66],"even":[67],"when":[68],"operator":[70],"blind":[72],"treatment":[75],"type.":[76],"Here,":[77],"we":[78],"report":[79],"newly":[80],"designed":[81],"software,":[83,248],"floodSeg,":[84],"which":[85],"greatly":[86],"aids":[87],"through":[89,158],"semiautomated":[90],"segmentation,":[91],"followed":[92,141],"automated":[94],"computation":[95],"entry.":[98],"The":[99,131,190],"program":[100],"includes":[101],"tools":[102],"both":[104],"rapid":[105],"component":[106],"selection,":[107],"precision":[109],"user-controlled":[110],"contour":[111],"correction.":[112],"In":[113],"practice,":[114],"occurs":[116],"following":[117],"selection":[119],"seed":[121],"points":[122],"corresponding":[124],"threshold":[125],"values,":[126],"desired":[129],"component.":[130],"flood":[132],"fill":[133],"algorithm":[134,145],"map":[138],"out":[139],"components,":[140],"Sklansky\u2019s":[143],"convex-hull":[144],"outer":[149],"contours.":[150],"If":[151],"necessary,":[152],"convexity":[153],"defects":[154],"can":[155],"be":[156],"overcome":[157],"point":[160],"placement":[161],"on":[162,202,245],"top":[163],"existing":[165],"points,":[166],"regeneration":[168],"contour.":[171],"floodSeg":[172,223],"was":[173,196,224],"tested":[174],"using":[175,222],"a":[176,255],"set":[177],"non-uniformly":[179],"stented":[181],"rat":[182],"arteries,":[183],"compared":[185],"against":[186],"manually":[187],"obtained":[188],"results.":[189],"accuracy":[191],"resulting":[194],"measurements":[195,205,234],"within":[197],"expected":[199],"limit":[200],"based":[201],"repeated":[203],"same":[208],"operator,":[209],"did":[211],"not":[212],"exceed":[213],"3%.":[214],"Most":[215],"notably,":[216],"duration":[218],"acquisition":[221],"less":[225],"than":[226],"20%":[227],"time":[230],"required":[231],"an":[236,243],"experienced":[237],"operator.":[238],"Thus,":[239],"our":[240],"contribution":[241],"improvement":[244],"widely":[246],"with":[249],"significant":[250],"potential":[251],"application":[253],"multitude":[256],"areas":[258],"pathology":[260],"practice.":[261]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-10-30T12:39:25.321706","created_date":"2020-02-07T00:00:00"}