{"id":"https://openalex.org/W2956739125","doi":"https://doi.org/10.1109/isbi.2019.8759200","title":"Automated Quantification With Sub-Micrometer Scale Precision In Volumetric Multicolor Multiphoton Microscopy Images","display_name":"Automated Quantification With Sub-Micrometer Scale Precision In Volumetric Multicolor Multiphoton Microscopy Images","publication_year":2019,"publication_date":"2019-04-01","ids":{"openalex":"https://openalex.org/W2956739125","doi":"https://doi.org/10.1109/isbi.2019.8759200","mag":"2956739125"},"language":"en","primary_location":{"id":"doi:10.1109/isbi.2019.8759200","is_oa":false,"landing_page_url":"https://doi.org/10.1109/isbi.2019.8759200","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5040928183","display_name":"Minh-Son Phan","orcid":"https://orcid.org/0000-0002-9916-1351"},"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/I142476485","display_name":"\u00c9cole Polytechnique","ror":"https://ror.org/05hy3tk52","country_code":"FR","type":"education","lineage":["https://openalex.org/I142476485","https://openalex.org/I4210145102"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"M.S. Phan","raw_affiliation_strings":["CNRS, INSERM, Ecole Polytechnique, Laboratory for Optics and Biosciences, Palaiseau, France","LOB - Laboratoire d'Optique et Biosciences (Ecole Polytechnique\r\n91128 PALAISEAU Cedex - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CNRS, INSERM, Ecole Polytechnique, Laboratory for Optics and Biosciences, Palaiseau, France","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I142476485","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"LOB - Laboratoire d'Optique et Biosciences (Ecole Polytechnique\r\n91128 PALAISEAU Cedex - France)","institution_ids":["https://openalex.org/I142476485"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062676612","display_name":"Katherine S. Matho","orcid":"https://orcid.org/0000-0002-6105-4219"},"institutions":[{"id":"https://openalex.org/I142476485","display_name":"\u00c9cole Polytechnique","ror":"https://ror.org/05hy3tk52","country_code":"FR","type":"education","lineage":["https://openalex.org/I142476485","https://openalex.org/I4210145102"]},{"id":"https://openalex.org/I2750212522","display_name":"Cold Spring Harbor Laboratory","ror":"https://ror.org/02qz8b764","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2750212522"]}],"countries":["FR","US"],"is_corresponding":false,"raw_author_name":"K. Matho","raw_affiliation_strings":["Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA","LOB - Laboratoire d'Optique et Biosciences (Ecole Polytechnique\r\n91128 PALAISEAU Cedex - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA","institution_ids":["https://openalex.org/I2750212522"]},{"raw_affiliation_string":"LOB - Laboratoire d'Optique et Biosciences (Ecole Polytechnique\r\n91128 PALAISEAU Cedex - France)","institution_ids":["https://openalex.org/I142476485"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057529735","display_name":"Lamiae Abdeladim","orcid":"https://orcid.org/0000-0002-5015-8653"},"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/I142476485","display_name":"\u00c9cole Polytechnique","ror":"https://ror.org/05hy3tk52","country_code":"FR","type":"education","lineage":["https://openalex.org/I142476485","https://openalex.org/I4210145102"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"L. Abdeladim","raw_affiliation_strings":["CNRS, INSERM, Ecole Polytechnique, Laboratory for Optics and Biosciences, Palaiseau, France","LOB - Laboratoire d'Optique et Biosciences (Ecole Polytechnique\r\n91128 PALAISEAU Cedex - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CNRS, INSERM, Ecole Polytechnique, Laboratory for Optics and Biosciences, Palaiseau, France","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I142476485","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"LOB - Laboratoire d'Optique et Biosciences (Ecole Polytechnique\r\n91128 PALAISEAU Cedex - France)","institution_ids":["https://openalex.org/I142476485"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014215458","display_name":"Jean Livet","orcid":"https://orcid.org/0000-0003-3079-4908"},"institutions":[{"id":"https://openalex.org/I1340951533","display_name":"Institut de la Vision","ror":"https://ror.org/000zhpw23","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1340951533","https://openalex.org/I39804081"]},{"id":"https://openalex.org/I2750212522","display_name":"Cold Spring Harbor Laboratory","ror":"https://ror.org/02qz8b764","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2750212522"]}],"countries":["FR","US"],"is_corresponding":false,"raw_author_name":"J. Livet","raw_affiliation_strings":["Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA","Institut de la Vision (17 Rue Moreau, 75012 Paris - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA","institution_ids":["https://openalex.org/I2750212522"]},{"raw_affiliation_string":"Institut de la Vision (17 Rue Moreau, 75012 Paris - France)","institution_ids":["https://openalex.org/I1340951533"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029886936","display_name":"Emmanuel Beaurepaire","orcid":"https://orcid.org/0000-0002-2082-8214"},"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/I142476485","display_name":"\u00c9cole Polytechnique","ror":"https://ror.org/05hy3tk52","country_code":"FR","type":"education","lineage":["https://openalex.org/I142476485","https://openalex.org/I4210145102"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"E. Beaurepaire","raw_affiliation_strings":["CNRS, INSERM, Ecole Polytechnique, Laboratory for Optics and Biosciences, Palaiseau, France","LOB - Laboratoire d'Optique et Biosciences (Ecole Polytechnique\r\n91128 PALAISEAU Cedex - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CNRS, INSERM, Ecole Polytechnique, Laboratory for Optics and Biosciences, Palaiseau, France","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I142476485","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"LOB - Laboratoire d'Optique et Biosciences (Ecole Polytechnique\r\n91128 PALAISEAU Cedex - France)","institution_ids":["https://openalex.org/I142476485"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023449502","display_name":"Anatole Chessel","orcid":"https://orcid.org/0000-0002-1326-6305"},"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/I142476485","display_name":"\u00c9cole Polytechnique","ror":"https://ror.org/05hy3tk52","country_code":"FR","type":"education","lineage":["https://openalex.org/I142476485","https://openalex.org/I4210145102"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"A. Chessel","raw_affiliation_strings":["CNRS, INSERM, Ecole Polytechnique, Laboratory for Optics and Biosciences, Palaiseau, France","LOB - Laboratoire d'Optique et Biosciences (Ecole Polytechnique\r\n91128 PALAISEAU Cedex - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CNRS, INSERM, Ecole Polytechnique, Laboratory for Optics and Biosciences, Palaiseau, France","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I142476485","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"LOB - Laboratoire d'Optique et Biosciences (Ecole Polytechnique\r\n91128 PALAISEAU Cedex - France)","institution_ids":["https://openalex.org/I142476485"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.04968857,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"521","last_page":"525"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10540","display_name":"Advanced Fluorescence Microscopy Techniques","score":0.9998999834060669,"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/T10540","display_name":"Advanced Fluorescence Microscopy Techniques","score":0.9998999834060669,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.9994999766349792,"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/T12015","display_name":"Photoacoustic and Ultrasonic Imaging","score":0.9965000152587891,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/microscopy","display_name":"Microscopy","score":0.6240532398223877},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5181828141212463},{"id":"https://openalex.org/keywords/computer-vision","display_name":"Computer vision","score":0.4897894859313965},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.4752090871334076},{"id":"https://openalex.org/keywords/optics","display_name":"Optics","score":0.4745510518550873},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.46853700280189514},{"id":"https://openalex.org/keywords/resolution","display_name":"Resolution (logic)","score":0.42941954731941223},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.38670170307159424},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.3308830261230469},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.2996254861354828},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.1565667986869812}],"concepts":[{"id":"https://openalex.org/C147080431","wikidata":"https://www.wikidata.org/wiki/Q1074953","display_name":"Microscopy","level":2,"score":0.6240532398223877},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5181828141212463},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.4897894859313965},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.4752090871334076},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.4745510518550873},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.46853700280189514},{"id":"https://openalex.org/C138268822","wikidata":"https://www.wikidata.org/wiki/Q1051925","display_name":"Resolution (logic)","level":2,"score":0.42941954731941223},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.38670170307159424},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.3308830261230469},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.2996254861354828},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.1565667986869812},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1109/isbi.2019.8759200","is_oa":false,"landing_page_url":"https://doi.org/10.1109/isbi.2019.8759200","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019)","raw_type":"proceedings-article"},{"id":"pmh:oai:repository.cshl.edu:38658","is_oa":false,"landing_page_url":"http://repository.cshl.edu/38658/","pdf_url":null,"source":{"id":"https://openalex.org/S4306402288","display_name":"Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Book"},{"id":"pmh:oai:HAL:hal-02372253v1","is_oa":false,"landing_page_url":"https://polytechnique.hal.science/hal-02372253","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI), IEEE, pp.521-525, 2019, IEEE ISBI, &#x27E8;10.1109/ISBI.2019.8759200&#x27E9;","raw_type":"Proceedings"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1609927754","display_name":"Imagerie et reconstruction multi\u00e9chelles de la morphogen\u00e8se. (Plateforme d'innovation technologique et m\u00e9thodologique pour l'imagerie in vivo et la reconstruction des dynamiques multi\u00e9chelles de la morphogen\u00e8se)","funder_award_id":"ANR-11-EQPX-0029","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"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":12,"referenced_works":["https://openalex.org/W1508135620","https://openalex.org/W1603300429","https://openalex.org/W1779718467","https://openalex.org/W2047468618","https://openalex.org/W2065045053","https://openalex.org/W2110232607","https://openalex.org/W2125637308","https://openalex.org/W2129650255","https://openalex.org/W2138398901","https://openalex.org/W2147607085","https://openalex.org/W2279851379","https://openalex.org/W2532163996"],"related_works":["https://openalex.org/W2770593030","https://openalex.org/W3154990682","https://openalex.org/W2560201613","https://openalex.org/W2171975302","https://openalex.org/W2022352247","https://openalex.org/W4312219546","https://openalex.org/W4377941617","https://openalex.org/W2518805858","https://openalex.org/W1568886124","https://openalex.org/W2156260160"],"abstract_inverted_index":{"Recent":[0],"multicolor":[1,60,163],"multiphoton":[2,164],"microscopy":[3],"schemes":[4],"are":[5],"opening":[6],"the":[7,37,49,75,85,92,126,138,146,151],"way":[8],"to":[9,29,70,83,145],"high":[10],"quality":[11],"fluorescence":[12],"color":[13,98],"imaging":[14],"at":[15],"near-micrometric":[16],"resolution":[17,35],"over":[18],"virtually":[19],"unlimited":[20],"volumes":[21],"of":[22,51,87,94,119,140,153,159],"brain":[23],"tissue.":[24],"However,":[25],"unavoidable":[26],"artifacts":[27],"related":[28],"depth,":[30],"chromatic":[31],"aberration":[32],"or":[33],"anisotropic":[34],"affect":[36],"resulting":[38],"images":[39],"and":[40,44,107,124],"can":[41],"bias":[42],"measurements":[43,56,155],"quantifications.":[45],"Here,":[46],"we":[47],"prove":[48],"possibility":[50],"performing":[52],"precise":[53],"automated":[54],"quantitative":[55],"on":[57,91],"such":[58],"tridimensional":[59],"images,":[61],"taking":[62],"as":[63],"a":[64,103,115],"model":[65],"fluorescently":[66],"labeled":[67],"axons":[68,89,127],"belonging":[69],"an":[71,80],"auditory":[72],"tract":[73],"in":[74,96],"mouse":[76],"brainstem.":[77],"We":[78,113],"present":[79],"analysis":[81],"pipeline":[82,142],"compute":[84],"diameter":[86],"these":[88],"based":[90],"calculation":[93],"distance":[95,111],"HSV":[97],"space,":[99],"its":[100],"binarization":[101],"using":[102],"random":[104],"walker":[105],"algorithm":[106],"skeleton":[108],"extraction":[109],"by":[110],"transform.":[112],"measure":[114],"biologically":[116],"meaningful":[117],"difference":[118],"about":[120],"500":[121],"nm":[122],"before":[123],"after":[125],"enter":[128],"their":[129],"target":[130],"nucleus":[131],"where":[132],"they":[133],"form":[134],"synaptic":[135],"connections,":[136],"proving":[137],"robustness":[139],"our":[141],"with":[143,162],"respect":[144],"aforementioned":[147],"limitations.":[148],"This":[149],"demonstrates":[150],"ability":[152],"sub-micrometric":[154],"across":[156],"tissue":[157],"depths":[158],"0.5":[160],"mm":[161],"microscopy.":[165]},"counts_by_year":[],"updated_date":"2026-07-02T09:51:11.867554","created_date":"2025-10-10T00:00:00"}
