{"id":"https://openalex.org/W7214192986","doi":"https://doi.org/10.64898/2026.09.18.752612","title":"BioAFMviewer AFM Analysis Arena A 3 \u2013 an interactive software platform for automated analysis of HS-AFM imaging","display_name":"BioAFMviewer AFM Analysis Arena A 3 \u2013 an interactive software platform for automated analysis of HS-AFM imaging","publication_year":2026,"publication_date":"2026-09-24","ids":{"openalex":"https://openalex.org/W7214192986","doi":"https://doi.org/10.64898/2026.09.18.752612"},"language":"en","primary_location":{"id":"doi:10.64898/2026.09.18.752612","doi":"https://doi.org/10.64898/2026.09.18.752612","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.18.752612","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/24/2026.09.18.752612.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/2026/09/24/2026.09.18.752612.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5072776057","display_name":"Romain Amyot","orcid":"https://orcid.org/0000-0002-3316-8462","observed_orcids":["https://orcid.org/0000-0002-3316-8462"]},"institutions":[{"id":"https://openalex.org/I10091056","display_name":"Kanazawa University","ror":"https://ror.org/02hwp6a56","country_code":"JP","type":"education","lineage":["https://openalex.org/I10091056"]},{"id":"https://openalex.org/I4405287064","display_name":"Nano Life Science Institute, Kanazawa University","ror":"https://ror.org/040xys054","country_code":"JP","type":"facility","lineage":["https://openalex.org/I10091056","https://openalex.org/I4405287064"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Romain Amyot","raw_affiliation_strings":["WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan","institution_ids":["https://openalex.org/I10091056","https://openalex.org/I4405287064"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5138923450","display_name":"Soma Yamamoto","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I10091056","display_name":"Kanazawa University","ror":"https://ror.org/02hwp6a56","country_code":"JP","type":"education","lineage":["https://openalex.org/I10091056"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Soma Yamamoto","raw_affiliation_strings":["Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa 920-1192, Japan","WISE Program for Nano-Precision Medicine, Science, and Technology, Kanazawa University, Kanazawa 920-1192, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa 920-1192, Japan","institution_ids":["https://openalex.org/I10091056"]},{"raw_affiliation_string":"WISE Program for Nano-Precision Medicine, Science, and Technology, Kanazawa University, Kanazawa 920-1192, Japan","institution_ids":["https://openalex.org/I10091056"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085945190","display_name":"Hiroki Konno","orcid":"https://orcid.org/0000-0002-1712-171X","observed_orcids":["https://orcid.org/0000-0002-1712-171X"]},"institutions":[{"id":"https://openalex.org/I10091056","display_name":"Kanazawa University","ror":"https://ror.org/02hwp6a56","country_code":"JP","type":"education","lineage":["https://openalex.org/I10091056"]},{"id":"https://openalex.org/I4405287064","display_name":"Nano Life Science Institute, Kanazawa University","ror":"https://ror.org/040xys054","country_code":"JP","type":"facility","lineage":["https://openalex.org/I10091056","https://openalex.org/I4405287064"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Hiroki Konno","raw_affiliation_strings":["WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan","institution_ids":["https://openalex.org/I10091056","https://openalex.org/I4405287064"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057583138","display_name":"Clemens M. Franz","orcid":"https://orcid.org/0000-0003-0104-4841","observed_orcids":["https://orcid.org/0000-0003-0104-4841"]},"institutions":[{"id":"https://openalex.org/I10091056","display_name":"Kanazawa University","ror":"https://ror.org/02hwp6a56","country_code":"JP","type":"education","lineage":["https://openalex.org/I10091056"]},{"id":"https://openalex.org/I4405287064","display_name":"Nano Life Science Institute, Kanazawa University","ror":"https://ror.org/040xys054","country_code":"JP","type":"facility","lineage":["https://openalex.org/I10091056","https://openalex.org/I4405287064"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Clemens Franz","raw_affiliation_strings":["WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan","institution_ids":["https://openalex.org/I10091056","https://openalex.org/I4405287064"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5059101377","display_name":"Holger Flechsig","orcid":"https://orcid.org/0000-0003-4984-9294","observed_orcids":["https://orcid.org/0000-0003-4984-9294"]},"institutions":[{"id":"https://openalex.org/I10091056","display_name":"Kanazawa University","ror":"https://ror.org/02hwp6a56","country_code":"JP","type":"education","lineage":["https://openalex.org/I10091056"]},{"id":"https://openalex.org/I4405287064","display_name":"Nano Life Science Institute, Kanazawa University","ror":"https://ror.org/040xys054","country_code":"JP","type":"facility","lineage":["https://openalex.org/I10091056","https://openalex.org/I4405287064"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Holger Flechsig","raw_affiliation_strings":["WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan","institution_ids":["https://openalex.org/I10091056","https://openalex.org/I4405287064"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5059101377"],"corresponding_institution_ids":["https://openalex.org/I10091056","https://openalex.org/I4405287064"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"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/T10923","display_name":"Force Microscopy Techniques and Applications","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/3107","display_name":"Atomic and Molecular Physics, and Optics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10923","display_name":"Force Microscopy Techniques and Applications","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/3107","display_name":"Atomic and Molecular Physics, and Optics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10540","display_name":"Advanced Fluorescence Microscopy Techniques","score":0.0003000000142492354,"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":0.0,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/high-speed-atomic-force-microscopy","display_name":"high-speed atomic force microscopy","score":0.9919999837875366},{"id":"https://openalex.org/keywords/automated-image-analysis","display_name":"automated image analysis","score":0.906000018119812},{"id":"https://openalex.org/keywords/molecule-detection","display_name":"molecule detection","score":0.7649999856948853},{"id":"https://openalex.org/keywords/dynamic-tracking","display_name":"dynamic tracking","score":0.8270000219345093},{"id":"https://openalex.org/keywords/single-molecule-dynamics","display_name":"single-molecule dynamics","score":0.9639999866485596},{"id":"https://openalex.org/keywords/software-platform","display_name":"software platform","score":0.37700000405311584}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7588000297546387},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6640999913215637},{"id":"https://openalex.org/C102951782","wikidata":"https://www.wikidata.org/wiki/Q49295","display_name":"Atomic force microscopy","level":2,"score":0.6141999959945679},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5938000082969666},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.5095999836921692},{"id":"https://openalex.org/C2775936607","wikidata":"https://www.wikidata.org/wiki/Q466845","display_name":"Tracking (education)","level":2,"score":0.5051000118255615},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.4456999897956848},{"id":"https://openalex.org/C132964779","wikidata":"https://www.wikidata.org/wiki/Q2110223","display_name":"Raw data","level":2,"score":0.4438000023365021},{"id":"https://openalex.org/C2984968299","wikidata":"https://www.wikidata.org/wiki/Q1077784","display_name":"Software tool","level":3,"score":0.4327000081539154},{"id":"https://openalex.org/C45206210","wikidata":"https://www.wikidata.org/wiki/Q2415817","display_name":"Nanoscopic scale","level":2,"score":0.4309000074863434},{"id":"https://openalex.org/C2986587452","wikidata":"https://www.wikidata.org/wiki/Q938438","display_name":"Statistical analysis","level":2,"score":0.39489999413490295},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.3806000053882599},{"id":"https://openalex.org/C2780977526","wikidata":"https://www.wikidata.org/wiki/Q42417149","display_name":"Data exploration","level":3,"score":0.37720000743865967},{"id":"https://openalex.org/C172367668","wikidata":"https://www.wikidata.org/wiki/Q6504956","display_name":"Data visualization","level":3,"score":0.3255999982357025},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.32519999146461487},{"id":"https://openalex.org/C147080431","wikidata":"https://www.wikidata.org/wiki/Q1074953","display_name":"Microscopy","level":2,"score":0.314300000667572},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.29260000586509705},{"id":"https://openalex.org/C64073096","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Interactive visualization","level":3,"score":0.28850001096725464},{"id":"https://openalex.org/C95986675","wikidata":"https://www.wikidata.org/wiki/Q185168","display_name":"Quantitative analysis (chemistry)","level":2,"score":0.2833999991416931},{"id":"https://openalex.org/C9417928","wikidata":"https://www.wikidata.org/wiki/Q1070689","display_name":"Image processing","level":3,"score":0.27399998903274536},{"id":"https://openalex.org/C55037315","wikidata":"https://www.wikidata.org/wiki/Q5421151","display_name":"Experimental data","level":2,"score":0.27000001072883606},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.2653000056743622},{"id":"https://openalex.org/C138827492","wikidata":"https://www.wikidata.org/wiki/Q6661985","display_name":"Data processing","level":2,"score":0.26429998874664307},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.263700008392334},{"id":"https://openalex.org/C175801342","wikidata":"https://www.wikidata.org/wiki/Q1988917","display_name":"Data analysis","level":2,"score":0.26260000467300415},{"id":"https://openalex.org/C31601959","wikidata":"https://www.wikidata.org/wiki/Q931309","display_name":"Medical imaging","level":2,"score":0.2542000114917755}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.09.18.752612","doi":"https://doi.org/10.64898/2026.09.18.752612","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.18.752612","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/24/2026.09.18.752612.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:10.64898/2026.09.18.752612","doi":"https://doi.org/10.64898/2026.09.18.752612","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.18.752612","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/24/2026.09.18.752612.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":[],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320318231","display_name":"Kanazawa University","ror":"https://ror.org/02hwp6a56"},{"id":"https://openalex.org/F4320320912","display_name":"Ministry of Education, Culture, Sports, Science and Technology","ror":"https://ror.org/048rj2z13"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7214192986.pdf","grobid_xml":"https://content.openalex.org/works/W7214192986.grobid-xml"},"referenced_works_count":1,"referenced_works":["https://openalex.org/W7117134965"],"related_works":["https://openalex.org/W4319871013","https://openalex.org/W2886047154","https://openalex.org/W4366191712","https://openalex.org/W4247665808","https://openalex.org/W2791780001","https://openalex.org/W7204159108","https://openalex.org/W4387564407","https://openalex.org/W2041018206","https://openalex.org/W2187098851","https://openalex.org/W2019058598"],"abstract_inverted_index":{"High-speed":[0],"atomic":[1],"force":[2],"microscopy":[3],"(HS-AFM)":[4],"experiments":[5],"provide":[6],"unique":[7],"insights":[8],"into":[9],"nanoscale":[10,141],"biological":[11],"processes":[12],"by":[13],"directly":[14],"visualizing":[15],"the":[16,37,50,57,66,126],"surface":[17],"topography":[18],"dynamics":[19],"of":[20,28,39,53,60,84,117],"biomolecules,":[21],"such":[22],"as":[23,75],"proteins,":[24],"over":[25],"extended":[26],"periods":[27],"time":[29],"and":[30,121],"generating":[31],"large":[32],"imaging":[33,87,103,112],"data":[34,44,55,88],"sets.":[35],"However,":[36],"lack":[38],"computational":[40],"methods":[41,116],"for":[42,56,79],"automated":[43],"analysis":[45,83],"has":[46],"thus":[47],"far":[48],"limited":[49],"full":[51],"utilization":[52],"these":[54],"quantitative":[58,82],"understanding":[59],"single-molecule":[61],"dynamic.":[62],"Here,":[63],"we":[64,114],"present":[65],"AFM":[67,85],"Analysis":[68],"Arena":[69],"(A":[70],"3":[71],")":[72],"within":[73,89],"BioAFMviewer":[74],"a":[76,90,96],"software":[77],"platform":[78],"automated,":[80],"high-throughput":[81],"topographic":[86],"user-friendly":[91],"interactive":[92],"graphical":[93],"interface,":[94],"implementing":[95],"convenient":[97],"workflow":[98],"from":[99,134],"raw":[100],"HS-AFM":[101,111,132],"(AFM)":[102],"to":[104,110,124,130],"statistical":[105],"analysis.":[106],"In":[107],"several":[108],"applications":[109],"data,":[113],"demonstrate":[115],"automatized":[118],"molecule":[119],"detection":[120],"dynamic":[122],"tracking":[123],"highlight":[125],"available":[127],"capacities,":[128],"aiming":[129],"transform":[131],"measurements":[133],"observations":[135],"towards":[136],"an":[137],"analytical":[138],"tool":[139],"in":[140],"biology.":[142]},"counts_by_year":[],"updated_date":"2026-11-06T12:05:46.655746","created_date":"2026-09-25T00:00:00"}
