{"id":"https://openalex.org/W3195710680","doi":"https://doi.org/10.1186/s12859-021-04324-z","title":"LLAMA: a robust and scalable machine learning pipeline for analysis of large scale 4D microscopy data: analysis of cell ruffles and filopodia","display_name":"LLAMA: a robust and scalable machine learning pipeline for analysis of large scale 4D microscopy data: analysis of cell ruffles and filopodia","publication_year":2021,"publication_date":"2021-08-19","ids":{"openalex":"https://openalex.org/W3195710680","doi":"https://doi.org/10.1186/s12859-021-04324-z","mag":"3195710680","pmid":"https://pubmed.ncbi.nlm.nih.gov/34412593"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-021-04324-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04324-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04324-z","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04324-z","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5029494537","display_name":"James Lefevre","orcid":"https://orcid.org/0000-0002-5945-9575"},"institutions":[{"id":"https://openalex.org/I165143802","display_name":"The University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"James G. Lefevre","raw_affiliation_strings":["Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia","institution_ids":["https://openalex.org/I165143802"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069756005","display_name":"Yvette W. H. Koh","orcid":"https://orcid.org/0000-0002-9963-0605"},"institutions":[{"id":"https://openalex.org/I165143802","display_name":"The University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Yvette W. H. Koh","raw_affiliation_strings":["Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia","institution_ids":["https://openalex.org/I165143802"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022945502","display_name":"Adam A. Wall","orcid":"https://orcid.org/0000-0001-8301-2899"},"institutions":[{"id":"https://openalex.org/I165143802","display_name":"The University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Adam A. Wall","raw_affiliation_strings":["Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia","institution_ids":["https://openalex.org/I165143802"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071296501","display_name":"Nicholas D. Condon","orcid":"https://orcid.org/0000-0002-1833-1129"},"institutions":[{"id":"https://openalex.org/I165143802","display_name":"The University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Nicholas D. Condon","raw_affiliation_strings":["Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia","institution_ids":["https://openalex.org/I165143802"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052494090","display_name":"Jennifer L. Stow","orcid":"https://orcid.org/0000-0002-5409-9101"},"institutions":[{"id":"https://openalex.org/I165143802","display_name":"The University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Jennifer L. Stow","raw_affiliation_strings":["Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia","institution_ids":["https://openalex.org/I165143802"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5072586243","display_name":"Nicholas Hamilton","orcid":"https://orcid.org/0000-0003-0331-3427"},"institutions":[{"id":"https://openalex.org/I165143802","display_name":"The University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Nicholas A. Hamilton","raw_affiliation_strings":["Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia. n.hamilton@imb.uq.edu.au","Research Computing Centre, The University of Queensland, Brisbane, QLD, Australia. n.hamilton@imb.uq.edu.au","Research Computing Centre, The University of Queensland, Brisbane, QLD, Australia"],"raw_orcid":"https://orcid.org/0000-0003-0331-3427","affiliations":[{"raw_affiliation_string":"Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia. n.hamilton@imb.uq.edu.au","institution_ids":["https://openalex.org/I165143802"]},{"raw_affiliation_string":"Research Computing Centre, The University of Queensland, Brisbane, QLD, Australia. n.hamilton@imb.uq.edu.au","institution_ids":["https://openalex.org/I165143802"]},{"raw_affiliation_string":"Research Computing Centre, The University of Queensland, Brisbane, QLD, Australia","institution_ids":["https://openalex.org/I165143802"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5072586243"],"corresponding_institution_ids":["https://openalex.org/I165143802"],"apc_list":{"value":2490,"currency":"USD","value_usd":2490},"apc_paid":{"value":2490,"currency":"USD","value_usd":2490},"fwci":1.0677,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.82523603,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":97},"biblio":{"volume":"22","issue":"1","first_page":"410","last_page":"410"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.8569999933242798,"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":0.8569999933242798,"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/T10379","display_name":"Cellular Mechanics and Interactions","score":0.039400000125169754,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell 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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.01679999940097332,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7789069414138794},{"id":"https://openalex.org/keywords/filopodia","display_name":"Filopodia","score":0.6455038785934448},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.6010084748268127},{"id":"https://openalex.org/keywords/terabyte","display_name":"Terabyte","score":0.5880364179611206},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.5620739459991455},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5611802935600281},{"id":"https://openalex.org/keywords/segmentation","display_name":"Segmentation","score":0.5098868608474731},{"id":"https://openalex.org/keywords/digital-pathology","display_name":"Digital pathology","score":0.4111374318599701},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3902389109134674},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.20426982641220093},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1033303439617157}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7789069414138794},{"id":"https://openalex.org/C90301020","wikidata":"https://www.wikidata.org/wiki/Q14859810","display_name":"Filopodia","level":3,"score":0.6455038785934448},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.6010084748268127},{"id":"https://openalex.org/C199683683","wikidata":"https://www.wikidata.org/wiki/Q8799","display_name":"Terabyte","level":2,"score":0.5880364179611206},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.5620739459991455},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5611802935600281},{"id":"https://openalex.org/C89600930","wikidata":"https://www.wikidata.org/wiki/Q1423946","display_name":"Segmentation","level":2,"score":0.5098868608474731},{"id":"https://openalex.org/C2777522853","wikidata":"https://www.wikidata.org/wiki/Q5276128","display_name":"Digital pathology","level":2,"score":0.4111374318599701},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3902389109134674},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.20426982641220093},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1033303439617157},{"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/C125705527","wikidata":"https://www.wikidata.org/wiki/Q185269","display_name":"Actin","level":2,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008264","descriptor_name":"Macrophages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008264","descriptor_name":"Macrophages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008264","descriptor_name":"Macrophages","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":"D011554","descriptor_name":"Pseudopodia","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011554","descriptor_name":"Pseudopodia","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011554","descriptor_name":"Pseudopodia","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-021-04324-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04324-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04324-z","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34412593","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34412593","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":"BMC bioinformatics","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8375126","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8375126","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:c5c8488c33194c0481b9480c83260689","is_oa":false,"landing_page_url":"https://doaj.org/article/c5c8488c33194c0481b9480c83260689","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 22, Iss 1, Pp 1-26 (2021)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-021-04324-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04324-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04324-z","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/10","score":0.5699999928474426,"display_name":"Reduced inequalities"}],"awards":[{"id":"https://openalex.org/G1272289860","display_name":null,"funder_award_id":"LE170100206","funder_id":"https://openalex.org/F4320334705","funder_display_name":"National Health and Medical Research Council"},{"id":"https://openalex.org/G1576124136","display_name":"Machine learning for organelle selection & feature detection in live cells","funder_award_id":"DP180101910","funder_id":"https://openalex.org/F4320334704","funder_display_name":"Australian Research Council"},{"id":"https://openalex.org/G5747412697","display_name":null,"funder_award_id":"APP1176209","funder_id":"https://openalex.org/F4320334704","funder_display_name":"Australian Research Council"},{"id":"https://openalex.org/G8657860356","display_name":"GTPase regulation of cellular pathways in inflammation and cancer","funder_award_id":"1176209","funder_id":"https://openalex.org/F4320334705","funder_display_name":"National Health and Medical Research Council"},{"id":"https://openalex.org/G8874556974","display_name":"Lattice light sheet microscopy for imaging biology in real space and time","funder_award_id":"LE170100206","funder_id":"https://openalex.org/F4320334704","funder_display_name":"Australian Research Council"}],"funders":[{"id":"https://openalex.org/F4320306082","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90"},{"id":"https://openalex.org/F4320306202","display_name":"Gordon and Betty Moore Foundation","ror":"https://ror.org/006wxqw41"},{"id":"https://openalex.org/F4320315254","display_name":"Innovative Research Group Project of the National Natural Science Foundation of China","ror":null},{"id":"https://openalex.org/F4320320390","display_name":"Australian Cancer Research Foundation","ror":"https://ror.org/0459phn12"},{"id":"https://openalex.org/F4320320984","display_name":"University of Queensland","ror":"https://ror.org/00rqy9422"},{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"},{"id":"https://openalex.org/F4320334704","display_name":"Australian Research Council","ror":"https://ror.org/05mmh0f86"},{"id":"https://openalex.org/F4320334705","display_name":"National Health and Medical Research Council","ror":"https://ror.org/011kf5r70"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3195710680.pdf","grobid_xml":"https://content.openalex.org/works/W3195710680.grobid-xml"},"referenced_works_count":42,"referenced_works":["https://openalex.org/W1570448133","https://openalex.org/W1865638244","https://openalex.org/W1901129140","https://openalex.org/W1980971505","https://openalex.org/W1999286245","https://openalex.org/W2004369799","https://openalex.org/W2006826186","https://openalex.org/W2018227909","https://openalex.org/W2030898714","https://openalex.org/W2053270078","https://openalex.org/W2066485305","https://openalex.org/W2070869225","https://openalex.org/W2087591542","https://openalex.org/W2099540110","https://openalex.org/W2116244722","https://openalex.org/W2116529502","https://openalex.org/W2118663558","https://openalex.org/W2167279371","https://openalex.org/W2222512263","https://openalex.org/W2229412420","https://openalex.org/W2335358468","https://openalex.org/W2336370554","https://openalex.org/W2467628122","https://openalex.org/W2528206395","https://openalex.org/W2562415513","https://openalex.org/W2580035316","https://openalex.org/W2601810315","https://openalex.org/W2759448220","https://openalex.org/W2806070179","https://openalex.org/W2807373645","https://openalex.org/W2888906615","https://openalex.org/W2895705408","https://openalex.org/W2963194837","https://openalex.org/W2972502550","https://openalex.org/W2999006993","https://openalex.org/W3014974815","https://openalex.org/W3019408206","https://openalex.org/W3046771764","https://openalex.org/W3046844007","https://openalex.org/W3093358384","https://openalex.org/W3112701542","https://openalex.org/W4233857083"],"related_works":["https://openalex.org/W2969269896","https://openalex.org/W2615823300","https://openalex.org/W2009321415","https://openalex.org/W1975394131","https://openalex.org/W4387095950","https://openalex.org/W894880941","https://openalex.org/W2950414472","https://openalex.org/W4387096203","https://openalex.org/W2031177229","https://openalex.org/W4387095997"],"abstract_inverted_index":{"BACKGROUND:":[0],"With":[1],"recent":[2],"advances":[3],"in":[4,12,78,234,241,311],"microscopy,":[5],"recordings":[6],"of":[7,47,73,92,99,104,112,114,118,127,152,209,237,265,303,332,343],"cell":[8,279],"behaviour":[9,344],"can":[10,50],"result":[11],"terabyte-size":[13],"datasets.":[14,44,156],"The":[15,45],"lattice":[16],"light":[17],"sheet":[18],"microscope":[19],"(LLSM)":[20],"images":[21],"cells":[22,49],"at":[23,32,130],"high":[24,27,193],"speed":[25],"and":[26,67,109,121,135,170,174,200,222,254,260,289,293,334,338,351],"3D":[28],"resolution,":[29],"accumulating":[30],"data":[31,106],"100":[33],"frames/second":[34],"over":[35,116],"hours,":[36],"presenting":[37],"a":[38,146,159,168,206,213,278,341],"major":[39],"challenge":[40],"for":[41,125,163,198,276,324],"interrogating":[42],"these":[43,105],"surfaces":[46],"vertebrate":[48],"rapidly":[51],"deform":[52],"to":[53,148,186,191,226,246,320],"create":[54],"projections":[55,63,115],"that":[56],"interact":[57],"with":[58,138,195],"the":[59,71,88,228,263,307,318],"microenvironment.":[60],"Such":[61],"surface":[62,72,90,239],"include":[64],"spike-like":[65],"filopodia":[66,352],"wave-like":[68,349],"ruffles":[69,249,337],"on":[70,188,284],"macrophages":[74],"as":[75],"they":[76],"engage":[77],"immune":[79,93],"surveillance.":[80],"LLSM":[81],"imaging":[82],"has":[83],"provided":[84],"new":[85,97],"insights":[86],"into":[87],"complex":[89],"behaviours":[91],"cells,":[94],"including":[95],"revealing":[96],"types":[98],"ruffles.":[100],"However,":[101],"full":[102],"use":[103,158],"requires":[107,133],"systematic":[108,150],"quantitative":[110],"analysis":[111,126,151,236,281,288],"thousands":[113],"hundreds":[117],"time":[119],"steps,":[120],"an":[122,235,271],"effective":[123,272,297],"system":[124,183,316],"individual":[128],"structures":[129],"this":[131],"scale":[132],"efficient":[134],"robust":[136,169],"methods":[137],"minimal":[139],"user":[140],"intervention.":[141],"RESULTS:":[142],"We":[143,157],"present":[144],"LLAMA,":[145],"platform":[147],"enable":[149,296],"terabyte-scale":[153],"4D":[154],"microscopy":[155,280],"machine":[160],"learning":[161],"method":[162],"semantic":[164,285],"segmentation,":[165,286],"followed":[166],"by":[167,251],"configurable":[171],"object":[172,179,287],"separation":[173],"tracking":[175],"algorithm,":[176],"generating":[177],"detailed":[178],"level":[180],"statistics.":[181],"Our":[182,315],"is":[184,205,232,244],"designed":[185],"run":[187],"high-performance":[189],"computing":[190],"achieve":[192],"throughput,":[194],"outputs":[196,295],"suitable":[197],"visualisation":[199,204,224],"statistical":[201,298],"analysis.":[202,314],"Advanced":[203],"key":[207],"element":[208],"LLAMA:":[210],"we":[211],"provide":[212],"specialised":[214],"tool":[215,275],"which":[216,242],"supports":[217],"interactive":[218],"quality":[219],"control,":[220],"optimisation,":[221],"output":[223],"processes":[225],"complement":[227],"processing":[229],"pipeline.":[230],"LLAMA":[231,269,328],"demonstrated":[233],"macrophage":[238,255],"projections,":[240],"it":[243,339],"used":[245],"i)":[247],"discriminate":[248],"induced":[250,336],"lipopolysaccharide":[252],"(LPS)":[253],"colony":[256],"stimulating":[257],"factor":[258],"(CSF-1)":[259],"ii)":[261],"determine":[262],"autonomy":[264],"ruffle":[266],"morphologies.":[267],"CONCLUSIONS:":[268],"provides":[270,317],"open":[273],"source":[274],"running":[277],"pipeline":[282],"based":[283],"tracking.":[290],"Detailed":[291],"numerical":[292],"visual":[294],"analysis,":[299],"identifying":[300],"distinct":[301,330],"patterns":[302],"increased":[304],"activity":[305],"under":[306],"two":[308],"interventions":[309],"considered":[310],"our":[312],"example":[313],"capacity":[319],"screen":[321],"large":[322],"datasets":[323],"specific":[325],"structural":[326],"configurations.":[327],"identified":[329,340],"features":[331],"LPS":[333],"CSF-1":[335],"continuity":[342],"between":[345],"tent":[346],"pole":[347],"ruffling,":[348],"ruffling":[350],"deployment.":[353]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":2}],"updated_date":"2026-08-28T12:50:07.497085","created_date":"2025-10-10T00:00:00"}