{"id":"https://openalex.org/W7160930307","doi":"https://doi.org/10.48550/arxiv.2605.08566","title":"MicroDiffuse3D: A Foundation Model for 3D Microscopy Imaging Restoration","display_name":"MicroDiffuse3D: A Foundation Model for 3D Microscopy Imaging Restoration","publication_year":2026,"publication_date":"2026-05-08","ids":{"openalex":"https://openalex.org/W7160930307","doi":"https://doi.org/10.48550/arxiv.2605.08566"},"language":"en","primary_location":{"id":"pmh:oai:pubmedcentral.nih.gov:13178444","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13178444/","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":"ArXiv","raw_type":"Text"},"type":"preprint","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13178444/","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100727702","display_name":"Yongkang Li","orcid":"https://orcid.org/0000-0002-3816-7071"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Li, Yongkang","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135981424","display_name":"Brian Wong","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wong, Brian","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135949962","display_name":"King Wai Chiu","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Chiu, King Wai","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042446084","display_name":"Hanwen Xu","orcid":"https://orcid.org/0000-0001-7797-5971"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Xu, Hanwen","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135983263","display_name":"Tangqi Fang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Fang, Tangqi","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135994512","display_name":"Erin Dunnington","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Dunnington, Erin","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5136000903","display_name":"Dan Fu","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Fu, Dan","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5135910724","display_name":"Sheng Wang","orcid":"https://orcid.org/0000-0002-3195-1701"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wang, Sheng","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"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/T10540","display_name":"Advanced Fluorescence Microscopy Techniques","score":0.7967000007629395,"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":0.7967000007629395,"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/T11897","display_name":"Digital Holography and Microscopy","score":0.05559999868273735,"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/T11996","display_name":"Random lasers and scattering media","score":0.0421999990940094,"subfield":{"id":"https://openalex.org/subfields/3102","display_name":"Acoustics and Ultrasonics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.5809000134468079},{"id":"https://openalex.org/keywords/segmentation","display_name":"Segmentation","score":0.5024999976158142},{"id":"https://openalex.org/keywords/microscopy","display_name":"Microscopy","score":0.4668000042438507},{"id":"https://openalex.org/keywords/image-restoration","display_name":"Image restoration","score":0.4088999927043915},{"id":"https://openalex.org/keywords/3d-model","display_name":"3d model","score":0.3693999946117401},{"id":"https://openalex.org/keywords/3d-reconstruction","display_name":"3D reconstruction","score":0.3472000062465668},{"id":"https://openalex.org/keywords/foundation","display_name":"Foundation (evidence)","score":0.3416000008583069},{"id":"https://openalex.org/keywords/iterative-reconstruction","display_name":"Iterative reconstruction","score":0.337799996137619},{"id":"https://openalex.org/keywords/image-quality","display_name":"Image quality","score":0.3377000093460083}],"concepts":[{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.5809000134468079},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5383999943733215},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.5332000255584717},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5170999765396118},{"id":"https://openalex.org/C89600930","wikidata":"https://www.wikidata.org/wiki/Q1423946","display_name":"Segmentation","level":2,"score":0.5024999976158142},{"id":"https://openalex.org/C147080431","wikidata":"https://www.wikidata.org/wiki/Q1074953","display_name":"Microscopy","level":2,"score":0.4668000042438507},{"id":"https://openalex.org/C106430172","wikidata":"https://www.wikidata.org/wiki/Q6002272","display_name":"Image restoration","level":4,"score":0.4088999927043915},{"id":"https://openalex.org/C3019007443","wikidata":"https://www.wikidata.org/wiki/Q568742","display_name":"3d model","level":2,"score":0.3693999946117401},{"id":"https://openalex.org/C109950114","wikidata":"https://www.wikidata.org/wiki/Q4464732","display_name":"3D reconstruction","level":2,"score":0.3472000062465668},{"id":"https://openalex.org/C2780966255","wikidata":"https://www.wikidata.org/wiki/Q5474306","display_name":"Foundation (evidence)","level":2,"score":0.3416000008583069},{"id":"https://openalex.org/C141379421","wikidata":"https://www.wikidata.org/wiki/Q6094427","display_name":"Iterative reconstruction","level":2,"score":0.337799996137619},{"id":"https://openalex.org/C55020928","wikidata":"https://www.wikidata.org/wiki/Q3813865","display_name":"Image quality","level":3,"score":0.3377000093460083},{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.3321000039577484},{"id":"https://openalex.org/C138268822","wikidata":"https://www.wikidata.org/wiki/Q1051925","display_name":"Resolution (logic)","level":2,"score":0.3172000050544739},{"id":"https://openalex.org/C124504099","wikidata":"https://www.wikidata.org/wiki/Q56933","display_name":"Image segmentation","level":3,"score":0.31610000133514404},{"id":"https://openalex.org/C99498987","wikidata":"https://www.wikidata.org/wiki/Q2210247","display_name":"Noise (video)","level":3,"score":0.31150001287460327},{"id":"https://openalex.org/C9417928","wikidata":"https://www.wikidata.org/wiki/Q1070689","display_name":"Image processing","level":3,"score":0.3073999881744385},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.28610000014305115},{"id":"https://openalex.org/C165998758","wikidata":"https://www.wikidata.org/wiki/Q1038886","display_name":"Imaging technology","level":2,"score":0.28610000014305115},{"id":"https://openalex.org/C115051666","wikidata":"https://www.wikidata.org/wiki/Q6522493","display_name":"Ranging","level":2,"score":0.2840999960899353},{"id":"https://openalex.org/C163294075","wikidata":"https://www.wikidata.org/wiki/Q581861","display_name":"Noise reduction","level":2,"score":0.28130000829696655},{"id":"https://openalex.org/C18555067","wikidata":"https://www.wikidata.org/wiki/Q8375051","display_name":"Joint (building)","level":2,"score":0.2793999910354614},{"id":"https://openalex.org/C3020199158","wikidata":"https://www.wikidata.org/wiki/Q210521","display_name":"High resolution","level":2,"score":0.27469998598098755},{"id":"https://openalex.org/C119666444","wikidata":"https://www.wikidata.org/wiki/Q5977280","display_name":"Temporal resolution","level":2,"score":0.26010000705718994},{"id":"https://openalex.org/C205372480","wikidata":"https://www.wikidata.org/wiki/Q210521","display_name":"Image resolution","level":2,"score":0.2558000087738037},{"id":"https://openalex.org/C172367668","wikidata":"https://www.wikidata.org/wiki/Q6504956","display_name":"Data visualization","level":3,"score":0.2554999887943268},{"id":"https://openalex.org/C160920958","wikidata":"https://www.wikidata.org/wiki/Q7662746","display_name":"Synthetic data","level":2,"score":0.25529998540878296},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.25429999828338623},{"id":"https://openalex.org/C61797465","wikidata":"https://www.wikidata.org/wiki/Q1188986","display_name":"Term (time)","level":2,"score":0.2533000111579895}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:pubmedcentral.nih.gov:13178444","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13178444/","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":"ArXiv","raw_type":"Text"},{"id":"doi:10.48550/arxiv.2605.08566","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2605.08566","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:13178444","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13178444/","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":"ArXiv","raw_type":"Text"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Chemical":[0],"imaging":[1],"enables":[2],"label-free":[3],"visualization":[4],"of":[5],"cells,":[6],"tissues":[7],"and":[8,96,98,132,138,159,171],"living":[9],"systems":[10],"while":[11],"providing":[12],"direct":[13],"biochemical":[14],"information":[15],"that":[16,63,173],"is":[17],"difficult":[18,176],"to":[19,34,177],"obtain":[20],"with":[21,129],"conventional":[22],"fluorescence":[23],"microscopy.":[24],"Despite":[25],"its":[26,37],"promise":[27],"in":[28,94,101,162],"applications":[29],"ranging":[30],"from":[31,68],"intraoperative":[32],"diagnosis":[33],"drug-response":[35],"analysis,":[36],"broader":[38],"use":[39],"remains":[40],"limited":[41],"by":[42,136,141],"slow":[43],"data":[44],"acquisition,":[45],"particularly":[46],"for":[47,58,155],"three-dimensional":[48],"imaging.":[49],"Here":[50],"we":[51],"present":[52],"MicroDiffuse3D,":[53],"a":[54,151],"pretrained":[55,147],"foundation":[56],"model":[57,110],"3D":[59,86,99,120,148],"microscopy":[60],"image":[61],"restoration":[62,83,149],"recovers":[64],"high-quality":[65],"volumetric":[66,90,163],"structure":[67],"degraded":[69],"low-resolution":[70],"measurements":[71],"acquired":[72],"at":[73,169],"substantially":[74],"higher":[75],"throughput.":[76],"We":[77],"evaluated":[78],"MicroDiffuse3D":[79,123],"across":[80,127],"three":[81],"challenging":[82],"settings,":[84],"including":[85],"super-resolution":[87,121],"under":[88],"16-fold":[89],"sparsity,":[91],"joint":[92],"degradation":[93],"resolution":[95],"noise,":[97],"denoising":[100],"the":[102,109,118,157],"low":[103],"signal-to-noise":[104],"ratio":[105],"(SNR)":[106],"regime,":[107],"where":[108],"delivered":[111],"clear":[112],"gains":[113],"over":[114],"strong":[115],"baselines.":[116],"Under":[117],"sparse":[119],"setting,":[122],"produced":[124],"clearer":[125],"continuity":[126],"depth":[128],"fewer":[130],"artifacts":[131],"improved":[133],"segmentation":[134],"quality":[135],"10.58%":[137],"line-profile":[139],"concordance":[140],"15.59%.":[142],"Together,":[143],"our":[144],"results":[145],"establish":[146],"as":[150],"broadly":[152],"applicable":[153],"strategy":[154],"overcoming":[156],"throughput":[158],"SNR":[160],"limitations":[161],"chemical":[164],"imaging,":[165],"enabling":[166],"high-resolution":[167],"analysis":[168],"scales":[170],"speeds":[172],"were":[174],"previously":[175],"achieve.":[178]},"counts_by_year":[],"updated_date":"2026-07-01T06:00:48.157686","created_date":"2026-05-13T00:00:00"}
