{"id":"https://openalex.org/W4389065219","doi":"https://doi.org/10.1109/tmi.2023.3337253","title":"Efficient Supervised Pretraining of Swin-Transformer for Virtual Staining of Microscopy Images","display_name":"Efficient Supervised Pretraining of Swin-Transformer for Virtual Staining of Microscopy Images","publication_year":2023,"publication_date":"2023-11-27","ids":{"openalex":"https://openalex.org/W4389065219","doi":"https://doi.org/10.1109/tmi.2023.3337253","pmid":"https://pubmed.ncbi.nlm.nih.gov/38010933"},"language":"en","primary_location":{"id":"doi:10.1109/tmi.2023.3337253","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tmi.2023.3337253","pdf_url":null,"source":{"id":"https://openalex.org/S58069681","display_name":"IEEE Transactions on Medical Imaging","issn_l":"0278-0062","issn":["0278-0062","1558-254X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Medical Imaging","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5048981603","display_name":"Jiabo Ma","orcid":"https://orcid.org/0000-0001-8532-4466"},"institutions":[{"id":"https://openalex.org/I200769079","display_name":"Hong Kong University of Science and Technology","ror":"https://ror.org/00q4vv597","country_code":"HK","type":"education","lineage":["https://openalex.org/I200769079"]}],"countries":["HK"],"is_corresponding":true,"raw_author_name":"Jiabo Ma","raw_affiliation_strings":["Department of Computer Science and Engineering, The Hong Kong University of Science and Technology, Hong Kong, China"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, The Hong Kong University of Science and Technology, Hong Kong, China","institution_ids":["https://openalex.org/I200769079"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100353596","display_name":"Hao Chen","orcid":"https://orcid.org/0000-0002-8400-3780"},"institutions":[{"id":"https://openalex.org/I200769079","display_name":"Hong Kong University of Science and Technology","ror":"https://ror.org/00q4vv597","country_code":"HK","type":"education","lineage":["https://openalex.org/I200769079"]},{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Hao Chen","raw_affiliation_strings":["Department of Computer Science and Engineering and the Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong, China","Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology and HKUST Shenzhen-Hong Kong Collaborative Innovation Research Institute, Futian, Shenzhen, China","Department of Computer Science and Engineering, The Hong Kong University of Science and Technology, China"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering and the Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong, China","institution_ids":["https://openalex.org/I200769079"]},{"raw_affiliation_string":"Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology and HKUST Shenzhen-Hong Kong Collaborative Innovation Research Institute, Futian, Shenzhen, China","institution_ids":["https://openalex.org/I200769079","https://openalex.org/I889458895"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, The Hong Kong University of Science and Technology, China","institution_ids":["https://openalex.org/I200769079"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5048981603"],"corresponding_institution_ids":["https://openalex.org/I200769079"],"apc_list":null,"apc_paid":null,"fwci":4.9339,"has_fulltext":false,"cited_by_count":14,"citation_normalized_percentile":{"value":0.94806246,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"43","issue":"4","first_page":"1388","last_page":"1399"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9995999932289124,"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":0.9995999932289124,"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/T13114","display_name":"Image Processing Techniques and Applications","score":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/2214","display_name":"Media Technology"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10862","display_name":"AI in cancer detection","score":0.9936000108718872,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/computer-science","display_name":"Computer science","score":0.7583881616592407},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.723763644695282},{"id":"https://openalex.org/keywords/pixel","display_name":"Pixel","score":0.5481881499290466},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.5222547650337219},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.516992449760437},{"id":"https://openalex.org/keywords/grid","display_name":"Grid","score":0.48058462142944336},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4458513855934143},{"id":"https://openalex.org/keywords/computer-vision","display_name":"Computer vision","score":0.3684844970703125},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3215823173522949},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1016029417514801}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7583881616592407},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.723763644695282},{"id":"https://openalex.org/C160633673","wikidata":"https://www.wikidata.org/wiki/Q355198","display_name":"Pixel","level":2,"score":0.5481881499290466},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.5222547650337219},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.516992449760437},{"id":"https://openalex.org/C187691185","wikidata":"https://www.wikidata.org/wiki/Q2020720","display_name":"Grid","level":2,"score":0.48058462142944336},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4458513855934143},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.3684844970703125},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3215823173522949},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1016029417514801},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0}],"mesh":[{"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":"D008853","descriptor_name":"Microscopy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013194","descriptor_name":"Staining and Labeling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013194","descriptor_name":"Staining and Labeling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013194","descriptor_name":"Staining and Labeling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013194","descriptor_name":"Staining and Labeling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1109/tmi.2023.3337253","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tmi.2023.3337253","pdf_url":null,"source":{"id":"https://openalex.org/S58069681","display_name":"IEEE Transactions on Medical Imaging","issn_l":"0278-0062","issn":["0278-0062","1558-254X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Medical Imaging","raw_type":"journal-article"},{"id":"pmid:38010933","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38010933","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":"IEEE transactions on medical imaging","raw_type":null},{"id":"pmh:oai:repository.hkust.edu.hk:1783.1-135152","is_oa":false,"landing_page_url":"http://repository.hkust.edu.hk/ir/Record/1783.1-135152","pdf_url":null,"source":{"id":"https://openalex.org/S4306401796","display_name":"Rare & Special e-Zone (The Hong Kong University of Science and Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I200769079","host_organization_name":"Hong Kong University of Science and Technology","host_organization_lineage":["https://openalex.org/I200769079"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/12","score":0.5199999809265137,"display_name":"Responsible consumption and production"}],"awards":[{"id":"https://openalex.org/G393849449","display_name":null,"funder_award_id":"62202403","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7074549279","display_name":null,"funder_award_id":"PRP/034/22FX","funder_id":"https://openalex.org/F4320324196","funder_display_name":"Innovation and Technology Commission - Hong Kong"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320324196","display_name":"Innovation and Technology Commission - Hong Kong","ror":"https://ror.org/04vf9tr09"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":62,"referenced_works":["https://openalex.org/W1522301498","https://openalex.org/W1583557840","https://openalex.org/W1901129140","https://openalex.org/W1998614190","https://openalex.org/W2108598243","https://openalex.org/W2114223486","https://openalex.org/W2129112648","https://openalex.org/W2140099710","https://openalex.org/W2343160907","https://openalex.org/W2752782242","https://openalex.org/W2797749376","https://openalex.org/W2900178951","https://openalex.org/W2904542956","https://openalex.org/W2909488080","https://openalex.org/W2944379858","https://openalex.org/W2949493305","https://openalex.org/W2951309741","https://openalex.org/W2962793481","https://openalex.org/W2962793691","https://openalex.org/W2963073614","https://openalex.org/W2964299526","https://openalex.org/W3001467249","https://openalex.org/W3002164240","https://openalex.org/W3011648454","https://openalex.org/W3096831136","https://openalex.org/W3098491829","https://openalex.org/W3104250195","https://openalex.org/W3119113183","https://openalex.org/W3122239467","https://openalex.org/W3138516171","https://openalex.org/W3171516518","https://openalex.org/W3198401109","https://openalex.org/W3199416604","https://openalex.org/W3214331391","https://openalex.org/W4206706211","https://openalex.org/W4213019189","https://openalex.org/W4225010001","https://openalex.org/W4225985635","https://openalex.org/W4249336316","https://openalex.org/W4281385110","https://openalex.org/W4281709991","https://openalex.org/W4282967624","https://openalex.org/W4282976788","https://openalex.org/W4288809219","https://openalex.org/W4295312788","https://openalex.org/W4312568229","https://openalex.org/W4312804044","https://openalex.org/W4313156423","https://openalex.org/W4319299929","https://openalex.org/W4319300001","https://openalex.org/W4322707229","https://openalex.org/W4323037718","https://openalex.org/W4385245566","https://openalex.org/W4387831664","https://openalex.org/W6631190155","https://openalex.org/W6758253779","https://openalex.org/W6766978945","https://openalex.org/W6779879114","https://openalex.org/W6784094891","https://openalex.org/W6795892075","https://openalex.org/W6837948907","https://openalex.org/W6838332116"],"related_works":["https://openalex.org/W2378211422","https://openalex.org/W4321353415","https://openalex.org/W2745001401","https://openalex.org/W2130974462","https://openalex.org/W2028665553","https://openalex.org/W2086519370","https://openalex.org/W4246352526","https://openalex.org/W2121910908","https://openalex.org/W915438175","https://openalex.org/W4230315250"],"abstract_inverted_index":{"Fluorescence":[0],"staining":[1,51,148],"is":[2,119],"an":[3,84],"important":[4],"technique":[5],"in":[6,22,63],"life":[7],"science":[8],"for":[9,180],"labeling":[10],"cellular":[11],"constituents.":[12],"However,":[13,53],"it":[14],"also":[15,128],"suffers":[16],"from":[17],"being":[18],"time-consuming,":[19],"having":[20],"difficulty":[21],"simultaneous":[23],"labeling,":[24,35],"etc.":[25],"Thus,":[26],"virtual":[27,50,147],"staining,":[28],"which":[29],"does":[30],"not":[31],"rely":[32],"on":[33,57,70,90,152,172,190],"chemical":[34],"has":[36],"been":[37,47],"introduced.":[38],"Recently,":[39],"deep":[40],"learning":[41],"models":[42],"such":[43],"as":[44],"transformers":[45],"have":[46],"applied":[48],"to":[49,102,134],"tasks.":[52],"their":[54,61],"performance":[55,205],"relies":[56],"large-scale":[58],"pretraining,":[59],"hindering":[60],"development":[62],"the":[64,68,91,109,124,181,195,199,203,220,223],"field.":[65],"To":[66],"reduce":[67,108],"reliance":[69],"large":[71],"amounts":[72],"of":[73,105,111,116,142,183,222],"computation":[74],"and":[75,82,99,107,155,176,194,208,216,229],"data,":[76],"we":[77,96,166],"construct":[78],"a":[79,130,161,168,178],"Swin-transformer":[80],"model":[81],"propose":[83],"efficient":[85],"supervised":[86,131],"pretraining":[87,114,225],"method":[88,118,201],"based":[89,151,171],"masked":[92,143],"autoencoder":[93],"(MAE).":[94],"Specifically,":[95],"adopt":[97],"downsampling":[98],"grid":[100],"sampling":[101],"mask":[103],"75%":[104],"pixels":[106],"number":[110],"tokens.":[112],"The":[113,227],"time":[115],"our":[117],"only":[120],"1/16":[121],"compared":[122],"with":[123,138],"original":[125],"MAE.":[126],"We":[127,186],"design":[129],"proxy":[132],"task":[133],"predict":[135],"stained":[136],"images":[137],"multiple":[139],"styles":[140],"instead":[141],"pixels.":[144],"Additionally,":[145],"most":[146],"approaches":[149],"are":[150,214,231],"private":[153],"datasets":[154,175],"evaluated":[156],"by":[157],"different":[158],"metrics,":[159],"making":[160],"fair":[162],"comparison":[163],"difficult.":[164],"Therefore,":[165],"develop":[167],"standard":[169],"benchmark":[170,192,228],"three":[173,191],"public":[174],"build":[177],"baseline":[179],"convenience":[182],"future":[184],"researchers.":[185],"conduct":[187],"extensive":[188],"experiments":[189],"datasets,":[193],"experimental":[196,217],"results":[197,218],"show":[198],"proposed":[200,224],"achieves":[202],"best":[204],"both":[206],"quantitatively":[207],"qualitatively.":[209],"In":[210],"addition,":[211],"ablation":[212],"studies":[213],"conducted,":[215],"illustrate":[219],"effectiveness":[221],"method.":[226],"code":[230],"available":[232],"at":[233],"https://github.com/birkhoffkiki/CAS-Transformer.":[234]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":2}],"updated_date":"2026-04-15T08:11:43.952461","created_date":"2025-10-10T00:00:00"}