{"id":"https://openalex.org/W7131300418","doi":"https://doi.org/10.1109/tmi.2026.3667612","title":"Masked Image Modeling for Generalizable Organelle Segmentation in Volume EM","display_name":"Masked Image Modeling for Generalizable Organelle Segmentation in Volume EM","publication_year":2026,"publication_date":"2026-02-24","ids":{"openalex":"https://openalex.org/W7131300418","doi":"https://doi.org/10.1109/tmi.2026.3667612","pmid":"https://pubmed.ncbi.nlm.nih.gov/41734129"},"language":"en","primary_location":{"id":"doi:10.1109/tmi.2026.3667612","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tmi.2026.3667612","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/A5126699096","display_name":"Yanchao Zhang","orcid":null},"institutions":[{"id":"https://openalex.org/I4210097554","display_name":"Center for Excellence in Brain Science and Intelligence Technology","ror":"https://ror.org/00vpwhm04","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210097554"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yanchao Zhang","raw_affiliation_strings":["State Key Laboratory of Brain Cognition and Brain-Inspired Intelligence Technology, Institute of Automation, Chinese Academy of Sciences, Beijing, China"],"raw_orcid":"https://orcid.org/0009-0008-9313-5815","affiliations":[{"raw_affiliation_string":"State Key Laboratory of Brain Cognition and Brain-Inspired Intelligence Technology, Institute of Automation, Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210097554"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Hao Zhai","orcid":"https://orcid.org/0000-0003-4149-3131"},"institutions":[{"id":"https://openalex.org/I4210097554","display_name":"Center for Excellence in Brain Science and Intelligence Technology","ror":"https://ror.org/00vpwhm04","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210097554"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hao Zhai","raw_affiliation_strings":["State Key Laboratory of Brain Cognition and Brain-Inspired Intelligence Technology, Institute of Automation, Chinese Academy of Sciences, Beijing, China"],"raw_orcid":"https://orcid.org/0000-0003-4149-3131","affiliations":[{"raw_affiliation_string":"State Key Laboratory of Brain Cognition and Brain-Inspired Intelligence Technology, Institute of Automation, Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210097554"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037260046","display_name":"Jinyue Guo","orcid":null},"institutions":[{"id":"https://openalex.org/I4210097554","display_name":"Center for Excellence in Brain Science and Intelligence Technology","ror":"https://ror.org/00vpwhm04","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210097554"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jinyue Guo","raw_affiliation_strings":["State Key Laboratory of Brain Cognition and Brain-Inspired Intelligence Technology, Institute of Automation, Chinese Academy of Sciences, Beijing, China"],"raw_orcid":"https://orcid.org/0009-0007-4042-8182","affiliations":[{"raw_affiliation_string":"State Key Laboratory of Brain Cognition and Brain-Inspired Intelligence Technology, Institute of Automation, Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210097554"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Zhenchen Li","orcid":"https://orcid.org/0000-0002-5015-3529"},"institutions":[{"id":"https://openalex.org/I4210097554","display_name":"Center for Excellence in Brain Science and Intelligence Technology","ror":"https://ror.org/00vpwhm04","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210097554"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhenchen Li","raw_affiliation_strings":["State Key Laboratory of Brain Cognition and Brain-Inspired Intelligence Technology, Institute of Automation, Chinese Academy of Sciences, Beijing, China"],"raw_orcid":"https://orcid.org/0000-0002-5015-3529","affiliations":[{"raw_affiliation_string":"State Key Laboratory of Brain Cognition and Brain-Inspired Intelligence Technology, Institute of Automation, Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210097554"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5126743244","display_name":"Jing Liu","orcid":null},"institutions":[{"id":"https://openalex.org/I4210097554","display_name":"Center for Excellence in Brain Science and Intelligence Technology","ror":"https://ror.org/00vpwhm04","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210097554"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jing Liu","raw_affiliation_strings":["State Key Laboratory of Brain Cognition and Brain-Inspired Intelligence Technology, Institute of Automation, Chinese Academy of Sciences, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Brain Cognition and Brain-Inspired Intelligence Technology, Institute of Automation, Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210097554"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5103543787","display_name":"Hua Han","orcid":null},"institutions":[{"id":"https://openalex.org/I4210097554","display_name":"Center for Excellence in Brain Science and Intelligence Technology","ror":"https://ror.org/00vpwhm04","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210097554"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hua Han","raw_affiliation_strings":["State Key Laboratory of Brain Cognition and Brain-Inspired Intelligence Technology, Institute of Automation, Chinese Academy of Sciences, Beijing, China"],"raw_orcid":"https://orcid.org/0000-0003-4713-4631","affiliations":[{"raw_affiliation_string":"State Key Laboratory of Brain Cognition and Brain-Inspired Intelligence Technology, Institute of Automation, Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210097554"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I4210097554"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.22938531,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"45","issue":"6","first_page":"3039","last_page":"3052"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10857","display_name":"Advanced Electron Microscopy Techniques and Applications","score":0.6906999945640564,"subfield":{"id":"https://openalex.org/subfields/1315","display_name":"Structural 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"}},"topics":[{"id":"https://openalex.org/T10857","display_name":"Advanced Electron Microscopy Techniques and Applications","score":0.6906999945640564,"subfield":{"id":"https://openalex.org/subfields/1315","display_name":"Structural 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/T12549","display_name":"Image and Object Detection Techniques","score":0.032099999487400055,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10739","display_name":"Electromagnetic Scattering and Analysis","score":0.03060000017285347,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/segmentation","display_name":"Segmentation","score":0.6607000231742859},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.5702999830245972},{"id":"https://openalex.org/keywords/masking","display_name":"Masking (illustration)","score":0.5327000021934509},{"id":"https://openalex.org/keywords/image-segmentation","display_name":"Image segmentation","score":0.4986000061035156},{"id":"https://openalex.org/keywords/redundancy","display_name":"Redundancy (engineering)","score":0.4571000039577484},{"id":"https://openalex.org/keywords/bridging","display_name":"Bridging (networking)","score":0.376800000667572},{"id":"https://openalex.org/keywords/semantics","display_name":"Semantics (computer science)","score":0.3508000075817108},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.34439998865127563},{"id":"https://openalex.org/keywords/neural-coding","display_name":"Neural coding","score":0.3418999910354614}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7268999814987183},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.7009000182151794},{"id":"https://openalex.org/C89600930","wikidata":"https://www.wikidata.org/wiki/Q1423946","display_name":"Segmentation","level":2,"score":0.6607000231742859},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.5702999830245972},{"id":"https://openalex.org/C2777402240","wikidata":"https://www.wikidata.org/wiki/Q6783436","display_name":"Masking (illustration)","level":2,"score":0.5327000021934509},{"id":"https://openalex.org/C124504099","wikidata":"https://www.wikidata.org/wiki/Q56933","display_name":"Image segmentation","level":3,"score":0.4986000061035156},{"id":"https://openalex.org/C152124472","wikidata":"https://www.wikidata.org/wiki/Q1204361","display_name":"Redundancy (engineering)","level":2,"score":0.4571000039577484},{"id":"https://openalex.org/C174348530","wikidata":"https://www.wikidata.org/wiki/Q188635","display_name":"Bridging (networking)","level":2,"score":0.376800000667572},{"id":"https://openalex.org/C184337299","wikidata":"https://www.wikidata.org/wiki/Q1437428","display_name":"Semantics (computer science)","level":2,"score":0.3508000075817108},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.34439998865127563},{"id":"https://openalex.org/C77637269","wikidata":"https://www.wikidata.org/wiki/Q7002051","display_name":"Neural coding","level":2,"score":0.3418999910354614},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.3379000127315521},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.3287999927997589},{"id":"https://openalex.org/C2776436953","wikidata":"https://www.wikidata.org/wiki/Q5163215","display_name":"Consistency (knowledge bases)","level":2,"score":0.3260999917984009},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.3222000002861023},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.3059999942779541},{"id":"https://openalex.org/C136389625","wikidata":"https://www.wikidata.org/wiki/Q334384","display_name":"Supervised learning","level":3,"score":0.2939999997615814},{"id":"https://openalex.org/C188198153","wikidata":"https://www.wikidata.org/wiki/Q1613840","display_name":"Limiting","level":2,"score":0.29249998927116394},{"id":"https://openalex.org/C124066611","wikidata":"https://www.wikidata.org/wiki/Q28684319","display_name":"Sparse approximation","level":2,"score":0.2913999855518341},{"id":"https://openalex.org/C177769412","wikidata":"https://www.wikidata.org/wiki/Q278090","display_name":"Prior probability","level":3,"score":0.28839999437332153},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.28519999980926514},{"id":"https://openalex.org/C173801870","wikidata":"https://www.wikidata.org/wiki/Q201413","display_name":"Heuristic","level":2,"score":0.2822999954223633},{"id":"https://openalex.org/C9417928","wikidata":"https://www.wikidata.org/wiki/Q1070689","display_name":"Image processing","level":3,"score":0.28119999170303345},{"id":"https://openalex.org/C2779304628","wikidata":"https://www.wikidata.org/wiki/Q3503480","display_name":"Face (sociological concept)","level":2,"score":0.2800999879837036},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.2777000069618225},{"id":"https://openalex.org/C141379421","wikidata":"https://www.wikidata.org/wiki/Q6094427","display_name":"Iterative reconstruction","level":2,"score":0.2766999900341034},{"id":"https://openalex.org/C168240541","wikidata":"https://www.wikidata.org/wiki/Q45948","display_name":"Organelle","level":2,"score":0.27639999985694885},{"id":"https://openalex.org/C75294576","wikidata":"https://www.wikidata.org/wiki/Q5165192","display_name":"Contextual image classification","level":3,"score":0.2669000029563904}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000094443","descriptor_name":"Volume Electron Microscopy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000094443","descriptor_name":"Volume Electron Microscopy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D015388","descriptor_name":"Organelles","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":true},{"descriptor_ui":"D015388","descriptor_name":"Organelles","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/tmi.2026.3667612","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tmi.2026.3667612","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:41734129","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41734129","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}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G226769338","display_name":null,"funder_award_id":"5254042","funder_id":"https://openalex.org/F4320334977","funder_display_name":"Beijing Municipal Natural Science Foundation"},{"id":"https://openalex.org/G5001389789","display_name":null,"funder_award_id":"32171461","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320334977","display_name":"Beijing Municipal Natural Science Foundation","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Accurate":[0],"segmentation":[1,41],"of":[2,63,206],"organelles":[3,64],"in":[4,39,54,70],"electron":[5],"microscopy":[6],"(EM)":[7],"volumes":[8,184],"is":[9,108,131,158],"essential":[10],"for":[11,151,160],"understanding":[12],"intracellular":[13],"organization.":[14],"While":[15],"promising,":[16],"deep":[17],"learning-based":[18],"methods":[19],"could":[20,57],"be":[21],"unstable":[22],"and":[23,65,98,185,200,233],"unreliable":[24],"without":[25],"sufficient":[26],"annotations.":[27],"Masked":[28],"image":[29],"modeling":[30],"(MIM),":[31],"a":[32,84,138,226],"powerful":[33],"pretraining":[34,75,210],"technique,":[35],"has":[36],"proven":[37],"effective":[38],"enhancing":[40],"by":[42,110,133,215],"extracting":[43],"meaningful":[44],"representations":[45,101],"from":[46,102,219],"large-scale":[47,170],"unlabeled":[48],"data.":[49,104],"However,":[50],"random":[51],"masking":[52,91,127],"strategies":[53,92],"classic":[55],"MIMs":[56],"overlook":[58],"the":[59,66,175,203,222],"unique":[60],"structural":[61,112],"patterns":[62,150],"spatial":[67],"redundancy":[68],"inherent":[69],"EM":[71,103,179,195],"volumes,":[72],"thus":[73],"limiting":[74],"efficiency.":[76],"To":[77,168],"address":[78],"this":[79],"issue,":[80],"we":[81,172],"propose":[82],"OrgMIM,":[83],"dual-branch":[85],"MIM":[86],"framework":[87],"that":[88,122,146],"integrates":[89],"complementary":[90],"to":[93,118,141],"capture":[94],"critical":[95],"subcellular":[96],"semantics":[97],"learn":[99],"organelle-specific":[100],"Specifically,":[105],"one":[106],"branch":[107],"guided":[109],"static":[111],"priors,":[113],"leveraging":[114],"visual":[115],"foundation":[116],"models":[117],"generate":[119],"affinity":[120],"maps":[121,145],"indicate":[123],"organelle":[124,149],"membranes":[125],"as":[126],"candidates.":[128],"The":[129],"other":[130],"driven":[132],"dynamic":[134],"reconstruction":[135],"feedback,":[136],"using":[137],"self-guidance":[139],"mechanism":[140],"compute":[142],"average":[143],"loss":[144],"highlight":[147],"intricate":[148],"heuristic":[152],"masking.":[153],"Moreover,":[154],"cross-branch":[155],"consistency":[156],"regularization":[157],"introduced":[159],"reliable":[161],"representation":[162],"learning":[163],"across":[164],"sparse":[165],"semantic":[166],"contexts.":[167],"support":[169],"pretraining,":[171],"construct":[173],"IsoOrg-1K,":[174],"first":[176],"organelle-centric":[177],"3D":[178],"dataset,":[180],"comprising":[181],"928":[182],"informative":[183],"over":[186,217],"120":[187],"billion":[188],"voxels.":[189],"Extensive":[190],"evaluations":[191],"on":[192,211,221],"three":[193],"public":[194],"datasets":[196],"with":[197,225],"varied":[198],"resolutions":[199],"appearances":[201],"validate":[202],"superior":[204],"performance":[205],"OrgMIM.":[207],"Notably,":[208],"OrgMIM":[209],"IsoOrg-1K":[212],"boosts":[213],"mIoU":[214],"28.78%":[216],"training":[218],"scratch":[220],"CMCC":[223],"dataset":[224],"Transformer-based":[227],"model.":[228],"All":[229],"datasets,":[230],"source":[231],"codes,":[232],"pretrained":[234],"weights":[235],"are":[236],"available":[237],"at":[238],"https://github.com/yanchaoz/OrgMIM.":[239]},"counts_by_year":[],"updated_date":"2026-06-26T08:34:08.712188","created_date":"2026-02-25T00:00:00"}
