{"id":"https://openalex.org/W7162086517","doi":"https://doi.org/10.1093/bioinformatics/btag327","title":"CryoPromptSeg: prompt-guided segmentation with integrated denoising for cryo-EM particle picking","display_name":"CryoPromptSeg: prompt-guided segmentation with integrated denoising for cryo-EM particle picking","publication_year":2026,"publication_date":"2026-05-20","ids":{"openalex":"https://openalex.org/W7162086517","doi":"https://doi.org/10.1093/bioinformatics/btag327","pmid":"https://pubmed.ncbi.nlm.nih.gov/42172598"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btag327","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag327","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bioinformatics/btag327","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5136729819","display_name":"Bin Yang","orcid":null},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]},{"id":"https://openalex.org/I24201400","display_name":"Chengdu University of Information Technology","ror":"https://ror.org/01yxwrh59","country_code":"CN","type":"education","lineage":["https://openalex.org/I24201400"]},{"id":"https://openalex.org/I4210125143","display_name":"Chengdu University","ror":"https://ror.org/034z67559","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210125143"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bin Yang","raw_affiliation_strings":["College of Computer Science, Sichuan University , Chengdu, 610065,"],"raw_orcid":"https://orcid.org/0009-0000-7994-3367","affiliations":[{"raw_affiliation_string":"College of Computer Science, Sichuan University , Chengdu, 610065,","institution_ids":["https://openalex.org/I4210125143","https://openalex.org/I24185976","https://openalex.org/I24201400"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5136778085","display_name":"Yujie You","orcid":null},"institutions":[{"id":"https://openalex.org/I4210131342","display_name":"Yibin University","ror":"https://ror.org/03w8m2977","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210131342"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yujie You","raw_affiliation_strings":["School of Computer Science and Engineering, Sichuan University of Science and Engineering , Yibin, 644000,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Sichuan University of Science and Engineering , Yibin, 644000,","institution_ids":["https://openalex.org/I4210131342"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5136794356","display_name":"Liang Jin","orcid":null},"institutions":[{"id":"https://openalex.org/I4210107668","display_name":"Guangzhou Regenerative Medicine and Health Guangdong Laboratory","ror":"https://ror.org/01n179w26","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210107668"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Liang Jin","raw_affiliation_strings":["Bioland Laboratory (Former Guangzhou Regenerative Medicine and Health-Guangdong Laboratory) , Guangzhou, 510005,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioland Laboratory (Former Guangzhou Regenerative Medicine and Health-Guangdong Laboratory) , Guangzhou, 510005,","institution_ids":["https://openalex.org/I4210107668"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102872803","display_name":"Hongyang Yu","orcid":"https://orcid.org/0000-0002-5608-5010"},"institutions":[{"id":"https://openalex.org/I4210107668","display_name":"Guangzhou Regenerative Medicine and Health Guangdong Laboratory","ror":"https://ror.org/01n179w26","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210107668"]},{"id":"https://openalex.org/I4210114178","display_name":"Suzhou Vocational Institute of Industrial Technology","ror":"https://ror.org/027rn2111","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210114178"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"HongYang Yu","raw_affiliation_strings":["Bioland Laboratory (Former Guangzhou Regenerative Medicine and Health-Guangdong Laboratory) , Guangzhou, 510005,","SIP-UCLA Institute for Technology Advancement , Suzhou, 215123,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioland Laboratory (Former Guangzhou Regenerative Medicine and Health-Guangdong Laboratory) , Guangzhou, 510005,","institution_ids":["https://openalex.org/I4210107668"]},{"raw_affiliation_string":"SIP-UCLA Institute for Technology Advancement , Suzhou, 215123,","institution_ids":["https://openalex.org/I4210114178"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100425653","display_name":"Li Zhang","orcid":"https://orcid.org/0000-0002-8565-6513"},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]},{"id":"https://openalex.org/I24201400","display_name":"Chengdu University of Information Technology","ror":"https://ror.org/01yxwrh59","country_code":"CN","type":"education","lineage":["https://openalex.org/I24201400"]},{"id":"https://openalex.org/I4210125143","display_name":"Chengdu University","ror":"https://ror.org/034z67559","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210125143"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Le Zhang","raw_affiliation_strings":["College of Computer Science, Sichuan University , Chengdu, 610065,"],"raw_orcid":"https://orcid.org/0000-0002-3708-1727","affiliations":[{"raw_affiliation_string":"College of Computer Science, Sichuan University , Chengdu, 610065,","institution_ids":["https://openalex.org/I4210125143","https://openalex.org/I24185976","https://openalex.org/I24201400"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5100425653","https://openalex.org/A5102872803"],"corresponding_institution_ids":["https://openalex.org/I24185976","https://openalex.org/I24201400","https://openalex.org/I4210107668","https://openalex.org/I4210114178","https://openalex.org/I4210125143"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.62349914,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"42","issue":"6","first_page":null,"last_page":null},"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":0.9491999745368958,"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":0.9491999745368958,"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/T10923","display_name":"Force Microscopy Techniques and Applications","score":0.004399999976158142,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.002899999963119626,"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/segmentation","display_name":"Segmentation","score":0.7081000208854675},{"id":"https://openalex.org/keywords/automation","display_name":"Automation","score":0.5641999840736389},{"id":"https://openalex.org/keywords/noise","display_name":"Noise (video)","score":0.5414999723434448},{"id":"https://openalex.org/keywords/particle-filter","display_name":"Particle filter","score":0.5242000222206116},{"id":"https://openalex.org/keywords/noise-reduction","display_name":"Noise reduction","score":0.5231999754905701},{"id":"https://openalex.org/keywords/particle","display_name":"Particle (ecology)","score":0.5076000094413757},{"id":"https://openalex.org/keywords/image-segmentation","display_name":"Image segmentation","score":0.415800005197525},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.38420000672340393}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7210000157356262},{"id":"https://openalex.org/C89600930","wikidata":"https://www.wikidata.org/wiki/Q1423946","display_name":"Segmentation","level":2,"score":0.7081000208854675},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6022999882698059},{"id":"https://openalex.org/C115901376","wikidata":"https://www.wikidata.org/wiki/Q184199","display_name":"Automation","level":2,"score":0.5641999840736389},{"id":"https://openalex.org/C99498987","wikidata":"https://www.wikidata.org/wiki/Q2210247","display_name":"Noise (video)","level":3,"score":0.5414999723434448},{"id":"https://openalex.org/C52421305","wikidata":"https://www.wikidata.org/wiki/Q1151499","display_name":"Particle filter","level":3,"score":0.5242000222206116},{"id":"https://openalex.org/C163294075","wikidata":"https://www.wikidata.org/wiki/Q581861","display_name":"Noise reduction","level":2,"score":0.5231999754905701},{"id":"https://openalex.org/C2778517922","wikidata":"https://www.wikidata.org/wiki/Q7140482","display_name":"Particle (ecology)","level":2,"score":0.5076000094413757},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.48170000314712524},{"id":"https://openalex.org/C124504099","wikidata":"https://www.wikidata.org/wiki/Q56933","display_name":"Image segmentation","level":3,"score":0.415800005197525},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.38420000672340393},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.3749000132083893},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3587999939918518},{"id":"https://openalex.org/C2780992000","wikidata":"https://www.wikidata.org/wiki/Q17016113","display_name":"Generator (circuit theory)","level":3,"score":0.3587000072002411},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.3427000045776367},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.28859999775886536},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.28630000352859497},{"id":"https://openalex.org/C3019060180","wikidata":"https://www.wikidata.org/wiki/Q184199","display_name":"Automated method","level":2,"score":0.2687000036239624},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.2632000148296356},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.26010000705718994},{"id":"https://openalex.org/C9417928","wikidata":"https://www.wikidata.org/wiki/Q1070689","display_name":"Image processing","level":3,"score":0.25540000200271606},{"id":"https://openalex.org/C65885262","wikidata":"https://www.wikidata.org/wiki/Q7429708","display_name":"Scale-space segmentation","level":4,"score":0.25450000166893005},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.2506999969482422}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020285","descriptor_name":"Cryoelectron Microscopy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059629","descriptor_name":"Signal-To-Noise Ratio","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btag327","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag327","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:42172598","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42172598","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:13241001","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13241001/","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btag327","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag327","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1705471998","display_name":null,"funder_award_id":"2024YFF0727300","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G2813597990","display_name":null,"funder_award_id":"62372316","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/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":23,"referenced_works":["https://openalex.org/W2001923477","https://openalex.org/W2008490358","https://openalex.org/W2013867005","https://openalex.org/W2047902460","https://openalex.org/W2104234755","https://openalex.org/W2299689158","https://openalex.org/W2587625522","https://openalex.org/W2793402357","https://openalex.org/W2952729952","https://openalex.org/W2963568497","https://openalex.org/W2977933365","https://openalex.org/W3093295276","https://openalex.org/W3093585353","https://openalex.org/W3127564879","https://openalex.org/W3131342469","https://openalex.org/W4292567336","https://openalex.org/W4381686770","https://openalex.org/W4392157400","https://openalex.org/W4399512708","https://openalex.org/W4405022378","https://openalex.org/W4406467464","https://openalex.org/W4406893733","https://openalex.org/W4411750178"],"related_works":[],"abstract_inverted_index":{"MOTIVATION:":[0],"Cryo-electron":[1],"microscopy":[2],"(Cryo-EM)":[3],"single":[4],"particle":[5,37,50,69,102,106,121,173,190,207,220,236],"analysis":[6],"(SPA)":[7],"is":[8,39],"a":[9,29,52,125,159,201,229],"key":[10],"technique":[11],"for":[12,43,120,206,232],"revealing":[13],"the":[14,26,44,57,143,166,169,177,181,194,233],"structure":[15],"of":[16,28,32,46,136,152,235],"biomacromolecules":[17],"by":[18,131,142],"three-dimensional":[19],"reconstruction.":[20],"Achieving":[21],"high-resolution":[22],"reconstruction":[23],"relies":[24],"on":[25],"acquisition":[27],"large":[30],"number":[31],"authentic":[33],"particles;":[34],"however,":[35],"manual":[36],"picking":[38,51,122,221],"inefficient":[40],"and":[41,104,138,168,223,241],"inadequate":[42],"demands":[45],"reconstruction,":[47],"making":[48],"automated":[49,68],"major":[53],"research":[54],"focus.":[55],"Although":[56],"foundational":[58],"segmentation":[59,72,151],"model":[60],"Segment":[61],"Anything":[62],"Model":[63],"(SAM)":[64],"has":[65],"recently":[66],"advanced":[67],"picking,":[70],"its":[71],"advantages":[73],"have":[74,86],"not":[75],"been":[76],"fully":[77],"realized":[78],"in":[79,218],"cryo-EM":[80,83,153],"applications.":[81],"Moreover,":[82],"images":[84],"often":[85],"significant":[87],"noise.":[88],"Conventional":[89],"denoising":[90,225],"decreases":[91],"noise":[92,185],"but":[93],"frequently":[94],"overlooks":[95],"high-level":[96],"semantic":[97,174],"information,":[98],"leading":[99],"to":[100,163,183,196],"oversmoothed":[101],"regions":[103],"reduced":[105],"distinguishability.":[107],"RESULTS:":[108],"To":[109,192],"address":[110],"these":[111],"challenges,":[112],"we":[113,199],"propose":[114],"CryoPromptSeg,":[115],"which":[116],"employs":[117,158],"prompt-guided":[118],"SAM":[119,137],"while":[123,186],"integrating":[124],"semantically":[126],"enhanced":[127],"image":[128,224],"denoiser.":[129],"Specifically,":[130],"performing":[132],"domain":[133],"adaptation":[134],"fine-tuning":[135],"incorporating":[139,172],"prompts":[140],"generated":[141],"proposed":[144],"automatic":[145],"prompt":[146,170,178],"generator,":[147,171],"it":[148,157],"achieves":[149],"precise":[150],"particles.":[154],"In":[155],"addition,":[156],"parallel":[160],"multi-task":[161],"framework":[162],"jointly":[164],"train":[165],"denoiser":[167,182],"information":[175],"from":[176],"generator":[179],"into":[180],"suppress":[184],"preserving":[187],"highly":[188],"distinguishable":[189],"structures.":[191],"lower":[193],"barrier":[195],"practical":[197],"application,":[198],"developed":[200],"user-friendly":[202],"online":[203],"prediction":[204],"platform":[205,242],"picking.":[208,237],"Experimental":[209],"results":[210],"demonstrate":[211],"that":[212],"CryoPromptSeg":[213],"outperforms":[214],"existing":[215],"mainstream":[216],"methods":[217],"both":[219],"accuracy":[222],"quality,":[226],"thus":[227],"providing":[228],"novel":[230],"solution":[231],"automation":[234],"AVAILABILITY:":[238],"The":[239],"code":[240],"are":[243],"available":[244],"at:":[245],"https://github.com/347251369/CryoPromptSeg.":[246]},"counts_by_year":[],"updated_date":"2026-06-18T08:10:14.011955","created_date":"2026-05-23T00:00:00"}