{"id":"https://openalex.org/W7154482421","doi":"https://doi.org/10.48550/arxiv.2604.12075","title":"OpenTME: An Open Dataset of AI-powered H&amp;E Tumor Microenvironment Profiles from TCGA","display_name":"OpenTME: An Open Dataset of AI-powered H&amp;E Tumor Microenvironment Profiles from TCGA","publication_year":2026,"publication_date":"2026-04-13","ids":{"openalex":"https://openalex.org/W7154482421","doi":"https://doi.org/10.48550/arxiv.2604.12075"},"language":null,"primary_location":{"id":"doi:10.48550/arxiv.2604.12075","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2604.12075","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":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},"type":"preprint","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.48550/arxiv.2604.12075","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5133658397","display_name":"Maaike Galama","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Galama, Maaike","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034908163","display_name":"Nina Kozar-Gillan","orcid":"https://orcid.org/0000-0002-3434-7884"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Kozar-Gillan, Nina","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114525080","display_name":"Christina Embacher","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Embacher, Christina","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008503327","display_name":"Todd Dembo","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Dembo, Todd","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051162791","display_name":"Cornelius B\u00f6hm","orcid":"https://orcid.org/0009-0007-3754-4182"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"B\u00f6hm, Cornelius","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028137405","display_name":"Evelyn Ramberger","orcid":"https://orcid.org/0000-0003-2760-2696"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ramberger, Evelyn","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085790556","display_name":"Julika Ribbat\u2010Idel","orcid":"https://orcid.org/0000-0003-1262-6572"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ribbat-Idel, Julika","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008804167","display_name":"Rosemarie Krupar","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Krupar, Rosemarie","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5133697012","display_name":"Verena Aumiller","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Aumiller, Verena","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038944725","display_name":"Miriam H\u00e4gele","orcid":"https://orcid.org/0000-0001-9251-5420"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"H\u00e4gele, Miriam","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019744186","display_name":"Kai Standvoss","orcid":"https://orcid.org/0000-0002-5739-6726"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Standvoss, Kai","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045182761","display_name":"Gerrit Erdmann","orcid":"https://orcid.org/0000-0002-4183-3995"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Erdmann, Gerrit","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072693540","display_name":"Blanca Pablos","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Pablos, Blanca","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5133683931","display_name":"Ari Angelo","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Angelo, Ari","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054151444","display_name":"Simon Schallenberg","orcid":"https://orcid.org/0000-0002-7897-7116"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Schallenberg, Simon","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075917916","display_name":"Andrew P. Norgan","orcid":"https://orcid.org/0000-0002-2955-2066"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Norgan, Andrew","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016310977","display_name":"Viktor Matyas","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Matyas, Viktor","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5133727202","display_name":"Klaus-Robert M\u00fcller","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"M\u00fcller, Klaus-Robert","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5133707270","display_name":"Maximilian Alber","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Alber, Maximilian","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016979661","display_name":"Lukas Ruff","orcid":"https://orcid.org/0000-0002-9707-297X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ruff, Lukas","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5133686831","display_name":"Frederick Klauschen","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Klauschen, Frederick","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":21,"corresponding_author_ids":["https://openalex.org/A5133658397"],"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/T10862","display_name":"AI in cancer detection","score":0.7322999835014343,"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"}},"topics":[{"id":"https://openalex.org/T10862","display_name":"AI in cancer detection","score":0.7322999835014343,"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"}},{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.1096000000834465,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.06459999829530716,"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/tumor-microenvironment","display_name":"Tumor microenvironment","score":0.8019000291824341},{"id":"https://openalex.org/keywords/digital-pathology","display_name":"Digital pathology","score":0.5295000076293945},{"id":"https://openalex.org/keywords/atlas","display_name":"Atlas (anatomy)","score":0.44830000400543213},{"id":"https://openalex.org/keywords/cancer","display_name":"Cancer","score":0.427700012922287},{"id":"https://openalex.org/keywords/biomarker","display_name":"Biomarker","score":0.4090999960899353},{"id":"https://openalex.org/keywords/h-e-stain","display_name":"H&E stain","score":0.40450000762939453},{"id":"https://openalex.org/keywords/lung-cancer","display_name":"Lung cancer","score":0.39010000228881836},{"id":"https://openalex.org/keywords/tumour-heterogeneity","display_name":"Tumour heterogeneity","score":0.38029998540878296}],"concepts":[{"id":"https://openalex.org/C2776107976","wikidata":"https://www.wikidata.org/wiki/Q1786433","display_name":"Tumor microenvironment","level":3,"score":0.8019000291824341},{"id":"https://openalex.org/C2777522853","wikidata":"https://www.wikidata.org/wiki/Q5276128","display_name":"Digital pathology","level":2,"score":0.5295000076293945},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5254999995231628},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.45910000801086426},{"id":"https://openalex.org/C2776673561","wikidata":"https://www.wikidata.org/wiki/Q655357","display_name":"Atlas (anatomy)","level":2,"score":0.44830000400543213},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.427700012922287},{"id":"https://openalex.org/C2781197716","wikidata":"https://www.wikidata.org/wiki/Q864574","display_name":"Biomarker","level":2,"score":0.4090999960899353},{"id":"https://openalex.org/C125473707","wikidata":"https://www.wikidata.org/wiki/Q9914","display_name":"H&E stain","level":3,"score":0.40450000762939453},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.39340001344680786},{"id":"https://openalex.org/C2776256026","wikidata":"https://www.wikidata.org/wiki/Q47912","display_name":"Lung cancer","level":2,"score":0.39010000228881836},{"id":"https://openalex.org/C2777306565","wikidata":"https://www.wikidata.org/wiki/Q15917291","display_name":"Tumour heterogeneity","level":3,"score":0.38029998540878296},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.36899998784065247},{"id":"https://openalex.org/C502942594","wikidata":"https://www.wikidata.org/wiki/Q3421914","display_name":"Cancer research","level":1,"score":0.34040001034736633},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.30570000410079956},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.2955000102519989},{"id":"https://openalex.org/C3017616150","wikidata":"https://www.wikidata.org/wiki/Q1069330","display_name":"Diagnostic biomarker","level":3,"score":0.29280000925064087},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.27880001068115234},{"id":"https://openalex.org/C544855455","wikidata":"https://www.wikidata.org/wiki/Q1070952","display_name":"Histopathology","level":2,"score":0.2777999937534332},{"id":"https://openalex.org/C3020616263","wikidata":"https://www.wikidata.org/wiki/Q1216998","display_name":"Tumor cells","level":2,"score":0.27399998903274536},{"id":"https://openalex.org/C124535831","wikidata":"https://www.wikidata.org/wiki/Q4915074","display_name":"Biomarker discovery","level":4,"score":0.27390000224113464},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.26179999113082886},{"id":"https://openalex.org/C45664433","wikidata":"https://www.wikidata.org/wiki/Q17029420","display_name":"Imaging biomarker","level":3,"score":0.2590999901294708},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.2563999891281128}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.48550/arxiv.2604.12075","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2604.12075","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":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"doi:10.48550/arxiv.2604.12075","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2604.12075","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":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"The":[0,60],"tumor":[1],"microenvironment":[2],"(TME)":[3],"plays":[4],"a":[5,133],"central":[6],"role":[7],"in":[8],"cancer":[9,50],"progression,":[10],"treatment":[11],"response,":[12],"and":[13,19,26,56,93,95,127,141],"patient":[14],"outcomes,":[15],"yet":[16],"large-scale,":[17],"consistent,":[18],"quantitative":[20,102],"TME":[21,40,148],"characterization":[22],"from":[23,43,59],"routine":[24],"hematoxylin":[25],"eosin":[27],"(H&amp;E)-stained":[28],"histopathology":[29],"remains":[30],"scarce.":[31],"We":[32,119],"introduce":[33],"OpenTME,":[34],"an":[35,72],"open-access":[36],"dataset":[37],"of":[38,80,144],"pre-computed":[39],"profiles":[41],"derived":[42],"3,634":[44],"H&amp;E-stained":[45],"whole-slide":[46],"images":[47],"across":[48],"five":[49],"types":[51],"(bladder,":[52],"breast,":[53],"colorectal,":[54],"liver,":[55],"lung":[57],"cancer)":[58],"Cancer":[61],"Genome":[62],"Atlas":[63,70,78],"(TCGA).":[64],"All":[65],"outputs":[66],"were":[67],"generated":[68],"using":[69],"H&amp;E-TME,":[71],"AI-powered":[73],"application":[74],"built":[75],"on":[76,116],"the":[77,142],"family":[79],"pathology":[81],"foundation":[82],"models,":[83],"which":[84],"performs":[85],"tissue":[86,89],"quality":[87],"control,":[88],"segmentation,":[90],"cell":[91],"detection":[92],"classification,":[94],"spatial":[96,138],"neighborhood":[97],"analysis,":[98],"yielding":[99],"over":[100,125],"4,500":[101],"readouts":[103],"per":[104],"slide":[105],"at":[106],"cell-level":[107],"resolution.":[108],"OpenTME":[109,124],"is":[110],"available":[111],"for":[112,135,147],"non-commercial":[113],"academic":[114],"research":[115],"Hugging":[117],"Face.":[118],"will":[120,130],"continue":[121],"to":[122],"expand":[123],"time":[126],"anticipate":[128],"it":[129],"serve":[131],"as":[132],"resource":[134],"biomarker":[136],"discovery,":[137],"biology":[139],"research,":[140],"development":[143],"computational":[145],"methods":[146],"analysis.":[149]},"counts_by_year":[],"updated_date":"2026-05-05T08:41:31.759640","created_date":"2026-04-16T00:00:00"}
