{"id":"https://openalex.org/W7164405006","doi":"https://doi.org/10.48550/arxiv.2606.12346","title":"Atlas H&amp;E-TME: Scalable AI-Based Tissue Profiling at Expert Pathologist-Level Accuracy","display_name":"Atlas H&amp;E-TME: Scalable AI-Based Tissue Profiling at Expert Pathologist-Level Accuracy","publication_year":2026,"publication_date":"2026-06-10","ids":{"openalex":"https://openalex.org/W7164405006","doi":"https://doi.org/10.48550/arxiv.2606.12346"},"language":null,"primary_location":{"id":"doi:10.48550/arxiv.2606.12346","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2606.12346","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"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":"Preprint"},"type":"preprint","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.48550/arxiv.2606.12346","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","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/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/A5138397486","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/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/A5084604245","display_name":"Jennifer Altsch\u00fcler","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Altsch\u00fcler, Jennifer","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/A5062268913","display_name":"Hans Pinckaers","orcid":"https://orcid.org/0000-0002-7570-9300"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Pinckaers, Hans","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/A5138407186","display_name":"Madleen Drinkwitz","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Drinkwitz, Madleen","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5138446924","display_name":"\u00c1d\u00e1m N\u00e1rai","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"N\u00e1rai, \u00c1d\u00e1m","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5122072244","display_name":"Alexander M\u00f6llers","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"M\u00f6llers, Alexander","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063085331","display_name":"Katja Lingelbach","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Lingelbach, Katja","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5138435396","display_name":"Sebastian Kons","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Kons, Sebastian","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012485692","display_name":"Luk\u00e1\u0161 H\u00f6nig","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"H\u00f6nig, Lukas","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5138413356","display_name":"Recepcan Adig\u00fczel","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Adig\u00fczel, Recepcan","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5138448831","display_name":"Joana Bai\u00e3o","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Bai\u00e3o, Joana","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5132876186","display_name":"Alberto Megina Gonzalo","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Gonzalo, Alberto Megina","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5138433932","display_name":"Marius Teodorescu","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Teodorescu, Marius","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014189154","display_name":"Marie\u2010Lisa Eich","orcid":"https://orcid.org/0000-0002-8601-4598"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Eich, Marie-Lisa","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5138462088","display_name":"Paolo Chetta","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Chetta, Paolo","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5138466335","display_name":"Shakil Merchant","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Merchant, Shakil","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/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/A5136912016","display_name":"Andrew Norgan","orcid":null},"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/A5138413020","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/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":"middle","author":{"id":"https://openalex.org/A5138413500","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":"last","author":{"id":"https://openalex.org/A5138399301","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":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/T10862","display_name":"AI in cancer detection","score":0.9836999773979187,"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":0.9836999773979187,"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":0.007499999832361937,"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/T12874","display_name":"Digital Imaging for Blood Diseases","score":0.002899999963119626,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/atlas","display_name":"Atlas (anatomy)","score":0.7986999750137329},{"id":"https://openalex.org/keywords/digital-pathology","display_name":"Digital pathology","score":0.4957999885082245},{"id":"https://openalex.org/keywords/ground-truth","display_name":"Ground truth","score":0.476500004529953},{"id":"https://openalex.org/keywords/ambiguity","display_name":"Ambiguity","score":0.42480000853538513},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.375900000333786},{"id":"https://openalex.org/keywords/modalities","display_name":"Modalities","score":0.357699990272522},{"id":"https://openalex.org/keywords/human-disease","display_name":"Human disease","score":0.3546000123023987},{"id":"https://openalex.org/keywords/profiling","display_name":"Profiling (computer programming)","score":0.3465999960899353}],"concepts":[{"id":"https://openalex.org/C2776673561","wikidata":"https://www.wikidata.org/wiki/Q655357","display_name":"Atlas (anatomy)","level":2,"score":0.7986999750137329},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6815000176429749},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5315999984741211},{"id":"https://openalex.org/C2777522853","wikidata":"https://www.wikidata.org/wiki/Q5276128","display_name":"Digital pathology","level":2,"score":0.4957999885082245},{"id":"https://openalex.org/C146849305","wikidata":"https://www.wikidata.org/wiki/Q370766","display_name":"Ground truth","level":2,"score":0.476500004529953},{"id":"https://openalex.org/C2780522230","wikidata":"https://www.wikidata.org/wiki/Q1140419","display_name":"Ambiguity","level":2,"score":0.42480000853538513},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.375900000333786},{"id":"https://openalex.org/C2779903281","wikidata":"https://www.wikidata.org/wiki/Q6888026","display_name":"Modalities","level":2,"score":0.357699990272522},{"id":"https://openalex.org/C2988867146","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Human disease","level":3,"score":0.3546000123023987},{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.3465999960899353},{"id":"https://openalex.org/C188087704","wikidata":"https://www.wikidata.org/wiki/Q369577","display_name":"Standardization","level":2,"score":0.32989999651908875},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.3294999897480011},{"id":"https://openalex.org/C19527891","wikidata":"https://www.wikidata.org/wiki/Q1120908","display_name":"Medical physics","level":1,"score":0.31929999589920044},{"id":"https://openalex.org/C89600930","wikidata":"https://www.wikidata.org/wiki/Q1423946","display_name":"Segmentation","level":2,"score":0.3003000020980835},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2994999885559082},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.2939999997615814},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.2935999929904938},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.2874999940395355},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.27379998564720154},{"id":"https://openalex.org/C158163496","wikidata":"https://www.wikidata.org/wiki/Q5937310","display_name":"Human Protein Atlas","level":4,"score":0.26989999413490295},{"id":"https://openalex.org/C138958017","wikidata":"https://www.wikidata.org/wiki/Q190087","display_name":"Data type","level":2,"score":0.2694999873638153},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.2685999870300293},{"id":"https://openalex.org/C58489278","wikidata":"https://www.wikidata.org/wiki/Q1172284","display_name":"Data set","level":2,"score":0.26260000467300415},{"id":"https://openalex.org/C2780385302","wikidata":"https://www.wikidata.org/wiki/Q367158","display_name":"Protocol (science)","level":3,"score":0.251800000667572}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.48550/arxiv.2606.12346","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2606.12346","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"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":"Preprint"}],"best_oa_location":{"id":"doi:10.48550/arxiv.2606.12346","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2606.12346","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"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":"Preprint"},"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":{"Hematoxylin":[0],"and":[1,48,82,111,144,170,190,207,210,216,244,259],"eosin":[2],"(H&amp;E)":[3],"staining":[4],"is":[5,73],"the":[6,35,83,196,225,229,242,251],"cornerstone":[7],"of":[8,14,38,86,180,254],"histopathology,":[9],"yet":[10],"scalable,":[11,238],"quantitative":[12,59,239],"analysis":[13],"H&amp;E":[15,148,226],"whole-slide":[16],"images":[17],"(WSIs)":[18],"remains":[19],"a":[20,101,134,237,248],"central":[21],"challenge":[22,68],"in":[23,233,257],"computational":[24],"pathology.":[25],"We":[26,97],"present":[27],"Atlas":[28,36,142,154,199,222],"H&amp;E-TME,":[29],"an":[30,118],"AI-based":[31],"system":[32],"built":[33],"on":[34,91,156],"family":[37],"pathology":[39,234],"foundation":[40,249],"models":[41],"that":[42,123],"predicts":[43],"tissue":[44,46],"quality,":[45],"region,":[47],"cell":[49],"type":[50],"labels":[51],"across":[52,163,212],"multiple":[53],"cancer":[54,168,184],"types,":[55],"yielding":[56],"over":[57,128,157],"4,500":[58],"readouts":[60],"per":[61,183],"slide":[62,227],"at":[63],"cell-level":[64],"resolution.":[65],"A":[66],"key":[67],"to":[69,78],"validating":[70],"such":[71,93],"systems":[72],"overcoming":[74],"morphological":[75,112,215],"ambiguity":[76],"inherent":[77],"H&amp;E-only":[79,130,160,205],"ground":[80],"truth":[81],"limited":[84],"scalability":[85],"more":[87],"informed":[88],"references":[89],"drawing":[90],"modalities":[92],"as":[94],"immunohistochemistry":[95],"(IHC).":[96],"address":[98],"this":[99,213],"with":[100,109,176],"dual":[102],"validation":[103],"framework":[104],"combining":[105],"biologically":[106],"grounded":[107,136],"depth":[108],"technical":[110,217],"breadth.":[113],"For":[114,150],"depth,":[115],"we":[116,140,152],"propose":[117],"IHC-informed":[119,197],"multi-pathologist":[120],"consensus":[121],"protocol":[122],"substantially":[124],"improves":[125],"inter-rater":[126],"agreement":[127],"conventional":[129],"annotation.":[131],"This":[132],"yields":[133],"molecularly":[135],"reference":[137],"against":[138,195],"which":[139],"compare":[141],"H&amp;E-TME":[143,155,200,223],"pathologists":[145],"working":[146],"from":[147,187],"alone.":[149],"breadth,":[151],"benchmark":[153],"200,000":[158],"high-confidence":[159],"pathologist":[161,204],"annotations":[162],"1,500+":[164],"cases":[165,182],"spanning":[166],"eight":[167],"types":[169],"their":[171],"most":[172,230],"common":[173],"metastatic":[174],"sites,":[175],"subtypes":[177],"covering":[178],"&gt;90%":[179],"clinical":[181,260],"type,":[185],"drawn":[186],"25+":[188],"sources":[189],"8+":[191],"scanner":[192],"models.":[193],"Benchmarked":[194],"consensus,":[198],"matches":[201],"or":[202],"exceeds":[203],"performance":[206],"generalizes":[208],"consistently":[209],"robustly":[211],"broad":[214],"scope.":[218],"In":[219],"doing":[220],"so,":[221],"turns":[224],"--":[228,235],"ubiquitous":[231],"data":[232],"into":[236,241],"window":[240],"tumor":[243],"its":[245],"microenvironment,":[246],"laying":[247],"for":[250],"next":[252],"generation":[253],"tissue-based":[255],"biomarkers":[256],"translational":[258],"research.":[261]},"counts_by_year":[],"updated_date":"2026-07-28T07:46:37.118299","created_date":"2026-06-12T00:00:00"}
