{"id":"https://openalex.org/W7129079562","doi":"https://doi.org/10.1093/bioinformatics/btag073","title":"InSituPy: a framework for histology-guided, multi-sample analysis of single-cell spatial omics data","display_name":"InSituPy: a framework for histology-guided, multi-sample analysis of single-cell spatial omics data","publication_year":2026,"publication_date":"2026-02-12","ids":{"openalex":"https://openalex.org/W7129079562","doi":"https://doi.org/10.1093/bioinformatics/btag073","pmid":"https://pubmed.ncbi.nlm.nih.gov/41692967"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btag073","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag073","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/btag073","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5037516157","display_name":"Johannes Wirth","orcid":"https://orcid.org/0000-0002-2216-3332"},"institutions":[{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Johannes Wirth","raw_affiliation_strings":["Institute of Pathology, School of Medicine and Health, Technical University of Munich , Munich,"],"affiliations":[{"raw_affiliation_string":"Institute of Pathology, School of Medicine and Health, Technical University of Munich , Munich,","institution_ids":["https://openalex.org/I62916508"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5116609128","display_name":"Anna Chernysheva","orcid":null},"institutions":[{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Anna Chernysheva","raw_affiliation_strings":["Institute of Pathology, School of Medicine and Health, Technical University of Munich , Munich,"],"affiliations":[{"raw_affiliation_string":"Institute of Pathology, School of Medicine and Health, Technical University of Munich , Munich,","institution_ids":["https://openalex.org/I62916508"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5116609129","display_name":"Birthe Lemke","orcid":null},"institutions":[{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Birthe Lemke","raw_affiliation_strings":["Institute of Pathology, School of Medicine and Health, Technical University of Munich , Munich,"],"affiliations":[{"raw_affiliation_string":"Institute of Pathology, School of Medicine and Health, Technical University of Munich , Munich,","institution_ids":["https://openalex.org/I62916508"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5116609130","display_name":"Isabel Giray","orcid":null},"institutions":[{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Isabel Giray","raw_affiliation_strings":["Institute of Pathology, School of Medicine and Health, Technical University of Munich , Munich,"],"affiliations":[{"raw_affiliation_string":"Institute of Pathology, School of Medicine and Health, Technical University of Munich , Munich,","institution_ids":["https://openalex.org/I62916508"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5124166186","display_name":"K. Steiger","orcid":null},"institutions":[{"id":"https://openalex.org/I17937529","display_name":"German Cancer Research Center","ror":"https://ror.org/04cdgtt98","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I17937529"]},{"id":"https://openalex.org/I4210127591","display_name":"German Centre for Cardiovascular Research","ror":"https://ror.org/031t5w623","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210127591","https://openalex.org/I4405256427"]},{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Katja Steiger","raw_affiliation_strings":["German Cancer Consortium (DKTK) Partner Site Munich , Munich,","Institute of Pathology, School of Medicine and Health, Technical University of Munich , Munich,"],"affiliations":[{"raw_affiliation_string":"German Cancer Consortium (DKTK) Partner Site Munich , Munich,","institution_ids":["https://openalex.org/I4210127591","https://openalex.org/I17937529"]},{"raw_affiliation_string":"Institute of Pathology, School of Medicine and Health, Technical University of Munich , Munich,","institution_ids":["https://openalex.org/I62916508"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5037516157"],"corresponding_institution_ids":["https://openalex.org/I62916508"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.39084949,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"42","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9664000272750854,"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"}},"topics":[{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9664000272750854,"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"}},{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.00559999980032444,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T14393","display_name":"Health, Environment, Cognitive Aging","score":0.002099999925121665,"subfield":{"id":"https://openalex.org/subfields/2307","display_name":"Health, Toxicology and Mutagenesis"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4296000003814697},{"id":"https://openalex.org/keywords/spatial-analysis","display_name":"Spatial analysis","score":0.31940001249313354},{"id":"https://openalex.org/keywords/data-exploration","display_name":"Data exploration","score":0.2667999863624573},{"id":"https://openalex.org/keywords/noisy-data","display_name":"Noisy data","score":0.2621999979019165}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6963000297546387},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5177000164985657},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4296000003814697},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3538999855518341},{"id":"https://openalex.org/C159620131","wikidata":"https://www.wikidata.org/wiki/Q1938983","display_name":"Spatial analysis","level":2,"score":0.31940001249313354},{"id":"https://openalex.org/C2780977526","wikidata":"https://www.wikidata.org/wiki/Q42417149","display_name":"Data exploration","level":3,"score":0.2667999863624573},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.26579999923706055},{"id":"https://openalex.org/C2781170535","wikidata":"https://www.wikidata.org/wiki/Q30587856","display_name":"Noisy data","level":2,"score":0.2621999979019165},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.2362000048160553},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.23280000686645508}],"mesh":[{"descriptor_ui":"D000071253","descriptor_name":"Metadata","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000071253","descriptor_name":"Metadata","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000071253","descriptor_name":"Metadata","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btag073","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag073","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:41692967","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41692967","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:12988772","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12988772/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"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/btag073","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag073","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/G6479141801","display_name":null,"funder_award_id":"01KD2206A","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"}],"funders":[{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":24,"referenced_works":["https://openalex.org/W1972618510","https://openalex.org/W2126537932","https://openalex.org/W2151013106","https://openalex.org/W2151103935","https://openalex.org/W2345356016","https://openalex.org/W2471536144","https://openalex.org/W2900569176","https://openalex.org/W2915848182","https://openalex.org/W2944545583","https://openalex.org/W2952481429","https://openalex.org/W2972445800","https://openalex.org/W3047081808","https://openalex.org/W3176444924","https://openalex.org/W4210583065","https://openalex.org/W4214876469","https://openalex.org/W4225157576","https://openalex.org/W4225678977","https://openalex.org/W4327857954","https://openalex.org/W4362737480","https://openalex.org/W4386623320","https://openalex.org/W4389938094","https://openalex.org/W4393004135","https://openalex.org/W4402533731","https://openalex.org/W4407107633"],"related_works":[],"abstract_inverted_index":{"j.wirth@tum.de,":[0],"katja.steiger@tum.de.":[1]},"counts_by_year":[],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2026-02-17T00:00:00"}
