{"doi":"10.1038/s41592-025-02617-2","title":"Optimizing Xenium In Situ data utility by quality assessment and best-practice analysis workflows","abstract":"The Xenium In Situ platform is a new spatial transcriptomics product commercialized by 10x Genomics, capable of mapping hundreds of genes in situ at subcellular resolution. Given the multitude of commercially available spatial transcriptomics technologies, recommendations in choice of platform and analysis guidelines are increasingly important. Herein, we explore 25 Xenium datasets generated from multiple tissues and species, comparing scalability, resolution, data quality, capacities and limitations with eight other spatially resolved transcriptomics technologies and commercial platforms. In addition, we benchmark the performance of multiple open-source computational tools, when applied to Xenium datasets, in tasks including preprocessing, cell segmentation, selection of spatially variable features and domain identification. This study serves as an independent analysis of the performance of Xenium, and provides best practices and recommendations for analysis of such datasets.","journal":"Nature Methods","year":2025,"id":9922,"datarank":1.3276000374945842,"base_score":4.007333185232471,"endowment":4.007333185232471,"self_citation_contribution":0.6010999777848708,"citation_network_contribution":0.7265000597097135,"self_endowment_contribution":0.6010999777848708,"citer_contribution":0.7265000597097135,"corpus_percentile":60.699755899104964,"corpus_rank":484,"citation_count":81,"citer_count":73,"citers_with_citation_signal":38,"citers_with_endowment":38,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.7998,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-03-13","fair_score":49.7917,"fair_percentile":77.9023746701847,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":58474,"name":"Louis Benedikt Kuemmerle","orcid":"0000-0002-9193-1243","position":1,"is_corresponding":false},{"id":85020,"name":"Christoffer Mattsson-Langseth","orcid":null,"position":2,"is_corresponding":false},{"id":85021,"name":"Sebastian Tismeyer","orcid":null,"position":3,"is_corresponding":false},{"id":85022,"name":"Christophe Avenel","orcid":"0000-0002-1835-921X","position":4,"is_corresponding":false},{"id":1998,"name":"Kuan-lin Huang","orcid":"0000-0002-3237-4248","position":5,"is_corresponding":false},{"id":85023,"name":"Habib Rehman","orcid":"0000-0002-8671-982X","position":6,"is_corresponding":false},{"id":84781,"name":"Marco Grillo","orcid":"0000-0003-2155-0645","position":7,"is_corresponding":false},{"id":85024,"name":"Paulo Czarnewski","orcid":"0000-0001-8150-4021","position":8,"is_corresponding":false},{"id":85025,"name":"Saga Helgadottir","orcid":null,"position":9,"is_corresponding":false},{"id":85026,"name":"Katarina Tiklova","orcid":null,"position":10,"is_corresponding":false},{"id":85027,"name":"Axel Andersson","orcid":"0000-0002-4714-3127","position":11,"is_corresponding":false},{"id":85028,"name":"Nima Rafati","orcid":"0000-0002-3687-9745","position":12,"is_corresponding":false},{"id":85029,"name":"Maria Chatzinikolaou","orcid":"0000-0002-3539-9088","position":13,"is_corresponding":false},{"id":42,"name":"Fabian Joachim Theis","orcid":"0000-0002-2419-1943","position":14,"is_corresponding":false},{"id":3578,"name":"Malte D. Luecken","orcid":"0000-0001-7464-7921","position":15,"is_corresponding":false},{"id":85030,"name":"Carolina Wählby","orcid":"0000-0002-4139-7003","position":16,"is_corresponding":false},{"id":58477,"name":"Naveed Ishaque","orcid":"0000-0002-8426-901X","position":17,"is_corresponding":false},{"id":24374,"name":"Mats Nilsson","orcid":"0000-0001-9985-0387","position":18,"is_corresponding":false},{"id":85031,"name":"Saga Helgadóttir","orcid":"0000-0001-8070-147X","position":19,"is_corresponding":false},{"id":85032,"name":"Katarína Tiklová","orcid":"0000-0002-9529-4552","position":20,"is_corresponding":false},{"id":27707,"name":"Sergio Marco Salas","orcid":"0000-0002-4636-0322","position":0,"is_corresponding":true}],"reference_count":58,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":"40082609","pmcid":"PMC11978515","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":"hybrid","license":"cc-by","views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":52.5,"fair_a":80.0,"fair_i":25.0,"fair_r":41.6667,"fair_zscore":0.4143,"fair_rationale":{"fair_score":49.79,"has_llm":true,"dimensions":{"F":{"name":"Findable","score":52.5,"criteria":[{"key":"f_has_doi","label":"Has a persistent DOI","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"DOI present","rationale":null},{"key":"f_repository_presence","label":"Indexed in repositories / literature DBs","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"datacite=0, pmcid=True, pmid=True","rationale":null},{"key":"f_persistent_ids","label":"Resolvable scholarly identifiers (OpenAlex)","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"no OpenAlex id","rationale":null},{"key":"f_metadata_richness","label":"Rich, machine-readable metadata","kind":"llm","weight":1.0,"fraction":0.25,"signal":null,"rationale":"The paper provides DOIs and URLs for datasets but lacks machine-readable metadata or structured descriptions beyond human-readable text."}]},"A":{"name":"Accessible","score":80.0,"criteria":[{"key":"a_open_access","label":"Open Access / files deposited","kind":"deterministic","weight":1.5,"fraction":1.0,"signal":"Open Access","rationale":null},{"key":"a_retrievable","label":"Free full text retrievable","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"0 OA location(s)","rationale":null},{"key":"a_access_protocol","label":"Clear data/code access protocol","kind":"llm","weight":1.0,"fraction":1.0,"signal":null,"rationale":"Clear and direct access to data via Zenodo DOIs and code via GitHub, with no authentication barriers and a CC BY 4.0 license for the article."}]},"I":{"name":"Interoperable","score":25.0,"criteria":[{"key":"i_linked_data","label":"Linked datasets / DataCite relations","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"linked_datasets=0, datacite=0","rationale":null},{"key":"i_standard_ids","label":"References data via standard accessions","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"accessions=0, trials=0","rationale":null},{"key":"i_standards","label":"Standard formats, vocabularies & identifiers","kind":"llm","weight":1.0,"fraction":0.5,"signal":null,"rationale":"Uses standard file formats (AnnData) and gene symbols, but does not explicitly adopt community ontologies or controlled vocabularies for cell types or anatomical regions."}]},"R":{"name":"Reusable","score":41.67,"criteria":[{"key":"r_license","label":"Clear, open reuse license","kind":"deterministic","weight":1.5,"fraction":0.0,"signal":"no license","rationale":null},{"key":"r_downloads","label":"Demonstrated reuse (downloads)","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"downloads=0","rationale":null},{"key":"r_version","label":"Versioned / maintained","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"no version chain","rationale":null},{"key":"r_dataset","label":"Classified as a data resource","kind":"deterministic","weight":0.5,"fraction":1.0,"signal":"is_dataset","rationale":null},{"key":"r_reusability","label":"Data-availability statement, license & reproducibility","kind":"llm","weight":2.0,"fraction":0.667,"signal":null,"rationale":"Comprehensive data availability statement with persistent identifiers and detailed methods, but lacks explicit licenses for the datasets and code in the paper text."}]}},"suggestions":["Explicitly state the license for each dataset and code repository in the data availability section.","Adopt standard ontologies (e.g., Cell Ontology, Uberon) for cell type and anatomical region annotations.","Include machine-readable metadata (e.g., schema.org or JSON-LD) for datasets in the paper or repository.","Provide a formal metadata file (e.g., ISA-Tab or RO-Crate) alongside each dataset to enhance findability and interoperability.","Ensure the code repository includes a clear license file and a README with installation and usage instructions."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v2","fulltext_source":"epmc_xml"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v2","fair_fulltext_source":"epmc_xml","fair_has_llm":true,"fair_computed_at":"2026-06-18T00:41:33.640120Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}