{"doi":"10.17504/protocols.io.x54v95m6pl3e/v1","title":"CoCo-ST detects global and local biological structures in spatial transcriptomics datasets v1","abstract":"A protocol describing the application of the CoCo-ST algorithm on spatial transcriptomics datasets to detect biologically relevant spatial structures. We demonstrate CoCo-ST's ability to detect low variance spatial structures driving tumor progression. Two main challenges with precancer analysis are: The high variance in global spatial patterns which might lead to the overlook of local, low-variance domains that hold significant biological relevance. The complexity of spatial domain detection across diverse tissue samples with varying spatial resolutions, necessitating a robust and scalable approach. Here, we show CoCo-ST’s contrastive learning approach for identifying both high and low-variance spatial structures, leveraging multi-sample data. This protocol is associated with our proposed CoCo-ST algorithm for spatial domain detection in Nature Cell Biology","journal":null,"year":2025,"id":556568,"datarank":0.16479184330021646,"base_score":1.0986122886681096,"endowment":1.0986122886681096,"self_citation_contribution":0.16479184330021646,"citation_network_contribution":0.0,"self_endowment_contribution":0.16479184330021646,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":2,"citer_count":1,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9626,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1287896,"name":"Bo Zhu","orcid":"0000-0001-6838-7406","position":1,"is_corresponding":false},{"id":4544,"name":"Natalie I. Vokes","orcid":"0000-0002-3766-5335","position":2,"is_corresponding":false},{"id":5676,"name":"Jia Wu","orcid":"0000-0001-8392-8338","position":3,"is_corresponding":false},{"id":24639,"name":"Jiexin Zhang","orcid":"0000-0001-9526-6730","position":4,"is_corresponding":false},{"id":5675,"name":"Muhammad Aminu","orcid":"0000-0002-9903-8812","position":0,"is_corresponding":true}],"reference_count":0,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T02:55:08.896385Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}