{"doi":"10.1002/cyto.a.24541","title":"MIRIAM: A machine and deep learning single‐cell segmentation and quantification pipeline for multi‐dimensional tissue images","abstract":"Increasingly, highly multiplexed tissue imaging methods are used to profile protein expression at the single-cell level. However, a critical limitation is the lack of robust cell segmentation tools for tissue sections. We present Multiplexed Image Resegmentation of Internal Aberrant Membranes (MIRIAM) that combines (a) a pipeline for cell segmentation and quantification that incorporates machine learning-based pixel classification to define cellular compartments, (b) a novel method for extending incomplete cell membranes, and (c) a deep learning-based cell shape descriptor. Using human colonic adenomas as an example, we show that MIRIAM is superior to widely utilized segmentation methods and provides a pipeline that is broadly applicable to different imaging platforms and tissue types.","journal":"Cytometry Part A","year":2022,"id":243730,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":32,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9481,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":876814,"name":"Justin Shao","orcid":null,"position":1,"is_corresponding":false},{"id":876815,"name":"Samuel T. Ellis","orcid":null,"position":2,"is_corresponding":false},{"id":86831,"name":"Cody N. Heiser","orcid":"0000-0002-1299-1628","position":3,"is_corresponding":false},{"id":86856,"name":"Joseph T. Roland","orcid":"0000-0001-9977-0520","position":4,"is_corresponding":false},{"id":876816,"name":"Mary C. Macedonia","orcid":null,"position":5,"is_corresponding":false},{"id":86832,"name":"Paige N. Vega","orcid":"0000-0003-2799-7587","position":6,"is_corresponding":false},{"id":876817,"name":"Susie Shin","orcid":null,"position":7,"is_corresponding":false},{"id":86857,"name":"Robert J. Coffey","orcid":"0000-0002-2180-3844","position":8,"is_corresponding":false},{"id":60556,"name":"Ken S. Lau","orcid":"0000-0001-8438-0319","position":9,"is_corresponding":false},{"id":86826,"name":"Eliot T. McKinley","orcid":"0000-0003-4802-3933","position":0,"is_corresponding":true}],"reference_count":36,"raw_metadata":null,"created_at":"2026-07-19T00:23:20.901576Z","pmid":"35084791","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":[]}