{"doi":"10.7554/elife.89050","title":"Automated cell annotation in multi-cell images using an improved CRF_ID algorithm","abstract":"Cell identification is an important yet difficult process in data analysis of biological images. Previously, we developed an automated cell identification method called CRF_ID and demonstrated its high performance in Caenorhabditis elegans whole-brain images (Chaudhary et al., 2021). However, because the method was optimized for whole-brain imaging, comparable performance could not be guaranteed for application in commonly used C. elegans multi-cell images that display a subpopulation of cells. Here, we present an advancement, CRF_ID 2.0, that expands the generalizability of the method to multi-cell imaging beyond whole-brain imaging. To illustrate the application of the advance, we show the characterization of CRF_ID 2.0 in multi-cell imaging and cell-specific gene expression analysis in C. elegans . This work demonstrates that high-accuracy automated cell annotation in multi-cell imaging can expedite cell identification and reduce its subjectivity in C. elegans and potentially other biological images of various origins.","journal":"eLife","year":2023,"id":396855,"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":2,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9554,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":531808,"name":"Jingting Liang","orcid":"0009-0004-4284-257X","position":1,"is_corresponding":false},{"id":564368,"name":"Shivesh Chaudhary","orcid":"0000-0002-1928-0933","position":2,"is_corresponding":false},{"id":861805,"name":"Sihoon Moon","orcid":"0000-0003-4540-9443","position":3,"is_corresponding":false},{"id":1172528,"name":"Zikai Yu","orcid":"0009-0004-1851-3493","position":4,"is_corresponding":false},{"id":355715,"name":"Taihong Wu","orcid":"0000-0002-9760-6978","position":5,"is_corresponding":false},{"id":355714,"name":"He Liu","orcid":"0000-0001-9418-9171","position":6,"is_corresponding":false},{"id":355713,"name":"Myung-Kyu Choi","orcid":"0000-0002-2660-1571","position":7,"is_corresponding":false},{"id":297565,"name":"Yun Zhang","orcid":"0000-0002-7631-858X","position":8,"is_corresponding":false},{"id":302031,"name":"Hang Lu","orcid":"0000-0002-6881-660X","position":9,"is_corresponding":false},{"id":1024083,"name":"Hyun Jee Lee","orcid":"0000-0001-9662-2063","position":0,"is_corresponding":true}],"reference_count":32,"raw_metadata":null,"created_at":"2026-07-19T01:19:35.497854Z","pmid":"39853076","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":[]}