{"doi":"10.64898/2026.01.21.700865","title":"The One Click Wonder: a retrained automated segmentation pipeline that enables quantitative and modular analysis of\n                  <i>C. elegans</i>\n                  embryos","abstract":"<jats:title>Abstract</jats:title>\n                <jats:p>\n                  High-throughput approaches have transformed the study of gene regulation by enabling quantitative, genome-scale analyses in both genomics and imaging. However, applying these methods to intact organisms remains challenging, particularly for high-throughput, 3D imaging. In\n                  <jats:italic>Caenorhabditis elegans</jats:italic>\n                  , generalist segmentation models often perform poorly due to rapid changes in nuclear size, shape, and density. To overcome this obstacle, we developed\n                  <jats:bold>One Click Wonder (OCW)</jats:bold>\n                  , an automated pipeline that pairs a retrained Cellpose model with stage-specific parameter selection to deliver accurate, high-throughput segmentation of embryos. We further introduce the\n                  <jats:bold>Biological Annotation and Association Mapper (BAAM)</jats:bold>\n                  , which integrates segmentation with spot detection, to enable single-cell quantitation. Applied to the pioneer factor\n                  <jats:italic>pha-4/FoxA</jats:italic>\n                  , this pipeline revealed distinct cell populations with an eight-fold range in transcriptional burst frequency. These findings demonstrate that OCW and BAAM provide a modular, scalable pipeline for quantitative, single-cell analysis of gene expression in\n                  <jats:italic>C. elegans</jats:italic>\n                  embryos.\n                </jats:p>","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2026,"id":924,"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":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.0506,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2026-01-22","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":11813,"name":"Tobias Evan Verheijen","orcid":"0009-0009-8456-1182","position":1,"is_corresponding":false},{"id":11814,"name":"Angelo Luiz Angonezi","orcid":"0009-0001-1455-6806","position":2,"is_corresponding":false},{"id":11815,"name":"Aude Andriollo","orcid":"0009-0006-0552-1472","position":3,"is_corresponding":false},{"id":11816,"name":"Sebastien Herbert","orcid":"0000-0002-3267-9156","position":4,"is_corresponding":false},{"id":11817,"name":"Gregory Roth","orcid":"0000-0003-0677-3293","position":5,"is_corresponding":false},{"id":11818,"name":"Jeffrey A. Chao","orcid":"0000-0002-5895-9156","position":6,"is_corresponding":false},{"id":11819,"name":"Susan E. Mango","orcid":"0000-0002-2146-3237","position":7,"is_corresponding":false},{"id":11812,"name":"Palmer Carlyn Bassett","orcid":"0000-0001-8535-725X","position":0,"is_corresponding":true}],"reference_count":44,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","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":[]}