{"doi":"10.1016/j.crmeth.2023.100692","title":"Using MitER for 3D analysis of mitochondrial morphology and ER contacts","abstract":"We have developed an open-source workflow that allows for quantitative single-cell analysis of organelle morphology, distribution, and inter-organelle contacts with an emphasis on the analysis of mitochondria and mitochondria-endoplasmic reticulum (mito-ER) contact sites. As the importance of inter-organelle contacts becomes more widely recognized, there is a concomitant increase in demand for tools to analyze subcellular architecture. Here, we describe a workflow we call MitER (pronounced \"mightier\"), which allows for automated calculation of organelle morphology, distribution, and inter-organelle contacts from 3D renderings by employing the animation software Blender. We then use MitER to quantify the variations in the mito-ER networks of Saccharomyces cerevisiae, revealing significantly more mito-ER contacts within respiring cells compared to fermenting cells. We then demonstrate how this workflow can be applied to mammalian systems and used to monitor mitochondrial dynamics and inter-organelle contact in time-lapse studies.","journal":"Cell Reports Methods","year":2024,"id":453975,"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":7,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9417,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1277657,"name":"Satyen Dhamankar","orcid":null,"position":1,"is_corresponding":false},{"id":988121,"name":"Saurabh Malani","orcid":"0009-0008-1564-0410","position":2,"is_corresponding":false},{"id":500571,"name":"William A. Hofstadter","orcid":"0000-0002-5872-6651","position":3,"is_corresponding":false},{"id":793471,"name":"Scott A. Wegner","orcid":null,"position":4,"is_corresponding":false},{"id":277733,"name":"Ileana M. Cristea","orcid":"0000-0002-6533-2458","position":5,"is_corresponding":false},{"id":256396,"name":"José L. Avalos‬","orcid":"0000-0002-7209-4208","position":6,"is_corresponding":false},{"id":1277238,"name":"Therese Kichuk","orcid":"0000-0001-9917-3785","position":0,"is_corresponding":true}],"reference_count":18,"raw_metadata":null,"created_at":"2026-07-19T02:03:07.923686Z","pmid":"38232737","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":[]}