{"doi":"10.1523/eneuro.0328-19.2019","title":"Capillary-Based and Stokes-Based Trapping of Serial Sections for Scalable 3D-EM Connectomics","abstract":"Abstract Serial section electron microscopy (ssEM), a technique where volumes of tissue can be anatomically reconstructed by imaging consecutive tissue slices, has proven to be a powerful tool for the investigation of brain anatomy. Between the process of cutting the slices, or “sections,” and imaging them, however, handling 10°−10 6 delicate sections remains a bottleneck in ssEM, especially for batches in the “mesoscale” regime, i.e., 10 2 –10 3 sections. We present a tissue section handling device that transports and positions sections, accurately and repeatability, for automated, robotic section pick-up and placement onto an imaging substrate. The device interfaces with a conventional ultramicrotomy diamond knife, accomplishing in-line, exact-constraint trapping of sections with 100-μm repeatability. An associated mathematical model includes capillary-based and Stokes-based forces, accurately describing observed behavior and fundamentally extends the modeling of water-air interface forces. Using the device, we demonstrate and describe the limits of reliable handling of hundreds of slices onto a variety of electron and light microscopy substrates without significant defects ( n = 8 datasets composed of 126 serial sections in an automated fashion with an average loss rate and throughput of 0.50% and 63 s/section, respectively. In total, this work represents an automated mesoscale serial sectioning system for scalable 3D-EM connectomics.","journal":"eNeuro","year":2020,"id":116585,"datarank":0.10397207708399181,"base_score":0.6931471805599453,"endowment":0.6931471805599453,"self_citation_contribution":0.10397207708399181,"citation_network_contribution":0.0,"self_endowment_contribution":0.10397207708399181,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":1,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9547,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2020-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":544340,"name":"Mighten C. Yip","orcid":"0000-0002-8463-0311","position":1,"is_corresponding":false},{"id":431969,"name":"Aditi Kumar","orcid":"0000-0003-1026-3173","position":2,"is_corresponding":false},{"id":544341,"name":"Colby F. Lewallen","orcid":"0000-0002-4424-2533","position":3,"is_corresponding":false},{"id":258635,"name":"Daniel J. Bumbarger","orcid":"0000-0001-6224-1633","position":4,"is_corresponding":false},{"id":258636,"name":"R. Clay Reid","orcid":"0000-0002-8697-6797","position":5,"is_corresponding":false},{"id":435740,"name":"Craig R. Forest","orcid":"0000-0001-5343-1769","position":6,"is_corresponding":false},{"id":544339,"name":"Timothy Lee","orcid":"0000-0002-3395-026X","position":0,"is_corresponding":true}],"reference_count":40,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-18T23:13:44.286758Z","pmid":"32094293","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":[]}