{"doi":"10.1101/2023.08.03.551845","title":"An end-to-end workflow for non-destructive 3D pathology","abstract":"Recent advances in 3D pathology offer the ability to image orders-of-magnitude more tissue than conventional pathology while providing a volumetric context that is lacking with 2D tissue sections, all without requiring destructive tissue sectioning. Generating high-quality 3D pathology datasets on a consistent basis is non-trivial, requiring careful attention to many details regarding tissue preparation, imaging, and data/image processing in an iterative process. Here we provide an end-to-end protocol covering all aspects of a 3D pathology workflow (using light-sheet microscopy as an illustrative imaging platform) with sufficient detail to perform well-controlled preclinical and clinical studies. While 3D pathology is compatible with diverse staining protocols and computationally generated color palettes for visual analysis, this protocol will focus on a fluorescent analog of hematoxylin and eosin (H&E), which remains the most common stain for gold-standard diagnostic determinations. We present our guidelines for a broad range of end-users (e.g., biologists, clinical researchers, and engineers) in a simple tutorial format.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2023,"id":391447,"datarank":0.31191623125197543,"base_score":2.0794415416798357,"endowment":2.0794415416798357,"self_citation_contribution":0.31191623125197543,"citation_network_contribution":0.0,"self_endowment_contribution":0.31191623125197543,"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":0.9359,"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":560155,"name":"Lindsey A. Barner","orcid":"0000-0002-9156-0024","position":1,"is_corresponding":false},{"id":1164170,"name":"Qinghua Han","orcid":"0000-0001-5527-5237","position":2,"is_corresponding":false},{"id":1164651,"name":"Elena Baraznenok","orcid":null,"position":3,"is_corresponding":false},{"id":1051528,"name":"Lydia Lan","orcid":null,"position":4,"is_corresponding":false},{"id":258186,"name":"Chetan Poudel","orcid":"0000-0002-8512-9238","position":5,"is_corresponding":false},{"id":560158,"name":"Gan Gao","orcid":"0000-0002-8100-7735","position":6,"is_corresponding":false},{"id":323421,"name":"Robert Serafin","orcid":"0000-0002-6646-353X","position":7,"is_corresponding":false},{"id":1091216,"name":"Sarah S. L. Chow","orcid":"0009-0005-7519-9346","position":8,"is_corresponding":false},{"id":279202,"name":"Adam K. Glaser","orcid":"0000-0003-3558-8994","position":9,"is_corresponding":false},{"id":247031,"name":"Andrew Janowczyk","orcid":"0000-0003-2982-4321","position":10,"is_corresponding":false},{"id":451833,"name":"David Brenes","orcid":"0000-0003-1969-5386","position":11,"is_corresponding":false},{"id":561077,"name":"Hongyi Huang","orcid":null,"position":12,"is_corresponding":false},{"id":1065843,"name":"Dominie Miyasato","orcid":"0000-0001-8977-7411","position":13,"is_corresponding":false},{"id":360871,"name":"Lawrence D. True","orcid":"0000-0001-5682-1228","position":14,"is_corresponding":false},{"id":758272,"name":"Soyoung Kang","orcid":"0000-0002-1022-9648","position":15,"is_corresponding":false},{"id":279206,"name":"Joshua C. Vaughan","orcid":"0000-0002-6550-8935","position":16,"is_corresponding":false},{"id":20776,"name":"Jonathan Liu","orcid":"0000-0001-5650-3086","position":17,"is_corresponding":false},{"id":353034,"name":"Kevin W. Bishop","orcid":"0000-0001-8722-6464","position":0,"is_corresponding":true}],"reference_count":98,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T01:18:47.408273Z","pmid":"37577615","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":[]}