{"doi":"10.1002/jbio.202400258","title":"A Simple and Fast Optical Clearing Method for Whole‐Mount Fluorescence In Situ Hybridization ( <scp>FISH</scp> ) Imaging","abstract":"We report a single-step optical clearing method that is compatible with RNA fluorescence in situ hybridization (FISH) imaging. We previously demonstrated microscopy imaging with immunohistochemistry and genetic reporters using a technique called lipid-preserving refractive index matching for prolonged imaging depth (LIMPID). Our protocol reliably produces high-resolution three-dimensional (3D) images with minimal aberrations using high magnification objectives, captures large field-of-view images of whole-mount tissues, and supports co-labeling with antibody and FISH probes. We also custom-designed FISH probes for quail embryos, demonstrating the ease of fabricating probes for use with less common animal models. Furthermore, we show high-quality 3D images using a conventional fluorescence microscope, without using more advanced depth sectioning instruments such as confocal or light-sheet microscopy. For broader adoption, we simplified and optimized 3D-LIMPID-FISH to minimize the barrier to entry, and we provide a detailed protocol to aid users with navigating the thick and thin of 3D microscopy.","journal":"Journal of Biophotonics","year":2024,"id":450757,"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":4,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9563,"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":523664,"name":"Yehe Liu","orcid":"0000-0002-0221-5676","position":1,"is_corresponding":false},{"id":796419,"name":"Jordan Smith","orcid":"0009-0005-7404-7738","position":2,"is_corresponding":false},{"id":523665,"name":"Michiko Watanabe","orcid":"0000-0002-6295-6759","position":3,"is_corresponding":false},{"id":391989,"name":"Andrew M. Rollins","orcid":"0000-0002-7780-4862","position":4,"is_corresponding":false},{"id":391990,"name":"Michael W. Jenkins","orcid":"0000-0002-8908-5383","position":5,"is_corresponding":false},{"id":1271235,"name":"Junwoo Suh","orcid":"0000-0002-9137-7270","position":0,"is_corresponding":true}],"reference_count":61,"raw_metadata":null,"created_at":"2026-07-19T02:02:28.969209Z","pmid":"39389582","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":[]}