{"doi":"10.7554/elife.68920","title":"Whole-organism 3D quantitative characterization of zebrafish melanin by silver deposition micro-CT","abstract":"We previously described X-ray histotomography, a high-resolution, non-destructive form of X-ray microtomography (micro-CT) imaging customized for three-dimensional (3D), digital histology, allowing quantitative, volumetric tissue and organismal phenotyping (Ding et al., 2019). Here, we have combined micro-CT with a novel application of ionic silver staining to characterize melanin distribution in whole zebrafish larvae. The resulting images enabled whole-body, computational analyses of regional melanin content and morphology. Normalized micro-CT reconstructions of silver-stained fish consistently reproduced pigment patterns seen by light microscopy, and further allowed direct quantitative comparisons of melanin content across wild-type and mutant samples, including subtle phenotypes not previously noticed. Silver staining of melanin for micro-CT provides proof-of-principle for whole-body, 3D computational phenomic analysis of a specific cell type at cellular resolution, with potential applications in other model organisms and melanocytic neoplasms. Advances such as this in whole-organism, high-resolution phenotyping provide superior context for studying the phenotypic effects of genetic, disease, and environmental variables.","journal":"eLife","year":2021,"id":161681,"datarank":0.5561348477542403,"base_score":2.833213344056216,"endowment":2.833213344056216,"self_citation_contribution":0.42498200160843247,"citation_network_contribution":0.13115284614580777,"self_endowment_contribution":0.42498200160843247,"citer_contribution":0.13115284614580777,"corpus_percentile":null,"corpus_rank":null,"citation_count":16,"citer_count":11,"citers_with_citation_signal":6,"citers_with_endowment":6,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9479,"is_data_producer":true,"deposit_databanks":{"Dryad":["10.5061/dryad.wwpzgmsjn"]},"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":676926,"name":"Maksim A. Yakovlev","orcid":"0000-0003-1846-3751","position":1,"is_corresponding":false},{"id":275305,"name":"Daniel J. Vanselow","orcid":"0000-0002-9221-8634","position":2,"is_corresponding":false},{"id":676927,"name":"Yifu Ding","orcid":"0000-0002-4629-5858","position":3,"is_corresponding":false},{"id":676928,"name":"Alex Y. Lin","orcid":"0000-0002-1653-4168","position":4,"is_corresponding":false},{"id":388241,"name":"Dilworth Y. Parkinson","orcid":"0000-0002-1817-0716","position":5,"is_corresponding":false},{"id":676929,"name":"Yuxin Wang","orcid":"0000-0002-6087-6544","position":6,"is_corresponding":false},{"id":676930,"name":"Victor A. Canfield","orcid":"0000-0002-4359-1790","position":7,"is_corresponding":false},{"id":676931,"name":"K.C. Ang","orcid":"0000-0001-7695-9953","position":8,"is_corresponding":false},{"id":264664,"name":"Keith C. Cheng","orcid":"0000-0002-5350-5825","position":9,"is_corresponding":false},{"id":676925,"name":"Spencer R. Katz","orcid":"0000-0002-5586-3562","position":0,"is_corresponding":true}],"reference_count":47,"raw_metadata":null,"created_at":"2026-07-18T23:44:56.409311Z","pmid":"34528510","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":[]}