{"doi":"10.1101/2025.10.01.679626","title":"Vis-OCT Explorer: an open-source software for visible-light optical coherence tomography data processing","abstract":"Background and objectives: Visible-light optical coherence tomography (vis-OCT) has enabled the visualization of retinal structures and functions beyond the capabilities of conventional OCTs. However, to reconstruct high-quality images, vis-OCT requires special post-processing, including balanced detection. An open-source, standardized vis-OCT data processing software is essential for clinical applications and translation of vis-OCT. Methods: We developed Vis-OCT Explorer, an open-source, modular Python-based software for processing vis-OCT images. In addition to the standard spectral-domain OCT processing pipeline - including k-space resampling, dispersion compensation, and fast Fourier transformation - Vis-OCT Explorer offers unique dual-spectrometer balanced detection, short-time-Fourier transformation (STFT) based dispersion compensation coefficient optimization, and GPU-accelerated processing. We evaluated the reconstruction performance by quantifying a quality index extracted from individual B-scan images. We also assessed the repeatability of retinal thickness measurements by five operators on images acquired from different testing sites using the intraclass correlation coefficient (ICC) analysis. Results: Balanced detection and STFT-based dispersion compensation significantly increased the quality index of reconstructed B-scan images. ICC values of the retinal nerve fiber layer (RNFL) and ganglion cell-inner plexiform layer (GCIPL) thickness measurements from four testing sites exceeded 0.8 in 87.5% of the macular-centered images. The ICC of RNFL thickness measurements on all optic nerve head-centered images is above 0.8, showing strong repeatability across users. Conclusions: Vis-OCT Explorer provides high-quality image processing and enables highly repeatable measurements on vis-OCT human retinal images. It facilitates future multicenter clinical tests to validate vis-OCT's clinical efficacy.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2025,"id":576732,"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":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9433,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1309160,"name":"Fengyuanshan Xu","orcid":null,"position":1,"is_corresponding":false},{"id":409027,"name":"Roman V. Kuranov","orcid":"0000-0002-9668-2960","position":2,"is_corresponding":false},{"id":583206,"name":"Ronald Zambrano","orcid":"0000-0002-6582-5308","position":3,"is_corresponding":false},{"id":430054,"name":"Jacqueline Chen","orcid":"0000-0002-9896-6262","position":4,"is_corresponding":false},{"id":1485554,"name":"Jiahui Wu","orcid":"0000-0001-6758-4635","position":5,"is_corresponding":false},{"id":1485555,"name":"Seung Hyen Lee","orcid":"0000-0003-2189-2821","position":6,"is_corresponding":false},{"id":1485974,"name":"Kenny Q. Trang","orcid":null,"position":7,"is_corresponding":false},{"id":770437,"name":"Rukhsana G. Mirza","orcid":"0000-0003-1351-5874","position":8,"is_corresponding":false},{"id":47324,"name":"S. Simon","orcid":null,"position":9,"is_corresponding":false},{"id":1296134,"name":"Fábio Lavinsky","orcid":"0000-0002-6925-1794","position":10,"is_corresponding":false},{"id":449686,"name":"Xiaorong Liu","orcid":"0000-0002-7655-6342","position":11,"is_corresponding":false},{"id":278863,"name":"Jeffrey L. Goldberg","orcid":"0000-0002-1390-7360","position":12,"is_corresponding":false},{"id":331867,"name":"Alex S. Huang","orcid":"0000-0001-9024-9608","position":13,"is_corresponding":false},{"id":6881,"name":"Joel S. Schuman","orcid":"0000-0002-8885-3766","position":14,"is_corresponding":false},{"id":409028,"name":"Hao F. Zhang","orcid":"0000-0001-5089-1196","position":15,"is_corresponding":false},{"id":998222,"name":"Weijia Fan","orcid":"0009-0002-8173-0760","position":0,"is_corresponding":true}],"reference_count":39,"raw_metadata":null,"created_at":"2026-07-19T02:58:00.620755Z","pmid":"41256529","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":[]}