{"doi":"10.1364/optcon.532996","title":"High-speed in vivo calcium recording using structured illumination with self-supervised denoising","abstract":"indicator GCaMP8f in CA1 pyramidal neurons using periodic structured illumination (SI) with computational image reconstruction. We implement what we believe to be a novel reconstruction method for data acquired using periodic structured illumination, termed pseudo-HiLo (pHiLo), that combines a pseudo-widefield (pWF) reconstruction with individual SI frames to perform a HiLo reconstruction. We compare this new technique to interleaved optical sectioning structured illumination microscopy (OS-SIM) and pWF reconstruction. We quantify the performance of each reconstruction by evaluating contrast, transient peak-to-noise ratio (PNR), pairwise correlation coefficients between ΔF/F time courses extracted from individual in-focus cells, and correlation coefficients between each cell with surrounding cell-free background pixels. We additionally incorporate a self-supervised deep learning method for real-time noise suppression (DeepCAD-RT) into our data preprocessing pipeline. At 500 Hz frame rates, we demonstrate a 75% increase in PNR using the denoised pHiLo reconstruction compared to pWF. Utilizing DeepCAD-RT, we show significant PNR improvements using both structured illumination (SI) reconstruction methods with OS-SIM showing a 59% increase in PNR after denoising. Both pHiLo and OS-SIM reconstructions result in a ≈65% decrease in the mean correlation coefficient of the ΔF/F time courses between ROIs in comparison with pWF, indicating the potential to remove background fluorescent transients from out-of-focus cells.","journal":"Optics Continuum","year":2024,"id":447617,"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":6,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9534,"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":1073617,"name":"Catherine A. Saladrigas","orcid":"0000-0001-5060-1996","position":1,"is_corresponding":false},{"id":140445,"name":"A.R. Teel","orcid":null,"position":2,"is_corresponding":false},{"id":1266234,"name":"Sean Vieau","orcid":null,"position":3,"is_corresponding":false},{"id":439248,"name":"Victor M. Bright","orcid":"0000-0001-5498-3071","position":4,"is_corresponding":false},{"id":439249,"name":"Juliet T. Gopinath","orcid":"0000-0003-2387-5371","position":5,"is_corresponding":false},{"id":552653,"name":"Cristin G. Welle","orcid":"0000-0001-8735-0983","position":6,"is_corresponding":false},{"id":372463,"name":"Diego Restrepo","orcid":"0000-0002-4972-446X","position":7,"is_corresponding":false},{"id":582488,"name":"Emily A. Gibson","orcid":"0000-0002-3436-1483","position":8,"is_corresponding":false},{"id":1074129,"name":"Forest Speed","orcid":null,"position":0,"is_corresponding":true}],"reference_count":39,"raw_metadata":null,"created_at":"2026-07-19T02:02:03.354708Z","pmid":"41550202","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":[]}