{"doi":"10.1016/j.jneumeth.2025.110495","title":"Using DeepLabCut-Live to probe state dependent neural circuits of behavior with closed-loop optogenetic stimulation","abstract":null,"journal":"Journal of Neuroscience Methods","year":2025,"id":646376,"datarank":0.26876392038420827,"base_score":1.791759469228055,"endowment":1.791759469228055,"self_citation_contribution":0.26876392038420827,"citation_network_contribution":0.0,"self_endowment_contribution":0.26876392038420827,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":5,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":807658,"name":"Mark A. Gradwell","orcid":"0000-0003-3308-8005","position":1,"is_corresponding":false},{"id":809336,"name":"Joshua K. Thackray","orcid":"0000-0003-2828-452X","position":2,"is_corresponding":false},{"id":1333736,"name":"Kanaksha K. Temkar","orcid":null,"position":3,"is_corresponding":false},{"id":1683539,"name":"Komal R. Patel","orcid":null,"position":4,"is_corresponding":false},{"id":644779,"name":"Victoria E. Abraira","orcid":"0000-0001-9936-9921","position":5,"is_corresponding":false},{"id":1307582,"name":"Melissa Gonzalez","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Using DeepLabCut-Live to probe state dependent neural circuits of behavior with closed-loop optogenetic stimulation","abstract":"BACKGROUND: Closed-loop behavior paradigms allow for real-time investigation of state-dependent neural circuits underlying behavior. However, studying context-dependent locomotor perturbations is challenging due to limitations in molecular tools and techniques for real-time manipulation of spinal circuits. NEW METHOD: We developed a novel closed-loop optogenetic stimulation paradigm that leverages DeepLabCut-Live pose estimation to manipulate primary sensory afferent activity at specific phases of the locomotor cycle in mice. A compact DeepLabCut model was trained to track hindlimb kinematics in real-time and integrated into the Bonsai visual programming framework. This system enabled LED triggered photo-stimulation of sensory neurons expressing channelrhodopsin based on user-defined pose-based criteria, such as stance or swing phase. RESULTS: sensory neurons during treadmill locomotion reliably evoked paw withdrawal responses. Stimulation during the stance phase generated a brief withdrawal and impacted the duration of the following swing phase. Stimulation during the swing phase increased the height of paw withdrawal during swing and reduced the duration of the following stance phase. COMPARISON WITH EXISTING METHODS: This method allows for high spatiotemporal precision in manipulating spinal circuits based on locomotor phase. Unlike previous approaches, this closed-loop system accounts for state-dependent nature of sensorimotor responses, enabling controlled, real-time modulation of locomotion. CONCLUSIONS: Integrating DeepLabCut-Live with optogenetics provides a powerful tool for dissecting the context-dependent role of sensory feedback and spinal interneurons in locomotion. This technique opens new avenues for uncovering the neural substrates of state-dependent behaviors and has broad applicability for studies of real-time closed-loop manipulation based on pose estimation.","is_dataset_classified":null,"base_score":1.791759469228055,"endowment":1.791759469228055,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"40436321","pmcid":null,"openalex_id":"https://openalex.org/W4410741062","authors":[],"funders":[{"funder_name":"National Institute of Neurological Disorders and Stroke","grant_id":"R01NS119268-S1","title":null},{"funder_name":"National Institute of Neurological Disorders and Stroke","grant_id":"K01NS116224","title":null},{"funder_name":"National Institute of Neurological Disorders and Stroke","grant_id":"R01NS124799","title":null},{"funder_name":"National Institute of Neurological Disorders and Stroke","grant_id":"K99NS133476","title":null},{"funder_name":"NINDS NIH HHS","grant_id":"R01 NS119268","title":null},{"funder_name":"National Institutes of Health","grant_id":"3R01NS124799-03S1","title":"Refining Oxytocin Therapy for Pain: Context is Key"},{"funder_name":"National Institutes of Health","grant_id":"5K01NS116224-03","title":"A new mechanistic and technological framework for uncovering the spinal cord neural systems important for functional recovery after injury"},{"funder_name":"National Institutes of Health","grant_id":"3R01NS119268-04S2","title":"Hannah's Diversity Supplement grant"},{"funder_name":"Whitehall Foundation","grant_id":"","title":null},{"funder_name":"New Jersey Commission on Spinal Cord Research","grant_id":"","title":null},{"funder_name":"Craig H. Neilsen Foundation","grant_id":"","title":null},{"funder_name":"PEW Charitable Trusts","grant_id":"","title":null}],"total_grants":12,"fwci":2.9688,"citation_percentile":0.90673925,"influential_citations":0,"citation_trend":[{"year":2025,"count":1},{"year":2026,"count":4}],"oa_status":"hybrid","license":"cc-by-nc","oa_locations":[{"url":"https://doi.org/10.1016/j.jneumeth.2025.110495","host_type":"journal"},{"url":"https://doi.org/10.1016/j.jneumeth.2025.110495","host_type":"HYBRID"},{"url":"https://doi.org/10.1016/j.jneumeth.2025.110495","host_type":"publisher"},{"url":"https://api.elsevier.com/content/article/PII:S0165027025001360?httpAccept=text/xml","host_type":"publisher"},{"url":"https://api.elsevier.com/content/article/PII:S0165027025001360?httpAccept=text/plain","host_type":"publisher"},{"url":"https://pubmed.ncbi.nlm.nih.gov/40436321","host_type":"repository"},{"url":"https://doi.org/10.1101/2024.07.28.605489","host_type":""},{"url":"https://pubmed.ncbi.nlm.nih.gov/39131312","host_type":""},{"url":"http://dx.doi.org/10.1101/2024.07.28.605489","host_type":""}],"fields_of_study":["Zebrafish Biomedical Research Applications","Photoreceptor and optogenetics research","Neurobiology and Insect Physiology Research","Medicine","Biology","05 social sciences","0501 psychology and cognitive sciences","Animals","Optogenetics","Mice","Locomotion","Male","Hindlimb","Mice, Inbred C57BL","TRPV Cation Channels","Channelrhodopsins","Biomechanical Phenomena","Mice, Transgenic","Sensory Receptor Cells","Spinal Cord","Behavior, Animal"],"mesh_terms":["Channelrhodopsins","Animals","Behavior, Animal","Biomechanical Phenomena","Hindlimb","Locomotion","Male","Mice, Inbred C57BL","Mice, Transgenic","Sensory Receptor Cells","Spinal Cord","TRPV Cation Channels","Mice","Optogenetics"],"keywords":["Optogenetics","Central pattern generator","Neuroscience","Biological neural network","Sensory system","Context (archaeology)","Channelrhodopsin","Computer science","Swing","Stimulation","Psychology","Rhythm","Biology","Engineering","Medicine","Locomotion","Pose Estimation","Near Real-time","State Dependent Behaviors","Male","Sensory Receptor Cells","Behavior, Animal","TRPV Cation Channels","Mice, Transgenic","Article","Hindlimb","Biomechanical Phenomena","Mice, Inbred C57BL","Mice","Channelrhodopsins","Spinal Cord","Animals"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-09T12:58:22.138459Z","pmid":null,"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":[]}