{"id":49535478,"url":"https://github.com/jiumao2/autocurationkilosort","last_synced_at":"2026-05-02T10:03:36.738Z","repository":{"id":284742023,"uuid":"898500378","full_name":"jiumao2/AutoCurationKilosort","owner":"jiumao2","description":"Automated Curation for Kilosort Output","archived":false,"fork":false,"pushed_at":"2026-03-04T14:09:08.000Z","size":2156,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2026-03-04T21:33:04.285Z","etag":null,"topics":["kilos","neuro","spike-sorting"],"latest_commit_sha":null,"homepage":"https://github.com/jiumao2/AutoCurationKilosort","language":"MATLAB","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/jiumao2.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2024-12-04T14:04:14.000Z","updated_at":"2026-03-04T14:09:14.000Z","dependencies_parsed_at":null,"dependency_job_id":"ba6cd8d2-b3dd-4ca2-be35-823d91bee397","html_url":"https://github.com/jiumao2/AutoCurationKilosort","commit_stats":null,"previous_names":["jiumao2/autocurationkilosort"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/jiumao2/AutoCurationKilosort","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jiumao2%2FAutoCurationKilosort","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jiumao2%2FAutoCurationKilosort/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jiumao2%2FAutoCurationKilosort/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jiumao2%2FAutoCurationKilosort/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/jiumao2","download_url":"https://codeload.github.com/jiumao2/AutoCurationKilosort/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jiumao2%2FAutoCurationKilosort/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":32530178,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-02T01:12:54.858Z","status":"online","status_checked_at":"2026-05-02T02:00:05.923Z","response_time":132,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["kilos","neuro","spike-sorting"],"created_at":"2026-05-02T10:03:25.169Z","updated_at":"2026-05-02T10:03:36.724Z","avatar_url":"https://github.com/jiumao2.png","language":"MATLAB","funding_links":[],"categories":[],"sub_categories":[],"readme":"# AutoCurationKilosort: Automated Curation for Kilosort Output\n\n[![View AutoCurationKilosort on GitHub](https://img.shields.io/badge/GitHub-AutoCurationKilosort-blue.svg)](https://github.com/jiumao2/AutoCurationKilosort)\n\n**AutoCurationKilosort** is a MATLAB-based pipeline designed to streamline and automate the curation of Kilosort outputs. By minimizing manual intervention while maintaining strict quality control, this tool helps researchers process large-scale electrophysiology datasets with greater speed, accuracy, and reproducibility.\n\n## 💡 Why Use AutoCurationKilosort?\n\nManual spike sorting curation is often laborious, error-prone, and inconsistent. This tool addresses these bottlenecks by offering:\n- **Time Efficiency:** Automatically discards obvious noise units, saving you from wasting time on unviable data.\n- **Reduced Fatigue:** Eliminates the need to manually review thousands of units once you have a clear understanding of your dataset.\n- **Automated Refinement:** Cleans up unit waveforms by removing large noise artifacts without requiring manual intervention.\n- **Objective Standardization:** Replaces inconsistent manual labeling with objective, metric-driven unit classification ('good' vs. 'mua').\n\n## ⚙️ The Pipeline\n\nThe tool processes your Kilosort output through a sequential, automated pipeline:\n\n1. **Noise Filtering:** Removes clearly bad units based on predefined Signal-to-Noise Ratio (SNR) thresholds.\n2. **Outlier Rejection:** Identifies and removes outliers within each cluster in the Principal Component (PC) feature space.\n3. **Split \u0026 Merge Detection:** Highlights potential splits and merges, allowing for either fully automatic or manual decision-making.\n4. **Metric Computation:** Calculates standardized quality metrics for each remaining unit.\n5. **Automated Labeling:** Classifies units as `'good'` or `'mua'` (multi-unit activity) based on the computed quality metrics.\n6. **Waveform Alignment:** Centers the troughs of the waveforms to the precise spike times for accurate visualization and downstream analysis.\n\n## 🚀 Getting Started\n\n### 1. Installation\nAdd the repository path to your MATLAB environment:\n```matlab\naddpath(genpath('path_to_AutoCurationKilosort'))\n```\n\n### 2. Configure Settings  \nEdit the settings.json file to set your specific curation parameters.\n\n### 3. Run the Curation\nCopy `AutoCurationKilosort.m` to your data folder. Edit the installation paths in the script to match your local setup:\n\n```matlab\nfolder_data = './catgt_Exp_g0';\nsetting_filenames = 'path_to_AutoCurationKilosort/settings.json';\n```\n\nFinally, run the script `AutoCurationKilosort.m` in MATLAB.\n\n## 📖 Documentation\nSee [Documentation.md](Documentation.md) for details on the pipeline algorithms and advanced configuration.\n\n## 📚 References for code\n\n* Siegle, J. H. et al. Survey of spiking in the mouse visual system reveals functional hierarchy. Nature 592, 86–92 (2021).\n* [Quality metrics](https://allensdk.readthedocs.io/en/latest/_static/examples/nb/ecephys_quality_metrics.html)\n* Sean Bone (2024). [JSON+C parsing for MATLAB](https://github.com/seanbone/matlab-json-c/releases/tag/v1.1), GitHub.\n* Algorithm AS 217 APPL. STATIST. (1985) Vol. 34. No.3 pg 322-325\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjiumao2%2Fautocurationkilosort","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjiumao2%2Fautocurationkilosort","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjiumao2%2Fautocurationkilosort/lists"}