{"id":33009087,"url":"https://github.com/kwikteam/klusta","last_synced_at":"2026-01-22T00:38:56.298Z","repository":{"id":52652507,"uuid":"54110163","full_name":"kwikteam/klusta","owner":"kwikteam","description":"Automatic spike sorting up to 64 channels","archived":false,"fork":false,"pushed_at":"2021-04-22T08:01:37.000Z","size":161,"stargazers_count":53,"open_issues_count":55,"forks_count":41,"subscribers_count":14,"default_branch":"master","last_synced_at":"2025-09-28T09:04:38.863Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/kwikteam.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}},"created_at":"2016-03-17T10:42:25.000Z","updated_at":"2025-02-05T04:00:49.000Z","dependencies_parsed_at":"2022-08-21T13:10:44.248Z","dependency_job_id":null,"html_url":"https://github.com/kwikteam/klusta","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/kwikteam/klusta","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kwikteam%2Fklusta","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kwikteam%2Fklusta/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kwikteam%2Fklusta/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kwikteam%2Fklusta/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/kwikteam","download_url":"https://codeload.github.com/kwikteam/klusta/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kwikteam%2Fklusta/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28648460,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-21T21:29:11.980Z","status":"ssl_error","status_checked_at":"2026-01-21T21:24:31.872Z","response_time":86,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":[],"created_at":"2025-11-13T16:00:27.190Z","updated_at":"2026-01-22T00:38:56.294Z","avatar_url":"https://github.com/kwikteam.png","language":"Python","funding_links":[],"categories":["Domain-specific libraries"],"sub_categories":["Neuroscience"],"readme":"# Klusta: automatic spike sorting up to 64 channels\n\n[![Build Status](https://img.shields.io/travis/kwikteam/klusta.svg)](https://travis-ci.org/kwikteam/klusta)\n[![codecov.io](https://img.shields.io/codecov/c/github/kwikteam/klusta.svg)](http://codecov.io/github/kwikteam/klusta?branch=master)\n[![Documentation Status](https://readthedocs.org/projects/klusta/badge/?version=latest)](http://klusta.readthedocs.org/en/latest/)\n[![PyPI release](https://img.shields.io/pypi/v/klusta.svg)](https://pypi.python.org/pypi/klusta)\n[![GitHub release](https://img.shields.io/github/release/kwikteam/klusta.svg)](https://github.com/kwikteam/klusta/releases/latest)\n\n[**klusta**](https://github.com/kwikteam/klusta) is an open source package for automatic spike sorting of multielectrode neurophysiological recordings made with probes containing up to a few dozens of sites.\n\nWe are also working actively on more sophisticated algorithms that will scale to hundreds/thousands of channels. This work is being done within the [phy project](https://github.com/kwikteam/phy), which is still experimental at this point.\n\n## Overview\n\n**klusta** implements the following features:\n\n* **Kwik**: An HDF5-based file format that stores the results of a spike sorting session.\n* **Spike detection** (also known as SpikeDetekt): an algorithm designed for probes containing tens of channels, based on a flood-fill algorithm in the adjacency graph formed by the recording sites in the probe.\n* **Automatic clustering** (also known as Masked KlustaKwik): an automatic clustering algorithm designed for high-dimensional structured datasets.\n\n\n## GUI\n\nYou will need a GUI to visualize the spike sorting results.\n\nWe have developed two GUI programs with the same features:\n\n* **phy KwikGUI**: newer project, scales to hundreds/thousands of channels, still relatively experimental. **It will be automatically installed if you follow the install instructions below.**\n* **[KlustaViewa](https://github.com/klusta-team/klustaviewa)**: widely used, but older and a bit hard to install since it relies on very old dependencies.\n\nBoth GUIs work with the same **Kwik** format.\n\n\n## Quick install guide\n\nThe following instructions will install both **klusta** and the **phy KwikGUI**.\n\n1. Make sure that you have [**miniconda**](http://conda.pydata.org/miniconda.html) installed. You can choose the Python 3.5 64-bit version for your operating system (Linux, Windows, or OS X).\n2. [Download the environment file.](https://raw.githubusercontent.com/kwikteam/klusta/master/installer/environment.yml)\n3. Open a terminal (on Windows, `cmd`, not Powershell) in the directory where you saved the file and type:\n\n    ```bash\n    conda env create -n klusta -f environment.yml\n    ```\n\n4. **Done**! Now, to use klusta and the phy KwikGUI, enter the directory that contains your files and type:\n\n    ```bash\n    source activate klusta  # omit the `source` on Windows\n    klusta yourfile.prm  # spikesort your data with a PRM file\n    phy kwik-gui yourfile.kwik  # open the GUI\n    ```\n\n    See the documentation for more details.\n\n\n### Updating the software\n\nTo get the latest version of the software, open a terminal and type:\n\n```\nsource activate klusta  # omit the `source` on Windows\npip install klusta phy phycontrib --upgrade\n```\n\n\n## Technical details\n\n**klusta** is written in pure Python. The clustering code, written in Python and Cython, currently lives in [another repository](https://github.com/kwikteam/klustakwik2/).\n\n\n## Links\n\n* [Documentation](http://klusta.readthedocs.org/en/latest/) (work in progress)\n* [Paper in Nature Neuroscience (April 2016)](http://www.nature.com/neuro/journal/vaop/ncurrent/full/nn.4268.html)\n* [Mailing list](https://groups.google.com/forum/#!forum/klustaviewas)\n* [Sample data repository](http://phy.cortexlab.net/data/) (work in progress)\n\n\n## Credits\n\n**klusta** is developed by [Cyrille Rossant](http://cyrille.rossant.net), [Shabnam Kadir](https://iris.ucl.ac.uk/iris/browse/profile?upi=SKADI56), [Dan Goodman](http://thesamovar.net/), [Max Hunter](https://iris.ucl.ac.uk/iris/browse/profile?upi=MLDHU99), and [Kenneth Harris](https://iris.ucl.ac.uk/iris/browse/profile?upi=KDHAR02), in the [Cortexlab](https://www.ucl.ac.uk/cortexlab), University College London.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkwikteam%2Fklusta","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkwikteam%2Fklusta","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkwikteam%2Fklusta/lists"}