{"id":190,"date":"2024-11-15T15:13:59","date_gmt":"2024-11-15T14:13:59","guid":{"rendered":"https:\/\/www.ephyswiki.org\/?post_type=yada_wiki&#038;p=190"},"modified":"2024-11-16T09:59:26","modified_gmt":"2024-11-16T08:59:26","slug":"neuropixels-recording-pipelines","status":"publish","type":"yada_wiki","link":"https:\/\/www.ephyswiki.org\/?yada_wiki=neuropixels-recording-pipelines","title":{"rendered":"Neuropixels Recording Pipelines"},"content":{"rendered":"<p>For the acquisition of the data coming directly from the Neuropixels probe, there are two packages:<\/p>\n<ul>\n<li><a href=\"https:\/\/github.com\/billkarsh\/SpikeGLX\">SpikeGLX\u00a0<\/a><\/li>\n<li><a href=\"https:\/\/open-ephys.github.io\/gui-docs\/index.html\">Open Ephys GUI<\/a><\/li>\n<\/ul>\n<p>There are a number of pipelines available for the whole process of Neuropixels recording. Here is a non-exhaustive list.<\/p>\n<ul>\n<li>Acquipix at <a href=\"https:\/\/github.com\/Herseninstituut\/Acquipix\">https:\/\/github.com\/Herseninstituut\/Acquipix<\/a>. This is a Matlab based pipeline to run experiment, building on SpikeGLX. It incoorporates eye tracking, and the probe mapping to histology, using SHARP-track or <a href=\"https:\/\/github.com\/JorritMontijn\/UniversalProbeFinder\">Universal Probe Finder<\/a>. See also <a href=\"https:\/\/www.ephyswiki.org\/?yada_wiki=acquipix\">Acquipix page<\/a> on this wiki.<\/li>\n<li>Power Pixels pipeline at <a href=\"https:\/\/github.com\/NeuroNetMem\/PowerPixelsPipeline\">https:\/\/github.com\/NeuroNetMem\/PowerPixelsPipeline<\/a>. It is a primarily Python-based pipeline combining existing tools: <a href=\"https:\/\/github.com\/spikeinterface\">SpikeInterface<\/a>, <a href=\"https:\/\/github.com\/int-brain-lab\/ibllib\">ibllib<\/a>, <a href=\"https:\/\/github.com\/MouseLand\/Kilosort\">Kilosort<\/a>, <a href=\"https:\/\/github.com\/Julie-Fabre\/bombcell\">Bombcell<\/a> and <a href=\"https:\/\/github.com\/JorritMontijn\/UniversalProbeFinder\">Universal Probe Finder<\/a>.<\/li>\n<\/ul>\n<p>Feel free to comment on these pipelines or suggest others.<\/p>\n","protected":false},"author":5,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"open","template":"","meta":{"_bbp_topic_count":0,"_bbp_reply_count":0,"_bbp_total_topic_count":0,"_bbp_total_reply_count":0,"_bbp_voice_count":0,"_bbp_anonymous_reply_count":0,"_bbp_topic_count_hidden":0,"_bbp_reply_count_hidden":0,"_bbp_forum_subforum_count":0,"footnotes":""},"wiki_cats":[11,13,12],"wiki_tags":[],"class_list":["post-190","yada_wiki","type-yada_wiki","status-publish","hentry","wiki_cats-analysis","wiki_cats-experiments","wiki_cats-tips"],"_links":{"self":[{"href":"https:\/\/www.ephyswiki.org\/index.php?rest_route=\/wp\/v2\/yada_wiki\/190","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ephyswiki.org\/index.php?rest_route=\/wp\/v2\/yada_wiki"}],"about":[{"href":"https:\/\/www.ephyswiki.org\/index.php?rest_route=\/wp\/v2\/types\/yada_wiki"}],"author":[{"embeddable":true,"href":"https:\/\/www.ephyswiki.org\/index.php?rest_route=\/wp\/v2\/users\/5"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ephyswiki.org\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=190"}],"version-history":[{"count":4,"href":"https:\/\/www.ephyswiki.org\/index.php?rest_route=\/wp\/v2\/yada_wiki\/190\/revisions"}],"predecessor-version":[{"id":246,"href":"https:\/\/www.ephyswiki.org\/index.php?rest_route=\/wp\/v2\/yada_wiki\/190\/revisions\/246"}],"wp:attachment":[{"href":"https:\/\/www.ephyswiki.org\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=190"}],"wp:term":[{"taxonomy":"wiki_cats","embeddable":true,"href":"https:\/\/www.ephyswiki.org\/index.php?rest_route=%2Fwp%2Fv2%2Fwiki_cats&post=190"},{"taxonomy":"wiki_tags","embeddable":true,"href":"https:\/\/www.ephyswiki.org\/index.php?rest_route=%2Fwp%2Fv2%2Fwiki_tags&post=190"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}