{"id":2989,"date":"2013-04-12T10:34:09","date_gmt":"2013-04-12T14:34:09","guid":{"rendered":"http:\/\/labrigger.com\/blog\/?p=2989"},"modified":"2013-04-20T13:31:12","modified_gmt":"2013-04-20T17:31:12","slug":"commoditizing-population-calcium-imaging-analysis","status":"publish","type":"post","link":"http:\/\/labrigger.com\/blog\/2013\/04\/12\/commoditizing-population-calcium-imaging-analysis\/","title":{"rendered":"Commoditizing population calcium imaging analysis"},"content":{"rendered":"<p align=\"center\"><img loading=\"lazy\" decoding=\"async\" src=\"http:\/\/labrigger.com\/blog\/wp-content\/uploads\/2013\/04\/tpp.png\" alt=\"tpp\" width=\"600\" height=\"274\" class=\"aligncenter size-full wp-image-2992\" srcset=\"http:\/\/labrigger.com\/blog\/wp-content\/uploads\/2013\/04\/tpp.png 600w, http:\/\/labrigger.com\/blog\/wp-content\/uploads\/2013\/04\/tpp-300x137.png 300w\" sizes=\"auto, (max-width: 600px) 100vw, 600px\" \/><\/p>\n<p align=\"center\"><img loading=\"lazy\" decoding=\"async\" src=\"http:\/\/labrigger.com\/blog\/wp-content\/uploads\/2013\/04\/s1.png\" alt=\"s1\" width=\"570\" height=\"539\" class=\"aligncenter size-full wp-image-2990\" srcset=\"http:\/\/labrigger.com\/blog\/wp-content\/uploads\/2013\/04\/s1.png 570w, http:\/\/labrigger.com\/blog\/wp-content\/uploads\/2013\/04\/s1-300x283.png 300w\" sizes=\"auto, (max-width: 570px) 100vw, 570px\" \/><\/p>\n<p><a href=\"http:\/\/uemweb.biomed.cas.cz\/tpp\/\">More open source software to check out.<\/a><\/p>\n<p>Two-Photon Processor and SeNeCA &#8211; A freely available software package to process data from two-photon calcium imaging at speeds down to several ms per frame.<br \/>\nJakub Tomek, Ondrej Novak, and Josef Syka<br \/>\n<a href=\"http:\/\/jn.physiology.org\/cgi\/content\/abstract\/jn.00087.2013v1?papetoc\">TJ Neurophysiol published 10 April 2013, 10.1152\/jn.00087.2013<\/a><\/p>\n<p>It&#8217;s notable in that it is an &#8220;all-in-one&#8221; package that&#8217;s freely available.<\/p>\n<p>The image processing to detect cells and draw ROIs seems to work pretty good, even with poor S:N. I&#8217;d like to see it operate on GCaMP images, since those are more challenging in some ways. Cells labeled with Oregon Green BAPTA-1 tend to exhibit spherical patterns of somatic fluorescence, but GCaMP, when it&#8217;s working well, does not brightly label the nucleus, so the shape of the ideal ROI is quite different. Plus, it&#8217;s nice to pick up dendrites and other features, not just somata.<\/p>\n<p>See also, <a href=\"http:\/\/optophysiology.org\">Vogelstein&#8217;s code for inferring action potentials in calcium imaging data<\/a>.<\/p>\n<p align=\"center\"><img loading=\"lazy\" decoding=\"async\" src=\"http:\/\/labrigger.com\/blog\/wp-content\/uploads\/2013\/04\/s2.png\" alt=\"s2\" width=\"511\" height=\"503\" class=\"aligncenter size-full wp-image-2991\" srcset=\"http:\/\/labrigger.com\/blog\/wp-content\/uploads\/2013\/04\/s2.png 511w, http:\/\/labrigger.com\/blog\/wp-content\/uploads\/2013\/04\/s2-300x295.png 300w\" sizes=\"auto, (max-width: 511px) 100vw, 511px\" \/><\/p>\n<p><em>Hat tip to Christian Wilms<\/em><br \/>\nEDIT: The code became available shortly after this post.<\/p>\n","protected":false},"excerpt":{"rendered":"<p align=\"center\">\n<p align=\"center\">\n<p><a href=\"http:\/\/uemweb.biomed.cas.cz\/tpp\/\">More open source software to check out.<\/a><\/p>\n<p>Two-Photon Processor and SeNeCA &#8211; A freely available&#8230;<\/p>\n<div class=\"read-more\"><a href=\"http:\/\/labrigger.com\/blog\/2013\/04\/12\/commoditizing-population-calcium-imaging-analysis\/\">Read More<\/a><\/div><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[7],"tags":[25,38,21,26,36],"class_list":["post-2989","post","type-post","status-publish","format-standard","hentry","category-software","tag-analysis","tag-calcium-imaging","tag-imaging","tag-matlab","tag-microscopy"],"_links":{"self":[{"href":"http:\/\/labrigger.com\/blog\/wp-json\/wp\/v2\/posts\/2989","targetHints":{"allow":["GET"]}}],"collection":[{"href":"http:\/\/labrigger.com\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/labrigger.com\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/labrigger.com\/blog\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/labrigger.com\/blog\/wp-json\/wp\/v2\/comments?post=2989"}],"version-history":[{"count":6,"href":"http:\/\/labrigger.com\/blog\/wp-json\/wp\/v2\/posts\/2989\/revisions"}],"predecessor-version":[{"id":3013,"href":"http:\/\/labrigger.com\/blog\/wp-json\/wp\/v2\/posts\/2989\/revisions\/3013"}],"wp:attachment":[{"href":"http:\/\/labrigger.com\/blog\/wp-json\/wp\/v2\/media?parent=2989"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/labrigger.com\/blog\/wp-json\/wp\/v2\/categories?post=2989"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/labrigger.com\/blog\/wp-json\/wp\/v2\/tags?post=2989"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}