{"id":4183,"date":"2015-02-06T11:09:32","date_gmt":"2015-02-06T16:09:32","guid":{"rendered":"http:\/\/labrigger.com\/blog\/?p=4183"},"modified":"2015-02-06T11:09:32","modified_gmt":"2015-02-06T16:09:32","slug":"focusstack-and-stimserver-for-matlab","status":"publish","type":"post","link":"http:\/\/labrigger.com\/blog\/2015\/02\/06\/focusstack-and-stimserver-for-matlab\/","title":{"rendered":"FocusStack and StimServer for MATLAB"},"content":{"rendered":"<p align=\"center\"><img loading=\"lazy\" decoding=\"async\" src=\"http:\/\/labrigger.com\/blog\/wp-content\/uploads\/2015\/02\/ss1.jpg\" alt=\"ss1\" width=\"850\" height=\"291\" class=\"alignnone size-full wp-image-4184\" srcset=\"http:\/\/labrigger.com\/blog\/wp-content\/uploads\/2015\/02\/ss1.jpg 850w, http:\/\/labrigger.com\/blog\/wp-content\/uploads\/2015\/02\/ss1-300x103.jpg 300w\" sizes=\"auto, (max-width: 850px) 100vw, 850px\" \/><\/p>\n<p>Dylan Muir and Bjorn Kampa created some MATLAB code for two-photon calcium imaging experiments. First up is FocusStack, which provides a suite of analysis tools. Next up is StimServer, which coordinates visual stimulus generation and presentation. <a href=\"http:\/\/journal.frontiersin.org\/Journal\/10.3389\/fninf.2014.00085\/full\">The paper<\/a> is open access.<\/p>\n<p>In particular, Dylan&#8217;s MATLAB functions <a href=\"http:\/\/se.mathworks.com\/matlabcentral\/fileexchange\/29694-mappedtensor-class-memory-mapped-files\">MappedTensor<\/a> and <a href=\"http:\/\/www.mathworks.com\/matlabcentral\/fileexchange\/32025-read-tiff-stacks-into-matlab-fast--with-lazy-loading\">TIFFStack<\/a> are worth checking out. Both provide ways to access large files on disk without having to load everything into memory at the same time.<\/p>\n<p><a href=\"http:\/\/dylan-muir.com\/projects\/focusstack_stimserver\/\">More from Dylan&#8217;s web site.<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p align=\"center\">\n<p>Dylan Muir and Bjorn Kampa created some MATLAB code for two-photon calcium imaging experiments. First up is FocusStack, which provides a suite of analysis tools. Next up is StimServer, which coordinates visual stimulus generation and&#8230;<\/p>\n<div class=\"read-more\"><a href=\"http:\/\/labrigger.com\/blog\/2015\/02\/06\/focusstack-and-stimserver-for-matlab\/\">Read More<\/a><\/div><\/p>\n","protected":false},"author":1,"featured_media":4184,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[7],"tags":[25,38,26,47],"class_list":["post-4183","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-software","tag-analysis","tag-calcium-imaging","tag-matlab","tag-two-photon"],"_links":{"self":[{"href":"http:\/\/labrigger.com\/blog\/wp-json\/wp\/v2\/posts\/4183","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=4183"}],"version-history":[{"count":1,"href":"http:\/\/labrigger.com\/blog\/wp-json\/wp\/v2\/posts\/4183\/revisions"}],"predecessor-version":[{"id":4185,"href":"http:\/\/labrigger.com\/blog\/wp-json\/wp\/v2\/posts\/4183\/revisions\/4185"}],"wp:featuredmedia":[{"embeddable":true,"href":"http:\/\/labrigger.com\/blog\/wp-json\/wp\/v2\/media\/4184"}],"wp:attachment":[{"href":"http:\/\/labrigger.com\/blog\/wp-json\/wp\/v2\/media?parent=4183"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/labrigger.com\/blog\/wp-json\/wp\/v2\/categories?post=4183"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/labrigger.com\/blog\/wp-json\/wp\/v2\/tags?post=4183"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}