{"id":1384,"date":"2021-10-18T11:40:38","date_gmt":"2021-10-18T11:40:38","guid":{"rendered":"https:\/\/www.ebi.ac.uk\/training\/materials\/microscopy-image-analysis-materials\/programme\/day-5-3\/"},"modified":"2022-01-26T11:05:12","modified_gmt":"2022-01-26T11:05:12","slug":"cellprofiler","status":"publish","type":"page","link":"https:\/\/www.ebi.ac.uk\/training\/materials\/microscopy-image-analysis-materials\/image-analysis-tools\/cellprofiler\/","title":{"rendered":"Cell profiler"},"content":{"rendered":"\n<p class=\"wp-block-paragraph\"><strong>Trainer:<\/strong>&nbsp;<a href=\"https:\/\/www.ebi.ac.uk\/training\/materials\/microscopy-image-analysis-materials\/trainer-biographies\/\">Beth Cimini<\/a><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Overview:<\/strong>&nbsp;<a href=\"https:\/\/cellprofiler.org\/\" target=\"_blank\" rel=\"noreferrer noopener\">CellProfiler<\/a> is an open source image analysis tool allowing users to create a reproducible workflow that can be scaled to a single image or &gt;1 million images. This session will cover how to tune object segmentations in CellProfiler based on principles of computer vision, how to use CellProfiler to create large measurement suites, and how to set up CellProfiler to run on large sets of images.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Learning outcomes<\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">By the end of this session you will be able to:<\/p>\n\n\n\n<ul class=\"wp-block-list\"><li>Explore the application of CellProfiler<\/li><li>Identify the functionalities of the CellProfiler software<\/li><\/ul>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Materials:<\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\"><li><a rel=\"noreferrer noopener\" href=\"https:\/\/drive.google.com\/file\/d\/1nADxINpBZKkZMHpyAiGH9V_QZqoxuCZ1\/view?usp=sharing\" target=\"_blank\">Presentation slides<\/a><\/li><li><a rel=\"noreferrer noopener\" href=\"https:\/\/cellprofiler.org\/\" target=\"_blank\">Web page<\/a><\/li><\/ul>\n\n\n\n<h2 class=\"wp-block-heading\">CellProfiler &#8211; Practical<\/h2>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Trainer:<\/strong>&nbsp;CellProfiler team<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Overview:<\/strong>&nbsp;For this exercise, find subset of the data from idr0036 (<a rel=\"noreferrer noopener\" href=\"https:\/\/idr.openmicroscopy.org\/webclient\/?show=screen-1952\" target=\"_blank\">https:\/\/idr.openmicroscopy.org\/webclient\/?show=screen-1952<\/a>) and apply CellProfiler for analysis. You will gain experience tuning a pipeline that can cope with not only different cell phenotypes but also images of empty wells, blurry wells, debris, and other real-world potential screen confounders.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Materials:<\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\"><li><a href=\"https:\/\/cellprofiler.org\/\" target=\"_blank\" rel=\"noreferrer noopener\">CellProfiler<\/a><\/li><li><a rel=\"noreferrer noopener\" href=\"https:\/\/idr.openmicroscopy.org\/webclient\/?show=screen-1952\" target=\"_blank\">idr0036<\/a> &#8211; Public data for images<\/li><li><a rel=\"noreferrer noopener\" href=\"https:\/\/github.com\/CellProfiler\/tutorials\/tree\/master\/AdvancedSegmentation\" target=\"_blank\">GitHub version of the data<\/a> &#8211; Find useful tutorials and pipeline at this GitHub page.<\/li><\/ul>\n\n\n\n<p class=\"wp-block-paragraph\"><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Trainer:&nbsp;Beth Cimini Overview:&nbsp;CellProfiler is an open source image analysis tool allowing users to create a reproducible workflow that can be scaled to a single image or &gt;1 million images. This session will cover how to tune object segmentations in CellProfiler based on principles of computer vision, how to use CellProfiler to create large measurement suites,&#8230;<\/p>\n","protected":false},"author":10,"featured_media":0,"parent":1678,"menu_order":1,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-1384","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/microscopy-image-analysis-materials\/wp-json\/wp\/v2\/pages\/1384","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/microscopy-image-analysis-materials\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/microscopy-image-analysis-materials\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/microscopy-image-analysis-materials\/wp-json\/wp\/v2\/users\/10"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/microscopy-image-analysis-materials\/wp-json\/wp\/v2\/comments?post=1384"}],"version-history":[{"count":11,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/microscopy-image-analysis-materials\/wp-json\/wp\/v2\/pages\/1384\/revisions"}],"predecessor-version":[{"id":1906,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/microscopy-image-analysis-materials\/wp-json\/wp\/v2\/pages\/1384\/revisions\/1906"}],"up":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/microscopy-image-analysis-materials\/wp-json\/wp\/v2\/pages\/1678"}],"wp:attachment":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/microscopy-image-analysis-materials\/wp-json\/wp\/v2\/media?parent=1384"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}