{"id":1432,"date":"2021-10-18T12:08:55","date_gmt":"2021-10-18T12:08:55","guid":{"rendered":"https:\/\/www.ebi.ac.uk\/training\/materials\/microscopy-image-analysis-materials\/programme\/day-1-2-2\/"},"modified":"2022-01-20T10:09:39","modified_gmt":"2022-01-20T10:09:39","slug":"segmentation","status":"publish","type":"page","link":"https:\/\/www.ebi.ac.uk\/training\/materials\/microscopy-image-analysis-materials\/introduction-to-image-analysis\/segmentation\/","title":{"rendered":"Segmentation with StarDist and SplineDist"},"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\/\">Martin Weigert, Soham Mandal, Virginie Uhlmann<\/a><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Overview:<\/strong>&nbsp;Segmentation is the process of partitioning a digital image into multiple image objects. This session will go over what segmentation is and introduce two methods: <a rel=\"noreferrer noopener\" href=\"https:\/\/github.com\/uhlmanngroup\/splinedist\" target=\"_blank\">SplineDist<\/a>, a machine learning framework for automated cell segmentation with spline curves, and StarDist, cell nuclei localisation via star-convex polygons.<\/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>Describe what segmentation is, it&#8217;s main challenges and outputs<\/li><li>Name main algorithms for segmentation<\/li><li>Give examples of ML applied to cell segmentation through spline curves and star-convex polygons<\/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=\"http:\/\/ftp.ebi.ac.uk\/pub\/training\/2021\/Microscopy_image_analysis_July2021\/Segmentation_with_StarDist_and_SplineDist-Weigert_Mandal_Ulman.pdf\" target=\"_blank\">Link to presentation slides<\/a><\/li><\/ul>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Suggested reading articles<\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\"><li><a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2020.10.27.357640v1\" target=\"_blank\" rel=\"noreferrer noopener\">SplineDist: Automated Cell Segmentation with Spline Curves<\/a><\/li><li><a href=\"https:\/\/arxiv.org\/abs\/1806.03535\" target=\"_blank\" rel=\"noreferrer noopener\">Cell Detection with Star-convex Polygons<\/a><\/li><\/ul>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Data repositories for SplineDist and StarDist<\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\" id=\"block-107d6e82-ea2a-4a57-8456-8b2d6e3d433e\"><li><a rel=\"noreferrer noopener\" href=\"https:\/\/github.com\/uhlmanngroup\/splinedist\" target=\"_blank\">SplineDist repository<\/a><\/li><li><a rel=\"noreferrer noopener\" href=\"https:\/\/github.com\/stardist\/stardist\" target=\"_blank\">StarDist repository<\/a><\/li><\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Trainer:&nbsp;Martin Weigert, Soham Mandal, Virginie Uhlmann Overview:&nbsp;Segmentation is the process of partitioning a digital image into multiple image objects. This session will go over what segmentation is and introduce two methods: SplineDist, a machine learning framework for automated cell segmentation with spline curves, and StarDist, cell nuclei localisation via star-convex polygons. Learning outcomes By the&#8230;<\/p>\n","protected":false},"author":10,"featured_media":0,"parent":1700,"menu_order":1,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-1432","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\/1432","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=1432"}],"version-history":[{"count":10,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/microscopy-image-analysis-materials\/wp-json\/wp\/v2\/pages\/1432\/revisions"}],"predecessor-version":[{"id":1784,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/microscopy-image-analysis-materials\/wp-json\/wp\/v2\/pages\/1432\/revisions\/1784"}],"up":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/microscopy-image-analysis-materials\/wp-json\/wp\/v2\/pages\/1700"}],"wp:attachment":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/microscopy-image-analysis-materials\/wp-json\/wp\/v2\/media?parent=1432"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}