{"id":16,"date":"2021-04-14T14:01:45","date_gmt":"2021-04-14T14:01:45","guid":{"rendered":"https:\/\/www.ebi.ac.uk\/training\/materials\/template\/day-5\/"},"modified":"2022-01-20T22:25:30","modified_gmt":"2022-01-20T22:25:30","slug":"bioimage-model-zoo","status":"publish","type":"page","link":"https:\/\/www.ebi.ac.uk\/training\/materials\/microscopy-image-analysis-materials\/image-analysis-tools\/bioimage-model-zoo\/","title":{"rendered":"Bioimage Model Zoo"},"content":{"rendered":"\n<h3 class=\"wp-block-heading\">BioImage Model Zoo &#8211; Lecture<\/h3>\n\n\n\n<p><strong>Trainer:<\/strong>\u00a0<a href=\"https:\/\/www.ebi.ac.uk\/training\/materials\/microscopy-image-analysis-materials\/trainer-biographies\/\">Anna Kreshuk<\/a><\/p>\n\n\n\n<p><strong>Lecture authors:<\/strong> <a href=\"https:\/\/www.ebi.ac.uk\/training\/materials\/microscopy-image-analysis-materials\/trainer-biographies\/\">Anna Kreshuk, Wei Ouyang, Esti Gomez De Mariscal<\/a> <\/p>\n\n\n\n<p><strong>Overview:<\/strong>&nbsp;This lecture will cover the <a href=\"https:\/\/bioimage.io\/#\/\" target=\"_blank\" rel=\"noreferrer noopener\">BioImage Model Zoo<\/a> &#8211; a community website for sharing neural networks pre-trained on bioimage analysis tasks. We will give the motivation behind the development of the zoo and demonstrate how it can be used together with ilastik, DeepImageJ and ImJoy softwares. We will look into several tasks, including image classification and segmentation, and show how one can create a shareable model and submit it to the website.<\/p>\n\n\n\n<p><strong>Learning outcomes<\/strong><\/p>\n\n\n\n<p>By the end of this session you will be able to:<\/p>\n\n\n\n<ul class=\"wp-block-list\"><li>Identify the main utilities of the BioImage Model Zoo portal<\/li><li>Perform basic interactions of the portal with ilastik, DeepImageJ and ImJoy softwares<\/li><\/ul>\n\n\n\n<p><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\/BioImage_Model_Zoo\/BioImageModelZoo-Kreshuk.pdf\" data-type=\"URL\" target=\"_blank\">Presentation slides Anna<\/a><\/li><li><a rel=\"noreferrer noopener\" href=\"https:\/\/slides.imjoy.io\/?slides=https:\/\/github.com\/oeway\/slides\/blob\/master\/2021\/bioimage-model-zoo-embl-training-2021.md\" target=\"_blank\">Presentation slides Wei<\/a><\/li><li><a rel=\"noreferrer noopener\" href=\"http:\/\/ftp.ebi.ac.uk\/pub\/training\/2021\/Microscopy_image_analysis_July2021\/BioImage_Model_Zoo\/BioImageModelZoo-Gomez_de_Mariscal.pdf\" target=\"_blank\">Presentation slides Estibalis<\/a><\/li><\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">BioImage Model Zoo &#8211; Practical<\/h3>\n\n\n\n<p><strong>Trainers:<\/strong>&nbsp;<a href=\"https:\/\/www.ebi.ac.uk\/training\/materials\/microscopy-image-analysis-materials\/trainer-biographies\/\">Anna Kreshuk, Dominik Kutrra, Wei Ouyang, Esti Gomez De Mariscal, Fynn Beuttenm\u00fcller<\/a><\/p>\n\n\n\n<p><strong>Overview:<\/strong>&nbsp;Follow the GitHub page for advanced bioimage analysis workflows, tools and datasets &#8211; <a rel=\"noreferrer noopener\" href=\"https:\/\/slides.imjoy.io\/?slides=https:\/\/github.com\/oeway\/slides\/blob\/master\/2021\/bioimage-model-zoo-embl-training-2021.md#\/17\" target=\"_blank\">Practical task<\/a><\/p>\n\n\n\n<p><\/p>\n","protected":false},"excerpt":{"rendered":"<p>BioImage Model Zoo &#8211; Lecture Trainer:\u00a0Anna Kreshuk Lecture authors: Anna Kreshuk, Wei Ouyang, Esti Gomez De Mariscal Overview:&nbsp;This lecture will cover the BioImage Model Zoo &#8211; a community website for sharing neural networks pre-trained on bioimage analysis tasks. We will give the motivation behind the development of the zoo and demonstrate how it can be&#8230;<\/p>\n","protected":false},"author":3,"featured_media":0,"parent":1678,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-16","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\/16","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\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/microscopy-image-analysis-materials\/wp-json\/wp\/v2\/comments?post=16"}],"version-history":[{"count":47,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/microscopy-image-analysis-materials\/wp-json\/wp\/v2\/pages\/16\/revisions"}],"predecessor-version":[{"id":1860,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/microscopy-image-analysis-materials\/wp-json\/wp\/v2\/pages\/16\/revisions\/1860"}],"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=16"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}