{"id":1864,"date":"2022-01-20T22:41:18","date_gmt":"2022-01-20T22:41:18","guid":{"rendered":"https:\/\/www.ebi.ac.uk\/training\/materials\/microscopy-image-analysis-materials\/technical-help-sheet\/"},"modified":"2022-01-25T12:05:04","modified_gmt":"2022-01-25T12:05:04","slug":"technical-help-sheet","status":"publish","type":"page","link":"https:\/\/www.ebi.ac.uk\/training\/materials\/microscopy-image-analysis-materials\/technical-help-sheet\/","title":{"rendered":"Technical help sheet"},"content":{"rendered":"\n<p class=\"wp-block-paragraph\">This course requires basic programming skills in Python. If you would like to refresh your Python skills for using these materials, please have a look at the following tutorial:<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><a href=\"https:\/\/www.w3schools.com\/python\/\">https:\/\/www.w3schools.com\/python\/<\/a><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">A few important links for practical materials used in this course:<\/p>\n\n\n\n<ul class=\"wp-block-list\"><li>Build and run a&nbsp;<a rel=\"noreferrer noopener\" href=\"https:\/\/snakemake.readthedocs.io\/en\/stable\/tutorial\/basics.html\" target=\"_blank\">Snakemake pipeline<\/a> &#8211; useful in preparing data for machine learning <\/li><li>GitHub link for BioStudies notebooks &#8211; <a rel=\"noreferrer noopener\" href=\"https:\/\/github.com\/EBIBioStudies\/biostudies-notebooks\" target=\"_blank\">Jupyter notebooks for loading and displaying data from BioStudies<\/a><\/li><li><a rel=\"noreferrer noopener\" href=\"https:\/\/github.com\/IDR\/idr-notebooks\" target=\"_blank\">Notebooks for the second part of the practical<\/a>&nbsp;\u2013 to demonstrate how to access the images and metadata from the&nbsp;<a rel=\"noreferrer noopener\" href=\"https:\/\/idr.openmicroscopy.org\/\" target=\"_blank\">Image Data Resource (IDR)<\/a>, including features and all descriptive tags<\/li><li><a rel=\"noreferrer noopener\" href=\"https:\/\/omero-guides.readthedocs.io\/en\/latest\/\" target=\"_blank\">Omero-guides containing other notebooks used in the practical<\/a>&nbsp;\u2013 The OMERO guide offers step-by-step instructions on how to use components of the OMERO platform.<\/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#\/17\" target=\"_blank\">GitHub page<\/a> for advanced bioimage analysis workflows, tools and datasets<\/li><li> <a rel=\"noreferrer noopener\" href=\"https:\/\/github.com\/CellProfiler\/tutorials\/tree\/master\/AdvancedSegmentation\" target=\"_blank\">GitHub page for CellProfiler practicals<\/a> &#8211; Find useful tutorials and pipelines<\/li><\/ul>\n","protected":false},"excerpt":{"rendered":"<p>This course requires basic programming skills in Python. If you would like to refresh your Python skills for using these materials, please have a look at the following tutorial: https:\/\/www.w3schools.com\/python\/ A few important links for practical materials used in this course: Build and run a&nbsp;Snakemake pipeline &#8211; useful in preparing data for machine learning GitHub&#8230;<\/p>\n","protected":false},"author":4,"featured_media":0,"parent":0,"menu_order":6,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-1864","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\/1864","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\/4"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/microscopy-image-analysis-materials\/wp-json\/wp\/v2\/comments?post=1864"}],"version-history":[{"count":8,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/microscopy-image-analysis-materials\/wp-json\/wp\/v2\/pages\/1864\/revisions"}],"predecessor-version":[{"id":1896,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/microscopy-image-analysis-materials\/wp-json\/wp\/v2\/pages\/1864\/revisions\/1896"}],"wp:attachment":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/microscopy-image-analysis-materials\/wp-json\/wp\/v2\/media?parent=1864"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}