{"id":60,"date":"2020-07-08T22:43:42","date_gmt":"2020-07-09T02:43:42","guid":{"rendered":"https:\/\/sites.temple.edu\/vahid\/?p=60"},"modified":"2020-07-08T22:43:43","modified_gmt":"2020-07-09T02:43:43","slug":"openslide-alternative-tifffile","status":"publish","type":"post","link":"https:\/\/sites.temple.edu\/vahid\/2020\/07\/08\/openslide-alternative-tifffile\/","title":{"rendered":"OpenSlide Alternative (tifffile)"},"content":{"rendered":"\n<p>I found the Python library tifffile can open SVS files.<\/p>\n\n\n\n<p>It can be installed from here<\/p>\n\n\n\n<p><a href=\"https:\/\/pypi.org\/project\/tifffile\/\">https:\/\/pypi.org\/project\/tifffile\/<\/a><\/p>\n\n\n\n<p>by running the command<\/p>\n\n\n\n<p>pip install tifffile<\/p>\n\n\n\n<p>as root.<\/p>\n\n\n\n<p>Also, it is necessary to install imagecodecs, too.<\/p>\n\n\n\n<p>pip install imagecodecs<\/p>\n\n\n\n<p>Then by simple command<\/p>\n\n\n\n<p>x = tifffile.imread(FILE_NAME, key=LEVEL_NUMBER)<\/p>\n\n\n\n<p>it reads the SVS file in specified level and return a Numpy array in x.<\/p>\n\n\n\n<p>Based on my experience it doesn&#8217;t read Alpha channel, which doesn&#8217;t seem important in our SVS dataset.<\/p>\n\n\n\n<p><\/p>\n","protected":false},"excerpt":{"rendered":"<p>I found the Python library tifffile can open SVS files. It can be installed from here https:\/\/pypi.org\/project\/tifffile\/ by running the command pip install tifffile as&#8230;<\/p>\n<div class=\"more-link-wrapper\"><a class=\"more-link\" href=\"https:\/\/sites.temple.edu\/vahid\/2020\/07\/08\/openslide-alternative-tifffile\/\">Continue reading<span class=\"screen-reader-text\">OpenSlide Alternative (tifffile)<\/span><\/a><\/div>\n","protected":false},"author":18759,"featured_media":0,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[14],"tags":[53,54,55,56,57],"class_list":["post-60","post","type-post","status-publish","format-standard","hentry","category-tools","tag-openslide","tag-svs","tag-tifffile","tag-whole-slide-image","tag-wsi","entry"],"_links":{"self":[{"href":"https:\/\/sites.temple.edu\/vahid\/wp-json\/wp\/v2\/posts\/60","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sites.temple.edu\/vahid\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/sites.temple.edu\/vahid\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/sites.temple.edu\/vahid\/wp-json\/wp\/v2\/users\/18759"}],"replies":[{"embeddable":true,"href":"https:\/\/sites.temple.edu\/vahid\/wp-json\/wp\/v2\/comments?post=60"}],"version-history":[{"count":0,"href":"https:\/\/sites.temple.edu\/vahid\/wp-json\/wp\/v2\/posts\/60\/revisions"}],"wp:attachment":[{"href":"https:\/\/sites.temple.edu\/vahid\/wp-json\/wp\/v2\/media?parent=60"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/sites.temple.edu\/vahid\/wp-json\/wp\/v2\/categories?post=60"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/sites.temple.edu\/vahid\/wp-json\/wp\/v2\/tags?post=60"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}