{"id":779,"date":"2025-11-03T15:51:29","date_gmt":"2025-11-03T13:51:29","guid":{"rendered":"https:\/\/sites.uef.fi\/cell-and-tissue-imaging-unit\/?page_id=779"},"modified":"2025-11-11T14:36:05","modified_gmt":"2025-11-11T12:36:05","slug":"image-analysis","status":"publish","type":"page","link":"https:\/\/sites.uef.fi\/cell-and-tissue-imaging-unit\/image-analysis\/","title":{"rendered":"Image Analysis"},"content":{"rendered":"\n<figure class=\"wp-block-image alignwide size-full\"><img loading=\"lazy\" decoding=\"async\" width=\"796\" height=\"265\" src=\"https:\/\/sites.uef.fi\/cell-and-tissue-imaging-unit\/wp-content\/uploads\/sites\/168\/2025\/11\/Analysis-Header-1.png\" alt=\"\" class=\"wp-image-856\" srcset=\"https:\/\/sites.uef.fi\/cell-and-tissue-imaging-unit\/wp-content\/uploads\/sites\/168\/2025\/11\/Analysis-Header-1.png 796w, https:\/\/sites.uef.fi\/cell-and-tissue-imaging-unit\/wp-content\/uploads\/sites\/168\/2025\/11\/Analysis-Header-1-300x100.png 300w, https:\/\/sites.uef.fi\/cell-and-tissue-imaging-unit\/wp-content\/uploads\/sites\/168\/2025\/11\/Analysis-Header-1-768x256.png 768w\" sizes=\"auto, (max-width: 796px) 100vw, 796px\" \/><\/figure>\n\n\n\n<p><\/p>\n\n\n\n<h3 class=\"wp-block-heading\">Software Downloads<\/h3>\n\n\n\n<p><strong>ZEN Lite<\/strong> is available for download from:<\/p>\n\n\n\n<div class=\"links-block\">\n\n    \n    <ul class=\"link-list\">\n        \n            \n            <li class=\"link-list-item\">\n                <a href=\"https:\/\/www.zeiss.com\/microscopy\/en\/products\/software\/zeiss-zen-lite.html#getzenlite\" class=\"link-reset link hover-scale-down\">\n                    <svg\n        width=\"43\" height=\"25\"\n        viewBox=\"0 0 43 25\"\n        xmlns=\"http:\/\/www.w3.org\/2000\/svg\">\n    <path\n        d=\"M30.027 0 43 12.5 30.027 25 27 22.083 34.351 15H0v-5h34.351L27 2.917z\"\n        fill=\"currentColor\"\n        fill-rule=\"evenodd\"\/>\n<\/svg>                    <div>Zen-Lite<\/div>\n                <\/a>\n                <div class=\"link-info\">\n                                            <div class=\"link-info-type\">Fill out the form to get will get the link for installation via email<\/div>\n                                    <\/div>\n            <\/li>\n\n                <\/ul>\n<\/div>\n\n\n<p><strong>LAS X <\/strong>for Leica Thunder Imager 3D Tissue can be downloaded from:<\/p>\n\n\n\n<div class=\"links-block\">\n\n    \n    <ul class=\"link-list\">\n        \n            \n            <li class=\"link-list-item\">\n                <a href=\"https:\/\/www.leica-microsystems.com\/products\/microscope-software\/p\/leica-las-x-ls\/downloads\/\" class=\"link-reset link hover-scale-down\">\n                    <svg\n        width=\"43\" height=\"25\"\n        viewBox=\"0 0 43 25\"\n        xmlns=\"http:\/\/www.w3.org\/2000\/svg\">\n    <path\n        d=\"M30.027 0 43 12.5 30.027 25 27 22.083 34.351 15H0v-5h34.351L27 2.917z\"\n        fill=\"currentColor\"\n        fill-rule=\"evenodd\"\/>\n<\/svg>                    <div>LAS X<\/div>\n                <\/a>\n                <div class=\"link-info\">\n                                    <\/div>\n            <\/li>\n\n                <\/ul>\n<\/div>\n\n\n<p><strong>FIJI<\/strong> open source software for image analysis:<\/p>\n\n\n\n<div class=\"links-block\">\n\n    \n    <ul class=\"link-list\">\n        \n            \n            <li class=\"link-list-item\">\n                <a href=\"https:\/\/imagej.net\/software\/fiji\/downloads\" class=\"link-reset link hover-scale-down\">\n                    <svg\n        width=\"43\" height=\"25\"\n        viewBox=\"0 0 43 25\"\n        xmlns=\"http:\/\/www.w3.org\/2000\/svg\">\n    <path\n        d=\"M30.027 0 43 12.5 30.027 25 27 22.083 34.351 15H0v-5h34.351L27 2.917z\"\n        fill=\"currentColor\"\n        fill-rule=\"evenodd\"\/>\n<\/svg>                    <div>FIJI<\/div>\n                <\/a>\n                <div class=\"link-info\">\n                                    <\/div>\n            <\/li>\n\n                <\/ul>\n<\/div>\n\n\n<p>QuPath an open source software for histological sample analysis<\/p>\n\n\n\n<div class=\"links-block\">\n\n    \n    <ul class=\"link-list\">\n        \n            \n            <li class=\"link-list-item\">\n                <a href=\"https:\/\/qupath.github.io\/\" class=\"link-reset link hover-scale-down\">\n                    <svg\n        width=\"43\" height=\"25\"\n        viewBox=\"0 0 43 25\"\n        xmlns=\"http:\/\/www.w3.org\/2000\/svg\">\n    <path\n        d=\"M30.027 0 43 12.5 30.027 25 27 22.083 34.351 15H0v-5h34.351L27 2.917z\"\n        fill=\"currentColor\"\n        fill-rule=\"evenodd\"\/>\n<\/svg>                    <div>QuPath<\/div>\n                <\/a>\n                <div class=\"link-info\">\n                                    <\/div>\n            <\/li>\n\n                <\/ul>\n<\/div>\n\n\n<p><\/p>\n\n\n\n<figure class=\"wp-block-image alignwide size-full\"><img loading=\"lazy\" decoding=\"async\" width=\"462\" height=\"132\" src=\"https:\/\/sites.uef.fi\/cell-and-tissue-imaging-unit\/wp-content\/uploads\/sites\/168\/2025\/11\/Orientation.png\" alt=\"\" class=\"wp-image-793\" srcset=\"https:\/\/sites.uef.fi\/cell-and-tissue-imaging-unit\/wp-content\/uploads\/sites\/168\/2025\/11\/Orientation.png 462w, https:\/\/sites.uef.fi\/cell-and-tissue-imaging-unit\/wp-content\/uploads\/sites\/168\/2025\/11\/Orientation-300x86.png 300w\" sizes=\"auto, (max-width: 462px) 100vw, 462px\" \/><\/figure>\n\n\n\n<h2 class=\"wp-block-heading\">Analysis resources<\/h2>\n\n\n\n<h5 class=\"wp-block-heading\">Fiji scripts<\/h5>\n\n\n\n<p>Macro for extracting single tif files out of the lif project:<\/p>\n\n\n\n<p><a href=\"https:\/\/github.com\/HGrobe\/CTIU_Kuopio\/blob\/main\/LIF_Extractor.ijm\">https:\/\/github.com\/HGrobe\/CTIU_Kuopio\/blob\/main\/LIF_Extractor.ijm<\/a><\/p>\n\n\n\n<div class=\"links-block\">\n\n    \n    <ul class=\"link-list\">\n            <\/ul>\n<\/div>\n\n\n<h5 class=\"wp-block-heading\">Reading material <\/h5>\n\n\n\n<ul class=\"wp-block-list\">\n<li>&#8220;Introduction to Bioimage Analysis&#8221; by Pete Bankhead<br><a href=\"https:\/\/bioimagebook.github.io\/index.html\">https:\/\/bioimagebook.github.io\/index.html<\/a><br><\/li>\n\n\n\n<li>&#8220;Bioimage Data Analysis Workflows&#8221; by Kota Miura<br><a href=\"https:\/\/link.springer.com\/book\/10.1007\/978-3-030-22386-1\">https:\/\/link.springer.com\/book\/10.1007\/978-3-030-22386-1<\/a><br><\/li>\n<\/ul>\n\n\n\n<p class=\"has-text-align-center\">If you need help with your analysis, don&#8217;t hesitate to reach out to us under: <br><strong>uef-ctiu@groups.uef.fi<\/strong><\/p>\n\n\n\n<p><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Software Downloads ZEN Lite is available for download from: LAS X for Leica Thunder Imager 3D Tissue can be downloaded from: FIJI open source software for image analysis: QuPath an open source software for histological sample analysis Analysis resources Fiji scripts Macro for extracting single tif files out of the lif project: https:\/\/github.com\/HGrobe\/CTIU_Kuopio\/blob\/main\/LIF_Extractor.ijm Reading material [&hellip;]<\/p>\n","protected":false},"author":1337,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":""},"class_list":["post-779","page","type-page","status-publish","hentry"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.1.1 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Image Analysis - Cell and Tissue Imaging Unit<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/sites.uef.fi\/cell-and-tissue-imaging-unit\/image-analysis\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" 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