{"id":638,"date":"2021-11-05T07:00:47","date_gmt":"2021-11-05T07:00:47","guid":{"rendered":"https:\/\/admin.acceleratingscience.com\/atomic-resolution\/2021\/11\/05\/correlative-microscopy-amira-software-understanding-cancer\/"},"modified":"2022-12-06T18:15:32","modified_gmt":"2022-12-06T18:15:32","slug":"correlative-microscopy-amira-software-understanding-cancer","status":"publish","type":"post","link":"https:\/\/www.thermofisher.com\/blog\/atomic-resolution\/correlative-microscopy-amira-software-understanding-cancer\/","title":{"rendered":"Correlative Microscopy: Using Amira Software to Understand the Spread of Cancer"},"content":{"rendered":"<p><span class=\"embed-youtube\" style=\"text-align:center; display: block;\"><iframe loading=\"lazy\" class=\"youtube-player\" width=\"760\" height=\"428\" src=\"https:\/\/www.youtube.com\/embed\/QMdNH3WcvJo?version=3&#038;rel=1&#038;showsearch=0&#038;showinfo=1&#038;iv_load_policy=1&#038;fs=1&#038;hl=en-US&#038;autohide=2&#038;wmode=transparent\" allowfullscreen=\"true\" style=\"border:0;\" sandbox=\"allow-scripts allow-same-origin allow-popups allow-presentation allow-popups-to-escape-sandbox\"><\/iframe><\/span><\/p>\n<h2 style=\"font-size: 100%\"><strong>What is correlative microscopy?<\/strong><\/h2>\n<p>One of the major challenges for scientists is correlative microscopy \u2014 collecting and integrating data from multiple imaging techniques to better explore their samples.<\/p>\n<p>How do you integrate this information? How do you make sure to precisely track regions of interest when moving between two imaging modalities using different resolutions?<\/p>\n<p>This was the issue facing Dr. Matthia Karreman when she was a post-doctoral fellow at the Neurology Clinic and National Center for Tumor Diseases at the University of Heidelberg, Germany. Working in collaboration with the German Consortium for Translational Cancer Research and the German Cancer Research Center, Karreman and her team were studying how brain cancer cells spread in mice\u2014specifically, how these tumor cells get carried out of blood vessels and into the brain.<\/p>\n<h2 style=\"font-size: 100%\"><strong>Tracking regions of interest with in vivo imaging<\/strong><\/h2>\n<p>To accomplish this goal, the research team captured in vivo images of brain tumor cells in live mice through small windows implanted into the skulls of their brains. Using intravital microscopy, the researchers were able to observe how the cancer progressed, but the resolution wasn\u2019t high enough to <a href=\"https:\/\/doi.org\/10.1242\/jcs.181842\">observe events occurring at the subcellular level or how the tumor cells interacted with the surrounding tissue<\/a>.<\/p>\n<p>For this higher-resolution analysis, the team needed to examine the mice cancer cells using 3D electron microscopy. Yet finding the same cell with an electron microscope that had already been captured using in vivo imaging was a difficult process. \u201cWe needed to find one cell in the mouse brain and somehow narrow down the volume that we were looking at and find the proper position inside the sample,\u201d says Karreman.<\/p>\n<h2 style=\"font-size: 100%\"><strong>Overlaying datasets using Amira Software<\/strong><\/h2>\n<p>To bridge these two imaging modalities, Karreman and her team used X-ray microCT imaging to capture an X-ray scan of the sample. The team then used <a href=\"https:\/\/ter.li\/xt8anr\">Amira Software<\/a> to build 3D models of the in vivo images showing the tumor cell and blood vessels with the X-ray images showing the blood vessels\u2014correlating this data to find the common points in both datasets.<\/p>\n<p>\u201cAmira Software is able to overlay the in vivo dataset right on top of the X-ray dataset so I can know exactly where the tumor cell is,\u201d Karreman says. \u201cThat allows me to very carefully remove all the brain material that I\u2019m not interested in so I can expose the tumor cell for 3D electron microscopy.\u201d<\/p>\n<h2 style=\"font-size: 100%\"><strong>A powerful correlative microscopy solution<\/strong><\/h2>\n<p>By correlating this data, <a href=\"https:\/\/admin.acceleratingscience.com\/microscopy\/amira-software-core-facility-3d-visualization-and-analysis\/\">Amira Software solved a problem that wasn\u2019t possible using other solutions<\/a>. \u201cI had a dataset from in vivo imaging and needed some way to manipulate and move it to a dataset coming from the X-ray machine,\u201d Karreman says. \u201cThe only software able to do that was Amira.\u201d<\/p>\n<p>Karreman believes the correlative microscopy workflow her team developed will have broad implications for other fields of biological research. Using the correlative microscopy features of Amira Software, scientists will easily be able to combine data from different imaging techniques. \u201cI recommend Amira because it\u2019s very powerful software that lets you do a lot with your images,\u201d Karreman says. \u201cIt has certain unique tools that are not offered by other image process tools.\u201d<\/p>\n<p>To learn more, see <a href=\"https:\/\/doi.org\/10.1242\/jcs.181842\">Karreman\u2019s correlative microscopy paper in the <em>Journal of Cell Science<\/em><\/a>. Also, visit our <a href=\"https:\/\/ter.li\/xt8anr\">Amira Software<\/a> webpage.<\/p>\n<p>\/\/<\/p>\n<p><em>Victoria Limosino is a marketing program manager at Thermo Fischer Scientific.<\/em><\/p>\n","protected":false},"excerpt":{"rendered":"<p>What is correlative microscopy? One of the major challenges for scientists is correlative microscopy \u2014 collecting and integrating data from multiple imaging techniques to better explore their samples. How do you integrate this information? How do you make sure to precisely track regions of interest when moving between two imaging modalities using different resolutions? This<\/p>\n","protected":false},"author":1515,"featured_media":639,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"_kad_blocks_custom_css":"","_kad_blocks_head_custom_js":"","_kad_blocks_body_custom_js":"","_kad_blocks_footer_custom_js":"","_monsterinsights_skip_tracking":false,"_genesis_hide_title":false,"_genesis_hide_breadcrumbs":false,"_genesis_hide_singular_image":false,"_genesis_hide_footer_widgets":false,"_genesis_custom_body_class":"","_genesis_custom_post_class":"","_genesis_layout":"","_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_feature_clip_id":0,"_jetpack_memberships_contains_paid_content":false,"footnotes":"","jetpack_post_was_ever_published":false},"categories":[24,51,33,185],"tags":[188,15,16,117,17],"division":[],"class_list":{"0":"post-638","1":"post","2":"type-post","3":"status-publish","4":"format-standard","5":"has-post-thumbnail","7":"category-cryo-electron-microscopy-cryo-em","8":"category-customer-spotlights","9":"category-general","10":"category-software","11":"tag-amira-software","12":"tag-cryo-electron-microscopy","13":"tag-cryo-em","14":"tag-drug-discovery","15":"tag-electron-microscopy","16":"entry"},"_selected_authors":"","_selected_reviewers":"","acf":[],"yoast_head":"<!-- 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The increasing\u2026","rel":"","context":"In &quot;Cryo EM Drug Discovery&quot;","block_context":{"text":"Cryo EM Drug Discovery","link":"https:\/\/admin.acceleratingscience.com\/atomic-resolution\/cryo-electron-microscopy-cryo-em\/cryo-em-drug-discovery\/"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/atomic-resolution\/wp-content\/uploads\/sites\/22\/2025\/12\/blog-8-banner-1920x450-1.jpg?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/atomic-resolution\/wp-content\/uploads\/sites\/22\/2025\/12\/blog-8-banner-1920x450-1.jpg?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/atomic-resolution\/wp-content\/uploads\/sites\/22\/2025\/12\/blog-8-banner-1920x450-1.jpg?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/atomic-resolution\/wp-content\/uploads\/sites\/22\/2025\/12\/blog-8-banner-1920x450-1.jpg?resize=700%2C400&ssl=1 2x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/atomic-resolution\/wp-content\/uploads\/sites\/22\/2025\/12\/blog-8-banner-1920x450-1.jpg?resize=1050%2C600&ssl=1 3x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/atomic-resolution\/wp-content\/uploads\/sites\/22\/2025\/12\/blog-8-banner-1920x450-1.jpg?resize=1400%2C800&ssl=1 4x"},"classes":[]},{"id":2016,"url":"https:\/\/www.thermofisher.com\/blog\/atomic-resolution\/how-artificial-intelligence-ai-improves-image-analysis-workflows-in-life-sciences\/","url_meta":{"origin":638,"position":4},"title":"How artificial intelligence (AI) improves image analysis workflows in life sciences","author":"Vinay S","date":"June 2, 2026","format":false,"excerpt":"Image acquisition is not the end of the story\u2014it is the starting point. Once images are captured, researchers typically move into preprocessing to improve quality, then they perform visualization, segmentation, and quantitative analysis to extract meaningful measurements. The goal is simple: turn images into understanding. In practice, however, image analysis\u2026","rel":"","context":"In &quot;Amira Software&quot;","block_context":{"text":"Amira Software","link":"https:\/\/admin.acceleratingscience.com\/atomic-resolution\/cryo-electron-microscopy-cryo-em\/amira-software\/"},"img":{"alt_text":"How artificial intelligence (AI) improves image analysis workflows in life sciences","src":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/atomic-resolution\/wp-content\/uploads\/sites\/22\/2026\/06\/amira-ai-tools-blog-header-1920x450-1.png?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/atomic-resolution\/wp-content\/uploads\/sites\/22\/2026\/06\/amira-ai-tools-blog-header-1920x450-1.png?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/atomic-resolution\/wp-content\/uploads\/sites\/22\/2026\/06\/amira-ai-tools-blog-header-1920x450-1.png?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/atomic-resolution\/wp-content\/uploads\/sites\/22\/2026\/06\/amira-ai-tools-blog-header-1920x450-1.png?resize=700%2C400&ssl=1 2x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/atomic-resolution\/wp-content\/uploads\/sites\/22\/2026\/06\/amira-ai-tools-blog-header-1920x450-1.png?resize=1050%2C600&ssl=1 3x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/atomic-resolution\/wp-content\/uploads\/sites\/22\/2026\/06\/amira-ai-tools-blog-header-1920x450-1.png?resize=1400%2C800&ssl=1 4x"},"classes":[]},{"id":2071,"url":"https:\/\/www.thermofisher.com\/blog\/atomic-resolution\/facilitating-soft-tissue-analysis-unraveling-complex-microct-imaging-data-with-amira-software\/","url_meta":{"origin":638,"position":5},"title":"Facilitating Soft Tissue Analysis \u2013 Unraveling Complex MicroCT Imaging Data with Amira Software","author":"Vinay S","date":"August 27, 2026","format":false,"excerpt":"Key takeaways Micro-computed X-ray tomography (microCT) can be used for high-resolution, 3D visualization of a range of biological samples, including soft tissues, but transforming this data into scientific insights requires the processing of increasingly large, complex datasets. Thermo Scientific Amira Software is a powerful data processing tool that can simplify\u2026","rel":"","context":"In &quot;Amira Software&quot;","block_context":{"text":"Amira Software","link":"https:\/\/admin.acceleratingscience.com\/atomic-resolution\/cryo-electron-microscopy-cryo-em\/amira-software\/"},"img":{"alt_text":"Facilitating Soft Tissue Analysis \u2013 Unraveling Complex MicroCT Imaging Data with Amira Software","src":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/atomic-resolution\/wp-content\/uploads\/sites\/22\/2026\/08\/blog-soft-tissue-micro-ct-research-header-1920x450-1.jpg?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/atomic-resolution\/wp-content\/uploads\/sites\/22\/2026\/08\/blog-soft-tissue-micro-ct-research-header-1920x450-1.jpg?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/atomic-resolution\/wp-content\/uploads\/sites\/22\/2026\/08\/blog-soft-tissue-micro-ct-research-header-1920x450-1.jpg?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/atomic-resolution\/wp-content\/uploads\/sites\/22\/2026\/08\/blog-soft-tissue-micro-ct-research-header-1920x450-1.jpg?resize=700%2C400&ssl=1 2x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/atomic-resolution\/wp-content\/uploads\/sites\/22\/2026\/08\/blog-soft-tissue-micro-ct-research-header-1920x450-1.jpg?resize=1050%2C600&ssl=1 3x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/atomic-resolution\/wp-content\/uploads\/sites\/22\/2026\/08\/blog-soft-tissue-micro-ct-research-header-1920x450-1.jpg?resize=1400%2C800&ssl=1 4x"},"classes":[]}],"jetpack_sharing_enabled":true,"jetpack_featured_media_url":"https:\/\/admin.acceleratingscience.com\/atomic-resolution\/wp-content\/uploads\/sites\/22\/2022\/04\/Untitled-design-28.png","_links":{"self":[{"href":"https:\/\/www.thermofisher.com\/blog\/atomic-resolution\/wp-json\/wp\/v2\/posts\/638","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.thermofisher.com\/blog\/atomic-resolution\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.thermofisher.com\/blog\/atomic-resolution\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.thermofisher.com\/blog\/atomic-resolution\/wp-json\/wp\/v2\/users\/1515"}],"replies":[{"embeddable":true,"href":"https:\/\/www.thermofisher.com\/blog\/atomic-resolution\/wp-json\/wp\/v2\/comments?post=638"}],"version-history":[{"count":0,"href":"https:\/\/www.thermofisher.com\/blog\/atomic-resolution\/wp-json\/wp\/v2\/posts\/638\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.thermofisher.com\/blog\/atomic-resolution\/wp-json\/wp\/v2\/media\/639"}],"wp:attachment":[{"href":"https:\/\/www.thermofisher.com\/blog\/atomic-resolution\/wp-json\/wp\/v2\/media?parent=638"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.thermofisher.com\/blog\/atomic-resolution\/wp-json\/wp\/v2\/categories?post=638"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.thermofisher.com\/blog\/atomic-resolution\/wp-json\/wp\/v2\/tags?post=638"},{"taxonomy":"division","embeddable":true,"href":"https:\/\/www.thermofisher.com\/blog\/atomic-resolution\/wp-json\/wp\/v2\/division?post=638"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}