{"id":2050,"date":"2022-12-06T04:39:13","date_gmt":"2022-12-06T09:39:13","guid":{"rendered":"https:\/\/courses.ideate.cmu.edu\/60-461\/f2022\/?p=2050"},"modified":"2022-12-06T13:28:28","modified_gmt":"2022-12-06T18:28:28","slug":"shrugbread-microscopic-scanning-pipeline","status":"publish","type":"post","link":"https:\/\/courses.ideate.cmu.edu\/60-461\/f2022\/shrugbread\/12\/06\/shrugbread-microscopic-scanning-pipeline\/","title":{"rendered":"shrugbread- microscopic scanning pipeline"},"content":{"rendered":"<p>For my final project I created a pipeline for obtaining super hi-res , stitched together images from the studio&#8217;s Unitron zoom microscope.<\/p>\n<p>The main components of the capture setup I have are the axidraw a3, a custom 3d printed build plate , and the Unitron Zoom HD microscope.<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" class=\"alignnone size-full wp-image-2069\" src=\"https:\/\/courses.ideate.cmu.edu\/60-461\/f2022\/wp-content\/uploads\/2022\/12\/excap-setup-diagram.png\" alt=\"\" width=\"3072\" height=\"3072\" srcset=\"https:\/\/courses.ideate.cmu.edu\/60-461\/f2022\/wp-content\/uploads\/2022\/12\/excap-setup-diagram.png 3072w, https:\/\/courses.ideate.cmu.edu\/60-461\/f2022\/wp-content\/uploads\/2022\/12\/excap-setup-diagram-480x480.png 480w, https:\/\/courses.ideate.cmu.edu\/60-461\/f2022\/wp-content\/uploads\/2022\/12\/excap-setup-diagram-1024x1024.png 1024w, https:\/\/courses.ideate.cmu.edu\/60-461\/f2022\/wp-content\/uploads\/2022\/12\/excap-setup-diagram-150x150.png 150w, https:\/\/courses.ideate.cmu.edu\/60-461\/f2022\/wp-content\/uploads\/2022\/12\/excap-setup-diagram-768x768.png 768w, https:\/\/courses.ideate.cmu.edu\/60-461\/f2022\/wp-content\/uploads\/2022\/12\/excap-setup-diagram-1536x1536.png 1536w, https:\/\/courses.ideate.cmu.edu\/60-461\/f2022\/wp-content\/uploads\/2022\/12\/excap-setup-diagram-2048x2048.png 2048w, https:\/\/courses.ideate.cmu.edu\/60-461\/f2022\/wp-content\/uploads\/2022\/12\/excap-setup-diagram-1200x1200.png 1200w\" sizes=\"(max-width: 709px) 85vw, (max-width: 909px) 67vw, (max-width: 1362px) 62vw, 840px\" \/><\/p>\n<p>These items are all connected to my laptop which is running a processing script that moves the axidraw build plate in a predetermined path, stopping along that path and outputting the microscope image at each point along the path. With this code I have full control over the variables that move the axidraw arm and can make scans with a specific number of images, image density, and the time interval that the capture is occuring.(This code was given to me by Golan Levin, and was edited in great collaboration by Himalini Gururaj, and Angelica Bonilla)<\/p>\n<figure id=\"attachment_2072\" aria-describedby=\"caption-attachment-2072\" style=\"width: 960px\" class=\"wp-caption alignnone\"><img decoding=\"async\" loading=\"lazy\" class=\"wp-image-2072 size-full\" src=\"https:\/\/courses.ideate.cmu.edu\/60-461\/f2022\/wp-content\/uploads\/2022\/12\/processing-window-screenshot.png\" alt=\"\" width=\"960\" height=\"1001\" srcset=\"https:\/\/courses.ideate.cmu.edu\/60-461\/f2022\/wp-content\/uploads\/2022\/12\/processing-window-screenshot.png 960w, https:\/\/courses.ideate.cmu.edu\/60-461\/f2022\/wp-content\/uploads\/2022\/12\/processing-window-screenshot-460x480.png 460w, https:\/\/courses.ideate.cmu.edu\/60-461\/f2022\/wp-content\/uploads\/2022\/12\/processing-window-screenshot-768x801.png 768w\" sizes=\"(max-width: 709px) 85vw, (max-width: 909px) 67vw, (max-width: 1362px) 62vw, 840px\" \/><figcaption id=\"caption-attachment-2072\" class=\"wp-caption-text\">the counter above displays the progress through the scan and below is an output window to check focus and placement of the mounting plate<\/figcaption><\/figure>\n<p>&nbsp;<\/p>\n<figure id=\"attachment_2071\" aria-describedby=\"caption-attachment-2071\" style=\"width: 483px\" class=\"wp-caption alignnone\"><img decoding=\"async\" loading=\"lazy\" class=\"wp-image-2071 size-full\" src=\"https:\/\/courses.ideate.cmu.edu\/60-461\/f2022\/wp-content\/uploads\/2022\/12\/image.png\" alt=\"\" width=\"483\" height=\"386\" \/><figcaption id=\"caption-attachment-2071\" class=\"wp-caption-text\">this is a simplified version of how the robot path is shaped<\/figcaption><\/figure>\n<p>From here I put the output images from the processing program into a software called gigapan stitch to have the edges of each photograph aligned and merged together. each photograph needs some amount of overlap for the software to be able to detect and match up edges<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" class=\"alignnone size-full wp-image-2075\" src=\"https:\/\/courses.ideate.cmu.edu\/60-461\/f2022\/wp-content\/uploads\/2022\/12\/Screenshot-2022-12-06-034455.png\" alt=\"\" width=\"1275\" height=\"860\" srcset=\"https:\/\/courses.ideate.cmu.edu\/60-461\/f2022\/wp-content\/uploads\/2022\/12\/Screenshot-2022-12-06-034455.png 1275w, https:\/\/courses.ideate.cmu.edu\/60-461\/f2022\/wp-content\/uploads\/2022\/12\/Screenshot-2022-12-06-034455-640x432.png 640w, https:\/\/courses.ideate.cmu.edu\/60-461\/f2022\/wp-content\/uploads\/2022\/12\/Screenshot-2022-12-06-034455-1024x691.png 1024w, https:\/\/courses.ideate.cmu.edu\/60-461\/f2022\/wp-content\/uploads\/2022\/12\/Screenshot-2022-12-06-034455-768x518.png 768w, https:\/\/courses.ideate.cmu.edu\/60-461\/f2022\/wp-content\/uploads\/2022\/12\/Screenshot-2022-12-06-034455-1200x809.png 1200w\" sizes=\"(max-width: 709px) 85vw, (max-width: 909px) 67vw, (max-width: 1362px) 62vw, 840px\" \/><\/p>\n<p>From here the images go straight to being hosted on the gigapan website and are accessible to all.<\/p>\n<p>Here are some I have made so far with this method.<\/p>\n<p><a href=\"http:\/\/www.gigapan.com\/gigapans\/231258\">http:\/\/www.gigapan.com\/gigapans\/231258<\/a><\/p>\n<p><a href=\"http:\/\/www.gigapan.com\/gigapans\/231255\">http:\/\/www.gigapan.com\/gigapans\/231255\u00a0<\/a><\/p>\n<p><a href=\"http:\/\/www.gigapan.com\/gigapans\/231253\">http:\/\/www.gigapan.com\/gigapans\/231253<\/a><\/p>\n<p><a href=\"http:\/\/www.gigapan.com\/gigapans\/231250\">http:\/\/www.gigapan.com\/gigapans\/231250<\/a><\/p>\n<p><a href=\"http:\/\/www.gigapan.com\/gigapans\/231241\">http:\/\/www.gigapan.com\/gigapans\/231241<\/a><\/p>\n<p><a href=\"http:\/\/www.gigapan.com\/gigapans\/231256\">http:\/\/www.gigapan.com\/gigapans\/231256<\/a><\/p>\n<p><a href=\"http:\/\/www.gigapan.com\/gigapans\/231259\">http:\/\/www.gigapan.com\/gigapans\/231259<\/a><\/p>\n<p>here&#8217;s a timelapse of a scan I couldn&#8217;t use:<\/p>\n<p><iframe loading=\"lazy\" title=\"turkey tail timelapsemp4\" width=\"840\" height=\"473\" src=\"https:\/\/www.youtube.com\/embed\/5qOM6FM4ACw?feature=oembed\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture\" allowfullscreen><\/iframe><\/p>\n<p><iframe loading=\"lazy\" title=\"microscopic gantry movement\" width=\"840\" height=\"473\" src=\"https:\/\/www.youtube.com\/embed\/31DgkQgQAZY?feature=oembed\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture\" allowfullscreen><\/iframe><\/p>\n<p>This process for scanning objects opens up scanning to a host of subjects that a flatbed scanner may not be able to capture. Such as objects with strange topology and subjects that ideally should not be dried out. I also believe that with a proper stitching software I will be able to record images with density and dpi that go beyond a typical flatbed scanner.<\/p>\n<p>I have a lot I would change about my project if I was given a chance to restart or work on it further. I didn&#8217;t have enough time to give softwares similar to gigapan a shot, and I think in many ways gigapan is a less-efficient, data capped method for image stitching than may be necessary for what I need. I\u00a0 also wish the range of objects I could capture did not have so many stipulations. At the moment I am only able to get a small sliver of the plane of my subject in focus. where I would have preferred to stitch together different focal planes. the subjects also have to be rigid enough to not deform or slosh around during axi-draw bed transit.\u00a0 With this project I am super excited to get a chance to photograph live mushroom cultures I have been growing and other biomaterial that does not scan well in a flat bed scanner.\u00a0 I want to utilize this setup to it&#8217;s fullest potential and be able to use the microscope near maximum magnification while having it be viewable.<\/p>\n<p>This project really tested a lot of my observational and hence problem solving skills. There were many moments where after viewing my exported images I was able to detect an issue in the way I was capturing that I could experiment with, such as realizing that increasing the amount of overlap between images doesn&#8217;t increase dpi unless I am actually increasing my magnification strength, or realizing with a zig zag path that half of my images are being stored in the wrong order.<\/p>\n<p>Once a again very big thanks to all of the people who helped me at every step of the way with this project. Y&#8217;all rock.<\/p>\n<p>&nbsp;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>For my final project I created a pipeline for obtaining super hi-res , stitched together images from the studio&#8217;s Unitron zoom microscope. The main components of the capture setup I have are the axidraw a3, a custom 3d printed build plate , and the Unitron Zoom HD microscope. These items are all connected to my &hellip; <a href=\"https:\/\/courses.ideate.cmu.edu\/60-461\/f2022\/shrugbread\/12\/06\/shrugbread-microscopic-scanning-pipeline\/\" class=\"more-link\">Continue reading<span class=\"screen-reader-text\"> &#8220;shrugbread- microscopic scanning pipeline&#8221;<\/span><\/a><\/p>\n","protected":false},"author":11,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":[],"categories":[20],"tags":[],"_links":{"self":[{"href":"https:\/\/courses.ideate.cmu.edu\/60-461\/f2022\/wp-json\/wp\/v2\/posts\/2050"}],"collection":[{"href":"https:\/\/courses.ideate.cmu.edu\/60-461\/f2022\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/courses.ideate.cmu.edu\/60-461\/f2022\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/courses.ideate.cmu.edu\/60-461\/f2022\/wp-json\/wp\/v2\/users\/11"}],"replies":[{"embeddable":true,"href":"https:\/\/courses.ideate.cmu.edu\/60-461\/f2022\/wp-json\/wp\/v2\/comments?post=2050"}],"version-history":[{"count":4,"href":"https:\/\/courses.ideate.cmu.edu\/60-461\/f2022\/wp-json\/wp\/v2\/posts\/2050\/revisions"}],"predecessor-version":[{"id":2125,"href":"https:\/\/courses.ideate.cmu.edu\/60-461\/f2022\/wp-json\/wp\/v2\/posts\/2050\/revisions\/2125"}],"wp:attachment":[{"href":"https:\/\/courses.ideate.cmu.edu\/60-461\/f2022\/wp-json\/wp\/v2\/media?parent=2050"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/courses.ideate.cmu.edu\/60-461\/f2022\/wp-json\/wp\/v2\/categories?post=2050"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/courses.ideate.cmu.edu\/60-461\/f2022\/wp-json\/wp\/v2\/tags?post=2050"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}