{"id":5550,"date":"2023-07-18T18:13:39","date_gmt":"2023-07-18T18:13:39","guid":{"rendered":"http:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/?p=5550"},"modified":"2025-03-14T20:59:30","modified_gmt":"2025-03-14T18:59:30","slug":"summer-workshop-2023","status":"publish","type":"post","link":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/summer-workshop-2023\/","title":{"rendered":"Summer Workshop 2023"},"content":{"rendered":"\n<figure class=\"wp-block-image size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"724\" height=\"1024\" src=\"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2023\/07\/2023_poster_summer_workshop_QR-724x1024.jpg\" alt=\"\" class=\"wp-image-5552\" srcset=\"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2023\/07\/2023_poster_summer_workshop_QR-724x1024.jpg 724w, https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2023\/07\/2023_poster_summer_workshop_QR-212x300.jpg 212w, https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2023\/07\/2023_poster_summer_workshop_QR-768x1086.jpg 768w, https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2023\/07\/2023_poster_summer_workshop_QR-1086x1536.jpg 1086w, https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2023\/07\/2023_poster_summer_workshop_QR-1448x2048.jpg 1448w, https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2023\/07\/2023_poster_summer_workshop_QR-scaled.jpg 1810w\" sizes=\"auto, (max-width: 724px) 100vw, 724px\" \/><\/figure>\n\n\n\n<ul class=\"wp-block-social-links is-layout-flex wp-block-social-links-is-layout-flex\"><li class=\"wp-social-link wp-social-link-twitter  wp-block-social-link\"><a rel=\"noopener nofollow\" target=\"_blank\" href=\"https:\/\/twitter.com\/IMCF_Vinicna\" class=\"wp-block-social-link-anchor\"><svg width=\"24\" height=\"24\" viewBox=\"0 0 24 24\" version=\"1.1\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" aria-hidden=\"true\" focusable=\"false\"><path d=\"M22.23,5.924c-0.736,0.326-1.527,0.547-2.357,0.646c0.847-0.508,1.498-1.312,1.804-2.27 c-0.793,0.47-1.671,0.812-2.606,0.996C18.324,4.498,17.257,4,16.077,4c-2.266,0-4.103,1.837-4.103,4.103 c0,0.322,0.036,0.635,0.106,0.935C8.67,8.867,5.647,7.234,3.623,4.751C3.27,5.357,3.067,6.062,3.067,6.814 c0,1.424,0.724,2.679,1.825,3.415c-0.673-0.021-1.305-0.206-1.859-0.513c0,0.017,0,0.034,0,0.052c0,1.988,1.414,3.647,3.292,4.023 c-0.344,0.094-0.707,0.144-1.081,0.144c-0.264,0-0.521-0.026-0.772-0.074c0.522,1.63,2.038,2.816,3.833,2.85 c-1.404,1.1-3.174,1.756-5.096,1.756c-0.331,0-0.658-0.019-0.979-0.057c1.816,1.164,3.973,1.843,6.29,1.843 c7.547,0,11.675-6.252,11.675-11.675c0-0.178-0.004-0.355-0.012-0.531C20.985,7.47,21.68,6.747,22.23,5.924z\"><\/path><\/svg><span class=\"wp-block-social-link-label screen-reader-text\">Twitter<\/span><\/a><\/li>\n\n<li class=\"wp-social-link wp-social-link-github  wp-block-social-link\"><a rel=\"noopener nofollow\" target=\"_blank\" href=\"https:\/\/github.com\/vmcf-konfmi\" class=\"wp-block-social-link-anchor\"><svg width=\"24\" height=\"24\" viewBox=\"0 0 24 24\" version=\"1.1\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" aria-hidden=\"true\" focusable=\"false\"><path d=\"M12,2C6.477,2,2,6.477,2,12c0,4.419,2.865,8.166,6.839,9.489c0.5,0.09,0.682-0.218,0.682-0.484 c0-0.236-0.009-0.866-0.014-1.699c-2.782,0.602-3.369-1.34-3.369-1.34c-0.455-1.157-1.11-1.465-1.11-1.465 c-0.909-0.62,0.069-0.608,0.069-0.608c1.004,0.071,1.532,1.03,1.532,1.03c0.891,1.529,2.341,1.089,2.91,0.833 c0.091-0.647,0.349-1.086,0.635-1.337c-2.22-0.251-4.555-1.111-4.555-4.943c0-1.091,0.39-1.984,1.03-2.682 C6.546,8.54,6.202,7.524,6.746,6.148c0,0,0.84-0.269,2.75,1.025C10.295,6.95,11.15,6.84,12,6.836 c0.85,0.004,1.705,0.114,2.504,0.336c1.909-1.294,2.748-1.025,2.748-1.025c0.546,1.376,0.202,2.394,0.1,2.646 c0.64,0.699,1.026,1.591,1.026,2.682c0,3.841-2.337,4.687-4.565,4.935c0.359,0.307,0.679,0.917,0.679,1.852 c0,1.335-0.012,2.415-0.012,2.741c0,0.269,0.18,0.579,0.688,0.481C19.138,20.161,22,16.416,22,12C22,6.477,17.523,2,12,2z\"><\/path><\/svg><span class=\"wp-block-social-link-label screen-reader-text\">GitHub<\/span><\/a><\/li><\/ul>\n\n\n\n<h2 class=\"wp-block-heading\"><span style=\"text-decoration: underline;\">SCHEDULE OF THE WORKSHOP<\/span><\/h2>\n\n\n\n<p><strong>Image Analysis and Data Processing (not only) in Super-Resolution Microscopy 2023<\/strong><\/p>\n\n\n<h2><strong>Day 1<\/strong><\/h2>\n<p>(Location: VMCF Vini\u010dn\u00e1, Microscopy Center, Vini\u010dn\u00e1 7, Praha 2, room P09)<\/p>\n<p><strong>\u00a0<\/strong><\/p>\n<p><strong>10:00 &#8211; 11:00<\/strong> \u00a0\u00a0\u00a0 Registration<\/p>\n<p><strong>11:00 \u2013 11:15<\/strong> \u00a0\u00a0 Welcome note in VMCF (RNDr.Miroslav Hyli\u0161,Ph.D., Martin Sch\u00e4tz,Ph.D., Zuzana Burdikova,Ph.D.)<\/p>\n<p><strong>11:20 \u2013 12:00<\/strong> \u00a0\u00a0 Introduction to super-resolution microscopy: methods, principles, theoretical background (Zuzana Burd\u00edkov\u00e1, Ph.D.)<\/p>\n<ul>\n<li>Image Formation in Fluorescence Microscopy<\/li>\n<li>Resolution and Noise<\/li>\n<li>Single-molecule localization microscopy (STORM, PALM, DNA-PAINT,\u2026)<\/li>\n<li>Structured Illumination Microscopy (SIM)<\/li>\n<\/ul>\n<p><strong>12:00 \u2013 13:20 \u00a0\u00a0 Lunch<\/strong><\/p>\n<p><strong>13:30 \u2013 14:00<\/strong>\u00a0\u00a0\u00a0\u00a0 Introduction to image processing (Karel \u0160t\u011bpka, Ph.D., Faculty of Informatics, MUNI)<\/p>\n<p><strong>14:00 \u2013 14:10<\/strong>\u00a0\u00a0\u00a0\u00a0 Coffee break\u00a0<\/p>\n<p><strong>14:10 \u2013 15:20<\/strong>\u00a0\u00a0\u00a0\u00a0 Image processing in FIJI, ImageJ<\/p>\n<p>(Karel \u0160t\u011bpka, Ph.D. Faculty of Informatics, MUNI)<\/p>\n<ul>\n<li>Two-channel colocalization (mitochondrial and membrane labeling)<\/li>\n<li>a p-Value of colocalization, data filtering<\/li>\n<li>Quantitative analysis<\/li>\n<li>Quantitative data (filtering, thresholding, background separation)<\/li>\n<li>Filter on photon count\u00a0<\/li>\n<li>Data visualization, 3D visualization<\/li>\n<li>Histogram, measurement of different parameters<\/li>\n<li>Pseudo-colors, pixel size, rendering mode, multicolor image<\/li>\n<li>Image export<\/li>\n<\/ul>\n<p><strong>15:20 \u2013 15:35<\/strong> \u00a0\u00a0 Coffee break<\/p>\n<p><strong>15:35 \u2013 17:00<\/strong> \u00a0\u00a0 Optional &#8211; ImageJ,Ilastik, Thunderstorm Installation (Martin Sch\u00e4tz, Jakub Soukup)<\/p>\n<p>Optional: Facility tour &#8211; KONFMI: Zeiss Elyra PS, Zeiss Axio Scan, Leica TCS SP8 (Pavel Krist, Jan Paces, Frantiasek Kitzberger)<\/p>\n<p>\u00a0<\/p>\n<h2><strong>Day 2<\/strong><\/h2>\n<p>(Location: VMCF Microscopy Center, Vini\u010dn\u00e1 7, Praha 2, Study room P09)<\/p>\n<p><strong>10:00 \u2013 10:40<\/strong> \u00a0\u00a0 Matlab Markus Hohle (QBM Munich: \u201cOptical Interferometry Imaging and Artificial Neural Networks for Fast Quality Screening of Cryo-EM Samples\u201d)\u00a0 30min + Q&amp;A)<\/p>\n<p><strong>10:40 \u2013 10:50<\/strong>\u00a0\u00a0\u00a0\u00a0 Coffee break<\/p>\n<p><strong>10:50 \u2013 12:00<\/strong> \u00a0\u00a0 ThunderSTORM: a comprehensive ImageJ plug-in for SMLM data analysis and super-resolution imaging (Zden\u011bk \u0160vindrych,Ph.D., Dartmouth College) https:\/\/zitmen.github.io\/thunderstorm\/<\/p>\n<ul>\n<li>Single Molecule Localisation (briefly)<\/li>\n<li>The idea behind ThunderSTORM<\/li>\n<li>Workflow &#8211; localization, filtering, rendering<\/li>\n<li>Simulation engine<\/li>\n<li>3D STORM &#8211; astigmatism method<\/li>\n<\/ul>\n<p><strong>12:00 \u2013 13:00\u00a0\u00a0\u00a0\u00a0 Lunch<\/strong><\/p>\n<p><strong>13:00 \u2013 13:40<\/strong>\u00a0\u00a0\u00a0\u00a0 Scientific lecture: Quantitative super-resolution microscopy reveals nuclear architecture in cells and tissues (Peter Hoboth, Ph.D.)<\/p>\n<ul>\n<li>Brief summary of SRM and overview of the quantitative approaches.<\/li>\n<li>Pros and cons of different SRM techniques to quantitatively study the nuclear antigens in cells and tissues.<\/li>\n<li>Commons and differences in the organization of gene expression compartments between cultured cells and human clinical tissue sections.<\/li>\n<\/ul>\n<p><strong>13:40 \u2013 14:00<\/strong>\u00a0\u00a0\u00a0\u00a0 Coffee break<\/p>\n<p>\u00a0<\/p>\n<p><strong><u>Practical part<\/u><\/strong><\/p>\n<p><strong>14:00 \u2013 16:00<\/strong>\u00a0\u00a0\u00a0\u00a0 ThunderSTORM hands-on sessions: Individual work with ThunderSTORM software<\/p>\n<p>(Zden\u011bk \u0160vindrych, Jakub Soukup, Zuzana Burd\u00edkov\u00e1, Martin Sch\u00e4tz, Peter Hoboth, Jan Paces, Frantisek Kitzberger)<\/p>\n<p><em>Group 1: beginners<\/em> (Zuzana Burd\u00edkov\u00e1, KONFMI, P\u0159FUK)<\/p>\n<p><em>Group 2: intermediate<\/em> (Ond\u0159ej \u0160ebesta, KONFMI, P\u0159FUK)<\/p>\n<p><em>Group 3: advanced<\/em> (Martin Sch\u00e4tz, KONFMI, P\u0159FUK, Peter Hoboth, KONFMI, P\u0159FUK)<\/p>\n<p>\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0<\/p>\n<p><strong>16:00 \u2013 16:30<\/strong>\u00a0\u00a0\u00a0\u00a0 Introduction to Ilastik (Martin Sch\u00e4tz, Jakub Soukup, Jan Paces, Zuzana Burdikova)<\/p>\n<p><strong>19:00 \u2013 22:00<\/strong>\u00a0\u00a0\u00a0\u00a0 Informal discussion in the Academic Club<\/p>\n<p>\u00a0<\/p>\n<h2><strong>Day 3<\/strong><\/h2>\n<p>(Location: VMCF Microscopy Center, Vini\u010dn\u00e1 7, Praha 2, study room B311)<\/p>\n<p>\u00a0<\/p>\n<p><strong>10:00 \u2013 11:00<\/strong>\u00a0\u00a0\u00a0\u00a0 Customizing Fiji\/ImageJ with ImageJ Macro with Hands-on (Marcelo Leomil Zoccoler, Ph.D., TU Dresden, Martin Schatz, Jakub Soukup, Jan Paces, Frantisek Kitzberger, Zuzana Burdikova)<\/p>\n<p><strong>11:00 \u2013 12:00<\/strong>\u00a0\u00a0\u00a0\u00a0 Interactive Design of GPU-accelerated Image Data Flow Graphs in Fiji\u00a0 with Hands-on (Marcelo Leomil Zoccoler, TU Dresden (Marcelo Leomil Zoccoler, Ph.D., TU Dresden, Martin Schatz, Jakub Soukup, Jan Paces, Frantisek Kitzberger)<\/p>\n<p><strong>12:00 \u2013 13:00\u00a0\u00a0\u00a0\u00a0 Lunch<\/strong><\/p>\n<p><strong>13:00-13:30<\/strong>\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 TissUUMaps Anna Klemm (University of Uppsala, Martin Sch\u00e4tz)<\/p>\n<p><strong>13:30- 14:00<\/strong>\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 Intro to Maker Institute, Prague 3D Printing: From Design to Fabrication<\/p>\n<p>(Martin Sch\u00e4tz)<\/p>\n<p><strong>14:00 \u2013 14:30<\/strong>\u00a0\u00a0\u00a0\u00a0 Coffee break<\/p>\n<p><strong>14:30 \u2013 16:30<\/strong> \u00a0\u00a0 Maker Institute, Prague 3D Printing: From Design to Fabrication with Hands-on (Martin Sch\u00e4tz)<\/p>\n<p><strong>16:30<\/strong>\u00a0\u00a0\u00a0\u00a0 \u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 Happy Wednesday Time in National Technical Library<\/p>\n<p>\u00a0<\/p>\n<h2><strong>Day 4<\/strong><\/h2>\n<p>(Location: IMCF Microscopy Center, Vini\u010dn\u00e1 7, Praha 2, study room B 311)<\/p>\n<p>\u00a0<\/p>\n<p><strong>10:00 \u2013 11:00<\/strong> \u00a0\u00a0 Object Detection Using StarDist and Noise2Void (Jakub Soukup, Martin Sch\u00e4tz, Zuzana Burdikova)\u00a0<\/p>\n<p><strong>11:00 \u2013 11:15<\/strong>\u00a0\u00a0\u00a0\u00a0 Coffee break<\/p>\n<p><strong>11:00 \u2013 12:15<\/strong> \u00a0\u00a0 Introduction to Napari (Marcelo Leomil Zoccoler, Ph.D., UT Dresden, Martin Sch\u00e4tz, Frantisek Kitzberger)<\/p>\n<ul>\n<li>Bio-Image Processing Using Napari Plugins<\/li>\n<li>An Image Segmentation Workflow with Napari: from Images to Labels to Surfaces<\/li>\n<li>Exporting Surfaces to 3D Printers Using napari-stl-exporter Plugin<\/li>\n<\/ul>\n<p><strong>12:15 \u2013 13:15\u00a0\u00a0\u00a0\u00a0 Lunch<\/strong><\/p>\n<p><strong>13:15 \u2013 14:15\u00a0\u00a0\u00a0\u00a0 <\/strong>Introduction to SIM and UC2 Microscope (Prof. Dr. Rainer Heintzmann, IPHT, Jena)<\/p>\n<p><strong>14:15 \u2013 14:30<\/strong>\u00a0\u00a0\u00a0\u00a0 Coffee break<\/p>\n<p><strong>14:30 &#8211; 16:30<\/strong> \u00a0\u00a0\u00a0 Practical demonstration of UC2 (Benedict Diedetrich, Ph.D., IPHT, Jena)<\/p>\n<p>practical demonstration of SIM UC2 microscope<\/p>\n<h2><strong>Day 5 &#8211; Zeiss\u00a0 and MesoSPIM WORKSHOP<\/strong><\/h2>\n<p>(Location: VMCF Microscopy Center, Vini\u010dn\u00e1 7, Praha 2, study room B 311)<\/p>\n<p>\u00a0<\/p>\n<p><strong>9:30 \u2013 10:00\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 <\/strong>Introduction to Airyscan Microscope (Pavel Krist, Ph.D., Zeiss)<\/p>\n<p><strong>10:00- 10:30<\/strong>\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 The mesoSPIM and open-hardware microscopy platforms for imaging cleared tissue. (Nikita Vladimirov, Ph.D., UZH Z\u00fcrich)<\/p>\n<p><strong>10:30 \u2013 10:45<\/strong>\u00a0\u00a0\u00a0\u00a0 Coffee break<\/p>\n<p><strong>10:45 \u2013 12:15\u00a0\u00a0\u00a0\u00a0 <\/strong>Handling of data for super-resolution microscopy in ARIVIS &#8211; big data, 3D visualization, tracking ( Maurizio Abbate, Ph.D., 4D Vision)<\/p>\n<p><strong>12:15 \u2013 13:15\u00a0\u00a0\u00a0\u00a0 Lunch<\/strong><\/p>\n<p><strong>13:15 \u2013 14:00<\/strong> \u00a0\u00a0 Practical demonstration MesoSPIM (Nikita Vladimirov, Ph.D., UZH Z\u00fcrich)<\/p>\n<p>case studies with a practical demonstration of mesoSPIM and mesoSPIM software<\/p>\n<p><strong>14:00 \u2013 15:15\u00a0\u00a0\u00a0\u00a0 <\/strong>Practical demonstration of\u00a0 Airyscan Microscope ( Pavel Krist, Ph.D., Zeiss)<\/p>\n<p>Parallel sessions<\/p>\n<p><strong>14:00 \u2013 15:15<\/strong> \u00a0\u00a0 Practical demonstration ARIVIS (Maurizio Abbate, 4D Vision)<\/p>\n<p><strong>15:15 \u2013 15:30<\/strong>\u00a0\u00a0\u00a0\u00a0 Coffee break<\/p>\n<p><strong>15:30 \u2013 16:45<\/strong> \u00a0\u00a0 Practical demonstration of\u00a0 Airyscan Microscope (Pavel Krist, Ph.D. Zeiss)<\/p>\n<p><strong>15:30 \u2013 16:45<\/strong> \u00a0\u00a0 Practical demonstration ARIVIS (Maurizio Abbate, Ph.D. 4D Vision)<\/p>\n<p>\u00a0<\/p>","protected":false},"excerpt":{"rendered":"<p>Image analysis and data processing in<br \/>\nsuper-resolution 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