Image Analysis and Data Processing (not only) in Super-Resolution Microscopy 2023#

DATE: 21.8. - 25.8.
PLACE: Vinicna 7, Prague 2, ROOM B2, 311
FORM: A hybrid form of presentation (hands-on in-person only)

Program for Summer Workshop 2023#

Program 21.8. – 25.8. 2023

Day 1#

Location: VMCF Viničná, Microscopy Center, Viničná 7, Praha 2, room P09

  • 10:00 - 11:00 Registration

  • 11:00 – 11:15 Welcome note in VMCF (Miroslav Hyliš, Ph.D., Martin Schätz, Ph.D., Zuzana Burdikova, Ph.D.)

  • 11:20 – 12:00 Introduction to super-resolution microscopy: methods, principles, theoretical background (Zuzana Burdíková, Ph.D.)

    • Image Formation in Fluorescence Microscopy

    • Resolution and Noise

    • Single-molecule localization microscopy (STORM, PALM, DNA-PAINT,…)

    • Structured Illumination Microscopy (SIM)

  • 12:00 – 13:20 Lunch

  • 13:30 – 14:00 Introduction to image processing (Karel Štěpka, Ph.D., Faculty of Informatics, MUNI)

  • 14:00 – 14:10 Coffee break

  • 14:10 – 15:20 Image processing in FIJI, ImageJ (Karel Štěpka, Ph.D., Faculty of Informatics, MUNI)

    • Two-channel colocalization (mitochondrial and membrane labeling)

    • A p-Value of colocalization, data filtering

    • Quantitative analysis

    • Quantitative data (filtering, thresholding, background separation)

    • Filter on photon count

    • Data visualization, 3D visualization

    • Histogram, measurement of different parameters

    • Pseudo-colors, pixel size, rendering mode, multicolor image

    • Image export

  • 15:20 – 15:35 Coffee break

  • 15:35 – 17:00 Optional - ImageJ, Ilastik, Thunderstorm Installation (Martin Schätz, Jakub Soukup)

    • Optional: Facility tour - KONFMI: Zeiss Elyra PS, Zeiss Axio Scan, Leica TCS SP8 (Pavel Krist, Jan Paces, Frantisek Kitzberger)

    • Refreshment included

Day 2#

Location: VMCF Microscopy Center, Viničná 7, Praha 2, Study room P09

  • 12:00 – 12:40 Matlab Markus Hohle (QBM Munich: “Optical Interferometry Imaging and Artificial Neural Networks for Fast Quality Screening of Cryo-EM Samples”) 30min + Q&A)

  • 12:40 – 12:50 Coffee break

  • 12:50 – 14:00 ThunderSTORM: a comprehensive ImageJ plug-in for SMLM data analysis and super-resolution imaging (Zdeněk Švindrych, Ph.D., Dartmouth College)

    • Single Molecule Localisation (briefly)

    • The idea behind ThunderSTORM

    • Workflow - localization, filtering, rendering

    • Simulation engine

    • 3D STORM - astigmatism method

  • 14:00 – 15:00 Lunch

  • 15:00 – 15:40 Scientific lecture: Quantitative super-resolution microscopy reveals nuclear architecture in cells and tissues (Peter Hoboth, Ph.D.)

    • Brief summary of SRM and overview of the quantitative approaches.

    • Pros and cons of different SRM techniques to quantitatively study the nuclear antigens in cells and tissues.

    • Commons and differences in the organization of gene expression compartments between cultured cells and human clinical tissue sections.

  • 15:40 – 16:00 Coffee break

Practical part

  • 16:00 – 17:00 ThunderSTORM hands-on sessions: Individual work with ThunderSTORM software (Zdeněk Švindrych, Jakub Soukup, Zuzana Burdíková, Martin Schätz, Peter Hoboth, Jan Paces, Frantisek Kitzberger)

    • Group 1: beginners (Zuzana Burdíková, VMCF, PřFUK)

    • Group 2: intermediate (Zdenek Svindrych, VMCF, PřFUK)

    • Group 3: advanced (Martin Schätz, VMCF, PřFUK, Peter Hoboth)

    • The coffee break included Refreshments included

  • 17:00 – 17:30 Introduction to Ilastik (Martin Schätz, Jakub Soukup, Jan Paces, Zuzana Burdikova)

  • 19:00 – 22:00 Informal discussion in the Academic Club Refreshment included

Day 3#

Location: VMCF Microscopy Center, Viničná 7, Praha 2, study room B311

  • 10:00 – 11:00 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)

  • 11:00 – 12:00 Interactive Design of GPU-accelerated Image Data Flow Graphs in Fiji with Hands-on (Marcelo Leomil Zoccoler, TU Dresden, Martin Schatz, Jakub Soukup, Jan Paces, Frantisek Kitzberger)

  • 12:00 – 13:00 Lunch

  • 13:00-13:30 TissUUMaps Anna Klemm (University of Uppsala, Martin Schätz)

  • 13:30-14:00 Intro to Maker Institute, Prague 3D Printing: From Design to Fabrication (Martin Schätz)

  • 14:00 – 14:30 Coffee break

  • 14:30 – 16:30 Maker Institute, Prague 3D Printing: From Design to Fabrication with Hands-on (Martin Schätz)

  • 16:30 Happy Wednesday Time in National Technical Library The coffee break included refreshments included

Day 4#

Location: IMCF Microscopy Center, Viničná 7, Praha 2, study room B 311

  • 10:00 – 11:00 Object Detection Using StarDist and Noise2Void (Jakub Soukup, Martin Schätz, Zuzana Burdikova)

  • 11:00 – 11:15 Coffee break

  • 11:00 – 12:15 Introduction to

Napari (Marcelo Leomil Zoccoler, Ph.D., UT Dresden, Martin Schätz, Frantisek Kitzberger)

  • Bio-Image Processing Using Napari Plugins

  • An Image Segmentation Workflow with Napari: from Images to Labels to Surfaces

  • Exporting Surfaces to 3D Printers Using napari-stl-exporter Plugin

  • 12:15 – 13:15 Lunch

  • 13:15 – 14:15 Introduction to SIM and UC2 Microscope (Prof. Dr. Rainer Heintzmann, IPHT, Jena)

  • 14:15 – 14:30 Coffee break

  • 14:30 - 16:30 Practical demonstration of UC2 (Benedict Diederich, Ph.D., IPHT, Jena)

    • Practical demonstration of SIM UC2 microscope

    • The coffee break is included. Refreshments included

Day 5#

Zeiss and MesoSPIM WORKSHOP Location: VMCF Microscopy Center, Viničná 7, Praha 2, study room B 311

  • 9:30 – 10:00 Introduction to Airyscan Microscope (Pavel Krist, Ph.D., Zeiss)

  • 10:00- 10:30 The mesoSPIM and open-hardware microscopy platforms for imaging cleared tissue. (Nikita Vladimirov, Ph.D., UZH Zürich)

  • 10:30 – 10:45 Coffee break

  • 10:45 – 12:15 Handling of data for super-resolution microscopy in ARIVIS - big data, 3D visualization, tracking (Maurizio Abbate, Ph.D., 4D Vision)

  • 12:15 – 13:15 Lunch

  • 13:15 – 14:00 Practical demonstration MesoSPIM (Nikita Vladimirov, Ph.D., UZH Zürich)

  • 14:00 – 15:15 Practical demonstration of Airyscan Microscope (Pavel Krist, Ph.D., Zeiss)

  • 14:00 – 15:15 Practical demonstration ARIVIS (Maurizio Abbate, 4D Vision)

  • 15:15 – 15:30 Coffee break

  • 15:30 – 16:45 Practical demonstration of Airyscan Microscope (Pavel Krist, Ph.D. Zeiss)

  • 15:30 – 16:45 Practical demonstration ARIVIS (Maurizio Abbate, Ph.D. 4D Vision)