Summer Workshop 2023
SCHEDULE OF THE WORKSHOP
Image Analysis and Data Processing (not only) in Super-Resolution Microscopy 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 (RNDr.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, Frantiasek Kitzberger)
Day 2
(Location: VMCF Microscopy Center, Viničná 7, Praha 2, Study room P09)
10:00 – 10:40 Matlab Markus Hohle (QBM Munich: “Optical Interferometry Imaging and Artificial Neural Networks for Fast Quality Screening of Cryo-EM Samples”) 30min + Q&A)
10:40 – 10:50 Coffee break
10:50 – 12:00 ThunderSTORM: a comprehensive ImageJ plug-in for SMLM data analysis and super-resolution imaging (Zdeněk Švindrych,Ph.D., Dartmouth College) https://zitmen.github.io/thunderstorm/
- Single Molecule Localisation (briefly)
- The idea behind ThunderSTORM
- Workflow – localization, filtering, rendering
- Simulation engine
- 3D STORM – astigmatism method
12:00 – 13:00 Lunch
13:00 – 13:40 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.
13:40 – 14:00 Coffee break
Practical part
14:00 – 16:00 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, KONFMI, PřFUK)
Group 2: intermediate (Ondřej Šebesta, KONFMI, PřFUK)
Group 3: advanced (Martin Schätz, KONFMI, PřFUK, Peter Hoboth, KONFMI, PřFUK)
16:00 – 16:30 Introduction to Ilastik (Martin Schätz, Jakub Soukup, Jan Paces, Zuzana Burdikova)
19:00 – 22:00 Informal discussion in the Academic Club
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 (Marcelo Leomil Zoccoler, Ph.D., 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
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 Diedetrich, Ph.D., IPHT, Jena)
practical demonstration of SIM UC2 microscope
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)
case studies with a practical demonstration of mesoSPIM and mesoSPIM software
14:00 – 15:15 Practical demonstration of Airyscan Microscope ( Pavel Krist, Ph.D., Zeiss)
Parallel sessions
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)