Image Analysis and Data Processing in Super-Resolution Microscopy 2022#

Program 22.8. – 25.8. 2022

Day 1#

Location: KONFMI, IMCF Vinicna, Microscopy Center, Viničná 7, Praha 2, room P09

10:00 - 11:00 Registration#

11:00 – 11:15 Welcome note in IMCF (Ondřej Šebesta, Martin Schätz, Miroslav Hyliš)#

11:20 – 12:00 ** Introduction to super-resolution microscopy: methods, principles, theoretical background** (Zuzana Burdíková)#

  • Image formation in Fluorescence Microscopy

  • Resolution and Noise

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

  • Structured Illumination Microscopy (SIM)

12:00 – 13:00 Lunch#

13:00 – 13:20 Call4Help#

13:30 – 14:00 Introduction to image processing (Karel Štěpka, Faculty of informatics, MUNI)#

14:00 – 14:10 Coffee break#

14:10 – 15:20 Image processing in FIJI, ImageJ#

(Karel Štěpka, Faculty of informatics, MUNI)

  • Two channel colocalization (mitochondrial and membrane labeling)

  • 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 – 16:00 Optional - ImageJ and Thunderstorm Installation (Ondřej Šebesta, Zuzana Burdíková, Martin Schätz, Peter Hoboth)#

16:00 – 16:15 Coffee break#

16:15 – 17:00 Optional: Facility tour - KONFMI: Zeiss Elyra PS, Zeiss Axio Scan, Leica TCS SP8 (Ondřej Šebesta, Zuzana Burdíková)#

Refreshment included

Day 2#

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

10:00 – 10:30 Data Management (Martin Schätz)#

10:30 – 10:40 Coffee break#

10:40 – 12:00 ThunderSTORM: a comprehensive ImageJ plug-in for SMLM data analysis and super-resolution imaging#

(Zdeněk Švindrych, 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 : 0 0 – 13 : 40 Scientific lecture: Phospholipid identity of the gene expression compartments revealed by quantitative super-resolution microscopy (Peter Hoboth)#

  • brief summary of dSTORM

  • overview of the quantitative approaches for the analysis of dSTORM data

  • dSTORM image reconstruction and quantitative analysis

  • quantitative evaluation of the nuclear phosphatidylinositol phosphates (nPIPs) within the gene expression compartments

  • co-patterning of nPIPs with the markers of subsequent stages of gene expression

13:40 – 14:00 Coffee break#

Practical part

14:00 – 16:00 ThunderSTORM hands-on sessions:** Individual work with ThunderSTORM software#

(Ondřej Šebesta, Zuzana Burdíková, Martin Schätz, Peter Hoboth)

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)

The coffee break included, Refreshments included

16:00 – 16:30 Leyla Yunis - Maker Institute, Prague#

3D Printing: From Design to Fabrication

19:00 – 22:00** Informal discussion in the Academic Club**#

Refreshment included

Day 3#

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

10:00 – 11:00 Customizing Fiji/ImageJ with ImageJ Macro#

(Robert Haase, TU Dresden)

11:00 – 12:00 Interactive Design of GPU-accelerated Image Data Flow Graphs in Fiji (Robert Haase, TU Dresden) Hands-on#

(Robert Haase; assisting: Zuzana Burdíková, Ondřej Šebesta, Martin Schätz)

12:00 – 13:00 Lunch#

13:00 – 14:00 Object Detection Using StarDist (Martin Schätz)#

14:00 – 14:30 Coffee break with Parrots in the Botanical Garden#

14:30 – 15:30 Noise2Void (Martin Schätz)#

15:40 – 15:50 Adaptive deconvolution LAS X Lightning and AIVIA software analysis options (Martin Kopecký, Pragolab)#

16:00 – 16:30 Happy Wednesday Time#

The coffee break included, Refreshments included

Day 4#

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

ANDOR AND IMARIS WORKSHOP#

9:30 – 10:30 Introduction to Andor BC43 Microscope and Imaris (Colin Wright, Blanka Forejtová)

10:30 – 11:00 Practical demonstration of Andor BC43 (Colin Wright; assisting: Blanka Forejtová**)**

  • case studies with a practical demonstration with Andor BC43 spinning disk confocal microscope and Imaris software

11:00 – 11:15 Coffee break

11:15 – 12:00 Practical demonstration of Andor BC43 hands-on part one (Colin Wright; assisting: Blanka Forejtová**)**

12:00 – 13:00 Lunch#

13:00 – 15:00** Practical demonstration of Andor BC43 hands-on part two **** (Colin Wright; assisting: Blanka Forejtová )**

15:00 – 15:15 Coffee break

15:15 – 16:30** Practical demonstration of Andor BC43 hands-on part three (Colin Wright; assisting: Blanka Forejtová )**