haesleinhuepf / FSUK_workshop21

Image analysis and data processing in superresolution microscopy workshop 2021, Faculty of Science, Charles University

FSUK_workshop21

Image analysis and data processing in superresolution microscopy workshop 2021, Faculty of Science, Charles University

What you can find in this repository

In this repository you will find mainly files for hands on part of workshop, instructions what and how to install apropriate free software, manuals and/or other usefull documentations for plugins. Also you will find here some of the presentations, if authors will agree to share them.

How to download whole repository

You can download whole repository as .zip file through this webpage:

It is also possible to clone whole repository, if you have git installed on your machine:

git clone https://github.com/martinschatz-cz/FSUK_workshop21.git

How to download single file

Or you can download single file through this webpage:

Copyright

Repository is under CC-0 licence, however some of the resources have their specific licences attached.

Program

Day 1

• 9:00 – 9:10 Welcome note (Ondřej Šebesta)

• 9:10 – 9:30 Introduction of new applications in KONFMI (Ondřej Šebesta, Martin Schätz)

• 9:40 – 10:20 Introduction to superresolution microscopy: methods, principles, theoretical background (Zuzana Burdíková)

• 10:30 – 11:00 Introduction to image processing (Karel Štěpka, Faculty of informatics, MUNI)

• 11:00 – 11:30 Coffee break

• 11:30 – 12:10 Image processing in FIJI, ImageJ (Karel Štěpka, Faculty of informatics, MUNI)

• 12:20 – 13:10 Image reconstruction of superresolution SIM data in ImageJ: fairSIM (Martin Schätz)

• 13:10 – 14:30 Lunch

Practical part

• 14:30 – 16:30 ImageJ, fairSIM hands-on

• 15:00 – 15:30 Coffee break

• 16:30 – 17:30 Optional: Facility tour - KONFMI: Zeiss Elyra PS, Zeiss Axio Scan (Ondřej Šebesta, Zuzana Burdíková) Refreshment included

Day 2

• 9:00 – 10:30 ThunderSTORM: a comprehensive ImageJ plug-in for SMLM data analysis and super-resolution imaging (Zdeněk Švindrych, Dartmouth College) https://zitmen.github.io/thunderstorm/

• 10:40 – 11:20 Scientific lecture Case Study part I: Nanoglance at the phospholipids of the gene expression compartments (Peter Hoboth)

• 11:20 – 11:40 Coffee break

• 11:40 – 12:20 Scientific lecture Case Study II (Peter Hoboth)

• 12:20 – 14:00 Lunch

• 14:00 – 14:30 CASE Study Methods for the quantitative analyses of SMLM data (Peter Hoboth) Coordinate-based colocalization / Nearest Neighbor Distance (NND) analysis in ThunderSTORM

Practical part

• 14:30 – 16:30 ThunderSTORM hands-on sessions: Individual work with ThunderSTORM software (Ondřej Šebesta, Zuzana Burdíková, Martin Schätz, Peter Hoboth) The coffee break included, Refreshment included

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

Day 3

• 09:00 – 9:30 Customizing Fiji/ImageJ with ImageJ Macro (Robert Haase)

• 09:30 – 10:00 Hands-on (Robert Haase; assisting: Zuzana Burdíková, Ondřej Šebesta, Martin Schätz)

• 10:00 – 10:15 Coffee break

• 10:15 – 10:45 Interactive Design of GPU-accelerated Image Data Flow Graphs in Fiji (Robert Haase)

• 10:45 – 11:30 Hands-on (Robert Haase; assisting: Zuzana Burdíková, Ondřej Šebesta, Martin Schätz)

• 11:30 – 12:30 Lunch

• 12:30 – 13:30 Introduction to Data Management and FAIR principles (Marian Novotny)

• 13:40 – 14:20 Scientific lecture Data interpretation and quantification of complex dynamical systems (Yoonsang Lee, Dartmouth College)

• 14:30 – 14:50 Pixel Classification Using ILASTIK (Martin Schätz)

• 15:00 – 15:20 Object Detection Using StarDist (Martin Schätz)

Practical part

• 15:30 – 17:00 ILASTIK or StarDist Hands-on (Ondřej Šebesta, Zuzana Burdíková, Martin Schätz, Peter Hoboth) The coffee break included, Refreshment included