Advanced 3D image visualization and quantification

This course is designed to introduce participants to the fundamentals of volumetric and time-lapse data processing. It covers various tools for processing, visualization, and quantitative analysis of 3D/4D microscopy data. The first part of the course will provide an introduction to Imaris software, while the second part will explore several other software options.

The course includes hands-on sessions, giving participants the opportunity to personally explore and use the tools. No prior knowledge of the software is required.

Date: June 19–20, 2024
Duration: 2 days
Language: English
Requirements: bring your own laptop

The course is organized in hybrid form and it is possible to join either in-person or online. The course will be the same for both groups.

Lecturers: Štěpán Kortus, Barbora Hyklová, Iva Švecová
Location: Turquoise Auditorium/online

Day 1, Wednesday 19.6.

Morning session: 9:00–11:30

9:00–9:10  Registration
9:10–9:30  Image processing options at the Microscopy service centre of IEM
9:30–10:15  Introduction to Imaris environment
10:15–10:30  Coffee break
10:30–11:30  Overview of Imaris modules (spots, surfaces, filaments)

Lunch break: 11:30–12:30

Afternoon session: 12:30–15:30

12:30–13:55  Exploration of Imaris modules (spots, surfaces, filaments)
13:55–14:15  Coffee break
14:15–15:30  Quantitative analysis in Imaris

Day 2, Thursday 20.6.

Morning session: 9:00–11:30

9:00–10:15  Imaris batch processing and other advanced functions
10:15–10:30  Coffee break
10:30–11:30  Stitching and Imaris Stitcher

Lunch break: 11:30–12:30

Afternoon session: 12:30–15:00

12:30–13:55  Freeware options for 3D image analysis
13:55–14:15  Coffee break
14:15–15:00  Introduction to Irbis (custom-made software for 3D image analysis)