Advanced 3D image visualization and quantification

Basic information

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)


Registration fee: free of charge
Deadline for registration: June 13, 2024