Advanced 3D image visualization and quantification 2026

This course introduces participants to the fundamentals of volumetric microscopy data processing, with a focus on visualization, segmentation, and quantitative analysis, primarily using fluorescence light microscopy data. The first day offers a hands-on introduction to Imaris, covering its core modules (Spots, Surfaces, and Filaments). The second day builds on this and includes a broader discussion on big data challenges, alternative 3D processing tools in ImageJ/Fiji, and options for data storage, sharing, and reuse (FAIR data).

Date: May 28-29, 2026
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.

Imaris is the main software used, and the course is designed to provide a comprehensive overview of its capabilities. As such, it is primarily aimed at participants with no or limited experience. However, advanced features and exercises will also be included to benefit those already familiar with the software.

Lecturers: Štěpán Kortus, Iva Švecová, Barbora Hyklová, Arzuv Čaryjeva
Location: Bordo Auditorium of the IEM CAS/online

Day 1

Morning session: 9:00–11:30

8:45-9:00   Registration
9:00-9:15   Image processing options at the IEM Microscopy service centre and Czech-Bioimaging
9:15-9:30   Visualization vs quantification of multidimensional images
9:30-10:15   Introduction to Imaris environment and workflow
10:15-10:30   Coffee break
10:30-11:30   Visualization and image preprocessing in Imaris

Lunch break: 11:30-12:30

Afternoon session: 12:30–16:45

12:30-12:45   Overview of Imaris modules (Spots, Surfaces, Filaments)
12:45-13:55   Exploring Imaris modules (Spots)
13:55-14:15   Coffee break
14:15-15:15   Exploring Imaris modules (Surfaces)
15:15-16:15   Exploring Imaris modules (Filaments)
16:15-16:45   Questions and wrap-up

Day 2

Morning session: 9:00–11:30

9:00-10:00   Qualitative and quantitative analysis in Imaris
10:00-10:15   Coffee break
10:15-11:30   Image stitching (Imaris Stitcher) and registration (Fiji)
11:00-11:30   3D processing in Fiji

Lunch break: 11:30-12:30

Afternoon session: 12:30–15:30

12:30-13:55   3D processing in Fiji
13:55-14:15   Coffee break
14:15-14:45   Introduction to big data and BigDataViewer
14:45-15:15   Data storage, sharing and reuse: a practical guide (by Arzuv Čaryjeva)
15:15-15:30   Questions and wrap-up

If you have any questions about the course, please contact Iva Švecová at iva.svecova@iem.cas.cz.

This event is organized by the National Infrastructure for Biological and Medical Imaging (Czech-BioImaging), supported by grants LM2023050 and CZ.02.01.01/00/23_015/0008205.