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    Advanced 3D image visualization and quantification 2025

    CourseCzech-BioimagingMicroscopy Published on 15. 01. 2025

    Basic information

    This course introduces participants to the fundamentals of volumetric and time-lapse microscopy data processing, with a focus on visualization, segmentation, and quantitative analysis. The first day offers a hands-on introduction to Imaris, covering its core modules (Spots, Surfaces, and Filaments). The second day builds on this by demonstrating specific workflows (using selected participants’ data) 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 22-23, 2025
    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.

    Target audience

    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.

    Program

    Lecturers: Štěpán Kortus, Barbora Hyklová, Iva Švecová, Arzuv Čaryjeva. Imaris experts (Andor)
    Location: Turquoise 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: 12:30–16:30

    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
    14:15-15:30   Exploring Imaris modules (Surfaces)
    15:30-16:00   Exploring Imaris modules (Filaments)
    16:00-16:30   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
    10:15-11:00   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

    12:30-14:00   Imaris workflow demonstration (by Imaris expert)
    14:00-14:20   Coffee break
    14:20-14:45   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

    Registration

    REGISTRATION IS CLOSED

    Registration fee

    • In-person participation: 500 CZK (excluding VAT)

    • Online participation: free

    In-person registration includes refreshments during coffee breaks and lunch. The activities are identical for both in-person and online participants; however, in-person participation is encouraged, as it offers better opportunities for interaction and direct support. In the event of limited time for questions or discussion, priority will be given to those attending in person.

    Capacity is limited to 15 participants on-site and 15 online.


      This event is organized by the National Infrastructure for Biological and Medical Imaging (Czech-BioImaging), supported by the grant LM2018129 of the Ministry of Education, Youth and Sports.