Fundamentals of bioimage analysis – May 26

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Overview

This 5-day workshop is designed to provide a thorough introduction to bioimage analysis for individuals with little to no prior experience. Participants will develop essential skills in image processing and analysis workflows using both open-source and proprietary software, namely Fiji/ImageJ and Arivis. Through hands-on sessions, you’ll explore techniques for image restoration, segmentation, feature extraction, and tracking—employing both classical methods and cutting-edge machine and deep learning tools. Most importantly, you’ll learn how to create reproducible data visualizations and manage your bioimage data effectively.

Upon successful completion of the course, participants will be awarded a digital microcertificate, aligning with the unified European framework.

What will you learn?

By the end of this workshop, you will be able to:

  • Understand Foundational Microscopy Techniques
    Gain insights into the principles of bioimage acquisition and analysis.
  • Apply Essential Image Processing Methods
    Use thresholding, segmentation, and preprocessing techniques to analyze bioimages.
  • Utilize Leading Software Tools
    Master FIJI/ImageJ for detailed analyses such as stitching, colocalization, and intensity comparisons; leverage ZEISS arivis for advanced 3D visualization, ML-based segmentation, and tracking.
  • Develop Reproducible Workflows
    Create consistent and reproducible data visualizations and analysis pipelines.
  • Engage in Real-World Projects
    Work on a final project to apply your newly acquired skills to an authentic bioimage analysis challenge.
  • Collaborate and Network
    Connect with peers and experts to foster professional relationships and knowledge exchange.

Workshop Agenda

Day 1: Introduction to Microscopy and Bioimage Analysis

  • Workshop Introduction and Overview
  • Microscopy Techniques: Principles, types, and applications
  • Image Acquisition: Methods and challenges
  • Image Preprocessing: Practical group exercises
  • Introduction to Thresholding and Segmentation
  • Partner lecture : Autonomous Microscopy Powered by AIVIA

Day 2: FIJI/ImageJ

  • Overview of the FIJI/ImageJ Interface and Key Functions
  • Hands-On Practice: Basic analysis workflows including segmentation and GPU-accelerated tools
  • Advanced Processing: Image stitching, intensity quantification, and pixel-based colocalization

Day 3: ZEISS arivis

  • Getting Started with ARIVIS: User interface, data import, and setup
  • 3D Visualization and Segmentation: Hands-on practice
  • Machine Learning in ARIVIS: Using Cellpose for ML-based segmentation, colocalization, and tracking

Day 4: Data Visualization and Reproducible Science

  • Creating Effective Visualizations for Data Analysis
  • Introduction to Reproducible Science: Best practices for consistent workflows
  • Project Work: Setting up your final project and defining objectives

Registration and Fees

For Registration, click here: Registration link

We offer tiered registration fees for:

  • Fee for a continuing education (CŽV) participant: 2956 Kč
  • Fee for a Charles University student: 541 Kč