Design microscopy experiment with examples

Course description:

The two-day course consists of lectures and hands-on sessions which will demonstrate basics in design of experiments, for instance hypothesizing, sampling, data dependency, statistical power or hypothesis testing in biology. The examples will be provided in the field of light microscopy and proteomics. The participants will learn the ways to correctly acquire data using high-end microscopes using a wide pallet of methods such as FLIM, SHG or CARS or proteomic approaches. In addition to that the participants will process and analyse the data using traditional approaches, stereology or AI tools or VR in Fiji or Python. Finally, the participants will be taught the data interpretation and presentation.

Although the course is biology science oriented, the skills you will acquire are valid and necessary in any area of research, development or industry. 

Registration and more information:

CANCELLED: 3D Bioimage Analysis Fundamentals Workshop

Course description:

This 5-day workshop is intended to give a thorough introduction to Bioimage analysis for individuals with little to no prior experience but who want to develop some basic skills in image processing and analysis workflows using both open-source and proprietary software. Participants will get hands-on experience with image restoration, segmentation techniques, feature extraction and tracking using classical and advanced machine and deep learning tools. Most importantly, students will gain insight in data visualization and analysis for reproducible research. By the end of the workshop, attendees will have the opportunity to work on a final project, in which they will be able to apply the newly learned skills on a real-world bioimage analysis challenge.

Workshop Objectives:

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

• Understand foundational microscopy techniques and the principles of bioimage acquisition and analysis.
• Apply essential image processing methods, such as thresholding and segmentation, to analyze bioimages effectively.
• Use FIJI/ImageJ for performing detailed image analysis, including stitching, colocalization, and intensity-based comparisons.
• Leverage ZEISS arivis for advanced 3D visualization, machine learning-based segmentation, and tracking.
• Create reproducible data visualizations and establish workflows for consistent bioimage data management.
• Engage in hands-on sessions designed to tackle real-world bioimage analysis challenges.
• Connect and collaborate with peers, fostering professional networking and knowledge exchange.

Registration and more information:

Advanced BioImage Analysis

Course description:

Join the comprehensive course organized by the Viničná Microscopy Core Facility at the Charles University, Prague to master image analysis using cutting-edge tools like ImageJ, Huygens, Arivis Vision4D, and Python. You’ll learn key techniques including deconvolution, segmentation, colocalization, and deep learning models, alongside practical applications in biological imaging.

Course Highlights:

• ImageJ: Learn segmentation, colocalization, and deep learning models.
• Huygens: Explore advanced deconvolution, stitching, and image corrections.
• Arivis Vision4D: Work with 3D imaging, segmentation, and tracking.
• Python: Master data analysis with Pandas, Bokeh, and statistical best practices.

Perfect for researchers and scientists looking to elevate their image analysis skills!

Course website:

To sign up contact the course organizer Mgr. Zuzana Burdíková, Ph.D. at burdika@natur.cuni.cz

BioImage Analysis

Course description:

TBD

Registration and more information: