Services & Facilities

Courses & Tutorials

Our team gives various courses and tutorials throughout the year. Most of our course materials are also publicly available and can be found here.



Introduction to Image Analysis using FIJI (18h)

  • Basic concepts: image characteristics, visualisation, regions of interest and measurements
  • Segmentation 1: thresholding, mask/region analysis, spot detection and skeletonisation
  • Segmentation 2: image filters such as erosion/dilation, distance maps and the watershed algorithm
  • Visualize and explore 3D images
  • Spot detection and segmentation in 3D datasets
  • Measurements in time sequences
  • Tracking basics

Data Analysis and Visualization with R (20h)

  • Introduction to R and Rstudio
  • Data import, manipulation (dplyr), plotting (ggplot2) & reshaping (tidyr)
  • Generating data analysis reports (RMarkdown)


Image J Macro basics 1: Introduction (3h)

  • Macro language basics: variables, comments, commands, etc.
  • Using the macro recorder
  • Writing a simple image processing macro
  • Good practices for reproducible results

ImageJ Macro basics 2: Batch Processing (3h)

  • Macro language elements, string manipulations
  • Flow statements: Conditions and Loops
  • Batch processing

3D Data Visualization & Analysis (3h)

  • Loading and visualizing 3D data
  • tools for analyzing 3D data (like segmentation)

Machine Learning & Illastik (3h)

  • Machine learning concepts
  • Pixel classification with random forest classifier
  • Introduction to the tool Illastik

Deconvolution using Huygens (2.5h)

  • Introduction to image deconvolution
  • Deconvolving images with Huygens Software