Bioimage Analysis Training Resources


This resource consists of a collection of training modules that have been used to teach a number of courses.

Each module can be tought in 30-45 min and covers a specific aspect of image analysis. Links to prerequisite and suggestions what could be tought next are give for each module. This provides trainers guidance on how to combine modules into a longer workshop. See also the module dependencies network.

The modules are meant to be taught hands-on, i.e. following the teacher’s guidance, students execute the relevant steps in an image analysis software on their computers. The modules provide those steps for several major image analysis platforms, such as ImageJ GUI, ImageJ Macro, Python and Galaxy. Please see our teaching tips.

We are a community of developers and trainers and we welcome any kind of collaboration! Please see our contributors guide and get in touch by writing an issue.

To get a sense for how this material may be used we compiled a selection of consolidated courses:

Basic Bioimage Inspection

Learn to inspect your images and visualize your data.

6 modules 4.5 hours 0.15 CP

Image Data Formats

Learn how to open and handle different image data formats.

5 modules 3.75 hours 0.125 CP

Basic Bioimage Analysis

Learn essential concepts of image analysis, such as segmentation, intensity measurements, and filtering.

12 modules 9 hours 0.3 CP

Basic Batch Analysis

Learn how to automatically process image analysis tasks on multiple images.

5 modules 3.75 hours 0.125 CP

Cloud Based Bioimage Analysis

Learn about executing bioimage analysis on remote compute resources.

2 modules 1.5 hours 0.05 CP

Bioimage Batch Analysis Essentials

Crash course to learn the essentials of how to devise a basic image analysis workflow and how automatically apply it on multiple images.

2 modules 3 hours 0.1 CP

Module dependecies network

Prerequiste dependencies between modules. Click on a module to highlight all his prerequisites. Shift-Click on a module to go the respective module