This resource consists of a collection of bioimage analysis training modules that have been used for several years to teach a number of courses.
The material is divided into small modules, where the teaching of each module should take about 30 minutes. Each module covers a specific aspect of image analysis. At the beginning of each module there is a list of modules containing prerequisite topics. At the end of each module there are suggestions of what could be taught next. This provides trainers guidance on how to combine modules into a longer workshop.
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.
Image Data Formats
Learn how to open and handle different image data formats.
Basic Bioimage Analysis
Learn essential concepts of image analysis, such as segmentation, intensity measurements, and filtering.
Basic Batch Analysis
Learn how to automatically process image analysis tasks on multiple images.
Cloud Based Bioimage Analysis
Learn about executing bioimage analysis on remote compute resources.
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.