Module 1: Introduction to image processing and analysis with ImageJ (3 days)

Day 1: Image processing for scientific illustration:

– What is Image J? Where can I find it? How do I install it?

– What is an image? How do I open proprietary image formats?

– What is the histogram of an image? How do I manipulate it?

– Colour images: the concept of a colour tables, different types of colour images (overlay, composite, etc.).

– Distance calibration of an image.

– Efficiently generating figures.

– Working with 3D images: 3D projections and visualisation.

Day 2: Image processing for analysis:

– Manipulating regions of interest and simple 2D measurements.

– Image enhancement prior to quantification: filters (linear, rank, frequency).

– Working on a binary image: morpho-mathematical concepts.

– Connected component analysis, enumeration and quantification of 2D and 3D objects.

– Image intensity calibration.

– Image segmentation (B&W and colour).

Day 3: On demand topics/Work on your images session

Examples:

– Advanced quantification (e.g. co-localisation, tracking etc).

– Introduction to task automation.

Module 2: Task automation in ImageJ: macros (3 days)

– Preparing for automation: defining basic tasks and the concept of algorithms.

– Simple task automation: macro-recorder and batch processing.

– Notion of variables, loops and conditional execution.

– Using ImageJ’s own functions in macros: filtering, regions of interest manager, morphometry, etc.

– Using functions added to ImageJ in macros: plug-ins.

– Representing results: data tables and graphs.

– Simplifying repeated actions and clarifying code: notions of functions.

– Interacting with the user: inputs and interfaces.

Module 3: Java programming for imageJ: plug-ins (3 days)

– Basic concepts of object-oriented programming.

– Choosing and using an IDE (Integrated Development Environment).

– Using ImageJ functions: configuring the IDE for its use.

– Elements of the ImageJ API: image management.

– Elements of the ImageJ API: representing data in graphical form.

– Creating a graphical interface using the IDE.