This hands-on course will introduce you to developing within and for the Fiji, ImageJ2, and KNIME ecosystems. Our aim is to introduce you to the core libraries and concepts behind those analysis tools, what software engineering infrastructure is commonly used, and how the existing community collaborates and communicates.
More specifically you will learn about IDE support, ImgLib2, SciJava, ImageJ ops, VisTools and BigDataViewer from a development point of view, KNIME image processing node generation, and more. This library knowledge will be complemented by introducing you to Maven and our communities’ deployment cycle. We will not cover Java programming in general, nor programming with Fiji macro language.
Ideally you join because you are or are planning to build bioimage analysis software within the above mentioned ecosystems. Having a concrete project in mind will help you to ask the right questions and will generally benefit the entire group.
How to develop for Fiji, ImageJ2, and KNIME Image Processing (KNIP).
Getting to know the fundamental libraries.
Getting to know the available software engineering infrastructure.
Hack-time: bring your ideas, solve your problems!
All participants are expected to have experience using Fiji/ImageJ. Ideally, you already are a person who creates useful scripts or macros within Fiji on a regular basis. Maybe you even come with some experience in making your own ImageJ plugins or KNIME nodes.
All participants are expected to have more than basic programming experience in Java, or can make up for the lack of it by having extensive experience with another object-oriented and template-capable programming language.
Registration + Selection Process:
You must register for this event. Since we have only limited space available we will need to select participants based on their knowledge and eagerness to learn. For that reason please wait until we contact you before you start booking your trip and your accommodation.
The registration fee is 200 EUR. If you would like to participate but cannot afford it please contact us to apply for a fellowship.