Educators:
Matthias Arzt, Florian Jug, Tobias Pietzsch, Vladimír Ulman, other core Fiji developers (CIBI / DAIS)
Date:
18.06.2017 – 24.06.2017
Location:
Center for Systems Biology Dresden / MPI-CBG
Contents:
This hands-on course will introduce you to developing within and for the Fiji, ImageJ2, and also 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, KNIP 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. During the last 2 days, we plan to work in groups on a number of real-world projects that should ideally result in Fiji plugins that will be made available to the general public.
Learning goals:
- 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-days: bring your ideas, solve your problems!
Prerequisites:
- All participants are expected to have experience using Fiji/ImageJ. Ideally, you should create useful scripts or macros within Fiji on a regular basis and maybe even come with some experience making your own ImageJ plugins.
- All participants are expected to have either programming experience in Java, or experience with another object-oriented and template-capable programming language and the ability to pick up Java fast during the course.
Keywords:
Java, Fiji, ImageJ2, KNIME, ImgLib2, scijava, BigDataViewer, ClearVolume
Tools:
Fiji, KNIME
Contact:
Florian Jug (
Tobias Pietzsch (
Pavel Tomancak (