ITK at the 2015 ImageJ User & Developer Conference

The 5th ImageJ User & Developer conference, held on September 3-4th at the University of Wisconsin-Madison, brought members of the ImageJ community from all around the world to improve software knowledge. The conference was organized by Kevin Eliceiri and team at the LOCI Lab. Presentations, lightning talks, workshops, and posters were a community forum to discuss recent developments, highlight case studies, plugins, and solutions to common problems.

Over 250 attendees at the ImageJ conference listens to Wayne Rasband’s keynote. Image credits: Kristy Wendt.

We gave a workshop on Image Registration with SimpleITK. The workshop introduced ITK / SimpleITK, how ITK/SimpleITK currently interoperates with ImageJ2 / Fiji, and how the image registration framework works in SimpleITK. Material was delivered in subsections as Python Jupyter notebooks. For each section, and short lecture introduced the material, then participants interactively went the tutorial material with their partner, and everyone went through the answers to exercises at the end. By clicking a URL for the conference, participants were immediately able to work on a dedicated Jupyter Docker image running on temporary cloud servers.

Following the conference, a productive, week-long hackathon was held. While dirtying whiteboards with the occasional running excursion around the trails of Lake Mendota, a lot of progress was made in ImageJ2 / ITK / SimpleITK integration by working with Mark Hiner, Curtis Rueden, Brian Northan, Tobias Pietzsch, Christian Dietz, Florian Jug, Stephan Saalfeld, and others. The SCIFIO ImageIO plugin for ITK, which allows ITK to read a number of microscopy formats via SCIFIO, was improved. Moreover, a new repository was created, where new exciting examples and code was added to call SimpleITK from Fiji:

• SimpleITK image <-> ImageJ2 dataset transparent conversion

• Call SimpleITK from a ImageJ2 Jython script

• Use a SimpleITK filter to implement an ImageJ2 Op

• Bundle SimpleITK’s native binaries for consumption via Maven​

Curtis Rueden explains ImageJ2 and Fiji. Image credits: Kristy Wendt

The ImageJ community continues to grow in open source image processing for the biosciences and beyond, and we look forward to future collaborations!