ImageJ

From Wednesday, September 20, 2017 through Friday, September 28, 2017, Christian Dietz of KNIME hosted ~20 developers at the KNIME Konstanz Regional Office for a hackathon to develop the KNIME Image Processing extensions along with the underlying ImageJ Ops library, as well as other related and/or supporting technologies such as Ilastik, ImgLib2 and BigDataViewer.

There was a big focus this time on machine learning, particularly deep learning networks applied to biological data.

Participants

• KNIME: Christian Dietz, Gabriel Einsdorf, Jon Fuller, Alexander Fillbrunn, Jonathan Hale, Martin Horn, Simon Schmid, Marcel Wiedenmann, Patrick Winter
• MPI-CBG Dresden: Florian Jug, Matthias Arzt, Tim-Oliver Buchholz, Tobias Pietzsch, Mangal Prakash, Deborah Schmidt, Vladimír Ulman, Benjamin Wilhelm
• Others: Jan Eglinger, Carsten Haubold, Stefan Helfrich, David Kolb, Klim Kolyvanov, Kevin Mader, Julianus Pfeuffer, Stephan Preibisch, Jonas Probst, René Rahn, Curtis Rueden

Hackathon progress

Curtis Rueden

• Worked with Stefan Helfrich on automating releases of SciJava components via Travis CI (1, 2, 3).
• Assisted Stefan Helfrich in improvements to the imagej-maven-plugin (1)
• Reviewed and merged Matthias Arzt's initial revamp of the SciJava log framework (1, 2).
• Reviewed and merged Jan Eglinger's work adding a SciJava widget for File[] inputs (1, 2, 3).
• With Jan Eglinger, began work on several related SciJava scripting enhancements (1).
• Helped Benjamin Wilhelm and Deborah Schmidt with ImageJ/TensorFlow integration and API improvements (PR(s) to imagej/imagej-tensorflow forthcoming).
• With Christian Dietz, continued work on the next-generation SciJava Struct API, including an overhauled widget framework and Swing widget implementations (as of this writing, on an unstable branch of scijava/scijava-ops repository; see here for a written update with illustration of progress).
• Helped Carsten Haubold set up his shiny new Ilastik-ImageJ integration with Travis CI and deploy it to the ImageJ Maven repository.

Florian Jug

• Worked on a KNIME workflow that starts IsoNet-type deep nets on a image column. Works well now, but we want to move tiled executions out from python and move it into KNIME (and also Fiji). This follow-up work will be performed by Deborah Schmidt and Benjamin Wilhelm.
• Received TGMM groin truth data an started working on Tr3d demo dataset.
• Started working on min cell-cycle constraints for Tr2d. This will make the ILP explode...
• Discussions with Curtis Rueden, Stefan Helfrich and Tobias Pietzsch about ImageJ Conference details for 2018.

Tim-Oliver Buchholz

• Worked on the Big Data Viewer GUI.
• Helped Matthias Arzt and Vladimír Ulman with KNIME Image Processing Node development.
• Fixed DefaultDifferenceVariance feature of the Haralick feature-set in imagej-ops (1).

Benjamin Wilhelm

• Worked on CSBDeep Fiji Plugin.
• Added Overlap to TiledView PR in imglib2.
• Worked on API improvements in imagej/imagej-tensorflow with the help of Curtis Rueden.
• Programmed KNIME Image Processing nodes which provied a loop over tiles of an image. See branch on GitHub.

Stefan Helfrich

• Worked on improvements to the imagej-maven-plugin (1, 2, 3)
• Got Carsten Haubold, Matthias Arzt, and Vladimír Ulman started on integrating their SciJava Commands as KNIME nodes
• Reviewed PRs of imagej-ops (1, 2, 3, 4)
• Looked into migration of algorithms from MorphoLibJ to Ops/ImgLib2
• Worked with Klim Kolyvanov on migrating an ImageJ1 plugin to a SciJava Command (and possibly Ops for computations)
• Fixed some bugs with respect to @Parameters (1, 2)
• Paired with Curtis Rueden to push the cloud-based build and deploy infrastructure

Tobias Pietzsch

• Worked on imglib2 discrete regions framework (imglib2-roi branch "cleaned-up", imglib-tests branch "roi").
• Reviewed imglib2-roi Masks PR, and worked on revision/re-implementation of core interfaces and operators (imglib2-roi branch "troi").
• Worked on reviewing and integrating "dynamic bookmarks" feature by Max Kleinhenz into BigDataViewer.
• Minor BigDataViewer features to help Tim-Oliver Buchholz with Big Data Viewer GUI.

Matthias Arzt

• Worked on revamp of the scijava logging framework.
• Worked on LoopBuilder, as tool for writing loops on images with imglib2.
• Got an introduction on KNIME Node development by Tim Oliver and Stefan Hilfrich
• Created a KNIME image processing plugin for image segmentation based on Labkit / Trainable Segmentation.

Technical discussions

• Fiji component and application releases: today and in the future (Curtis Rueden, Florian Jug, Tobias Pietzsch)
  • Next stable release (December 2017) will still follow the 'old' way of doing things.
  • In case the DFG grant comes in and we hired the 2 people they will start implementing the new way of cutting stable releases. This will be great!
• How to integrate ImageJ, KNIME and machine learning frameworks (particularly Keras and TensorFlow)