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2017-09-25 - KNIME Image Processing hackathon

From Wednesday, September 20, 2017 through Friday, September 28, 2017, Christian Birkhold (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.


Hackathon progress

Curtis Rueden

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

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 ImageJ 1.x 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

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)