Difference between revisions of "2017-09-25 - KNIME Image Processing hackathon"

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* With {{Person|Eglinger}}, began work on several related SciJava scripting enhancements ([https://github.com/scijava/scijava-common/issues/261#issuecomment-331487719 1]).
 
* With {{Person|Eglinger}}, began work on several related SciJava scripting enhancements ([https://github.com/scijava/scijava-common/issues/261#issuecomment-331487719 1]).
 
* Helped {{Person|HedgehogCode}} and {{Person|frauzufall}} with ImageJ/TensorFlow integration and API improvements (PR(s) to <code>imagej/imagej-tensorflow</code> forthcoming).
 
* Helped {{Person|HedgehogCode}} and {{Person|frauzufall}} with ImageJ/TensorFlow integration and API improvements (PR(s) to <code>imagej/imagej-tensorflow</code> forthcoming).
* With {{Person|Dietzc}}, continued work on the next-generation SciJava Struct API, including overhauled an widget framework and Swing widget implementations (as of this writing, on an unstable branch of <code>scijava/scijava-ops</code> repository; see [https://github.com/scijava/scijava-common/issues/42#issuecomment-332658377 here] for a written update with illustration of progress).
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* With {{Person|Dietzc}}, 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 <code>scijava/scijava-ops</code> repository; see [https://github.com/scijava/scijava-common/issues/42#issuecomment-332658377 here] for a written update with illustration of progress).
 
* Helped {{Person|chaubold}} set up his {{GitHub | org=ilastik | repo=ilastik4ij | label=shiny new Ilastik-ImageJ integration}} with [[Travis CI]] and deploy it to the ImageJ Maven repository.
 
* Helped {{Person|chaubold}} set up his {{GitHub | org=ilastik | repo=ilastik4ij | label=shiny new Ilastik-ImageJ integration}} with [[Travis CI]] and deploy it to the ImageJ Maven repository.
  

Revision as of 14:40, 28 September 2017

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

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 ({{GitHub | org=imagej | repo=imagej-maven-plugin | pr=24 | label=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

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.

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)