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

(Add Stelfrich's projects)
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* Fixed some bugs with respect to <code>@Parameters</code> ({{GitHub | org=imagej | repo=imagej-common | pr=69 | label=1}}, {{GitHub | org=imagej | repo=imagej-legacy | pr=171 | label=2}})
 
* Fixed some bugs with respect to <code>@Parameters</code> ({{GitHub | org=imagej | repo=imagej-common | pr=69 | label=1}}, {{GitHub | org=imagej | repo=imagej-legacy | pr=171 | label=2}})
 
* Paired with {{Person|Rueden}} to push the cloud-based build and deploy infrastructure
 
* Paired with {{Person|Rueden}} to push the cloud-based build and deploy infrastructure
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=== Tobias Pietzsch ===
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* Worked on imglib2 discrete regions framework (imglib2-roi branch [https://github.com/imglib/imglib2-roi/tree/8bafc8de2d83531aaef46ee36964731a78204589 "cleaned-up"], imglib-tests branch [https://github.com/imglib/imglib2-tests/tree/ec0df49bf5fc344f6ae5af5fec8584a36e3d2ca2 "roi"]).
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* Reviewed imglib2-roi {{GitHub | org=imglib | repo=imglib-roi | pr=29 | label=Masks PR}}, and worked on revision/re-implementation of core interfaces and operators  (imglib2-roi branch [https://github.com/imglib/imglib2-roi/tree/c41c93acf696b801e13f5023bf00527c04722263  "troi"]).
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* Worked on reviewing and integrating "dynamic bookmarks" feature by [https://github.com/maxkleinhenz/bigdataviewer-core Max Kleinhenz] into BigDataViewer.
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* Minor BigDataViewer features to help {{Person|tibuch}} with [https://github.com/knime-ip/knip-bdv Big Data Viewer GUI].
  
 
== Technical discussions ==
 
== Technical discussions ==

Latest revision as of 04:14, 6 October 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

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 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.

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)