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2018-12-06 - I2K 2018 Dresden Hackathon

From Monday, December 3, 2018 through Friday, December 7, 2018, the Max Planck Institute of Molecular Cell Biology and Genetics hosts ~10 developers at the Center for Systems Biology in Dresden, Germany for a hackathon to develop KNIME Image Processing and ImageJ2/Fiji core infrastructure and plugins.

Gitter channel:

Topics / Technical Discussions

TensorFlow (Debo, Curtis, Benny)

  • Plan for TensorFlow: ship native libs both CPU and GPU in lib/<platform> directly;
  • TensorFlow update sites and reconcile to new TF version – add tests

SCIFIO (Gabriel, Curtis)

  • Create, migrate LOCI samples, update website with a table of samples
  • Update scifio-bf-compat to split the mega-format into one per reader/writer


Google Scholar: citation count badges on wiki pages

  • What to do about NanoJ using google analytics – i.e. should we have usage stats?
    • [Action item] Ask Ricardo Henriques about it
    • Consider what to write onto code of conduct about what should be allowed

Meet at later point in time—and who is going to do it

  • What to do about the two different logos: ImageJ vs. Fiji
  • Upstream Java issues – send something shortly after January 15
    • [Action item for Ulrik] Writeup from Ulrik and Stephan S. about JavaFX
    • [Action item for Ulrik] Writeup from Tobias about Unsafe


  • doi in maven pom
  • citation badge on wiki pages

Servers (Gaby, Debo, Curtis)

  • Server infrastructure overview with Gaby

rsync mirror to

Labkit as Labeling Editor for KNIME Image Processing

  • Node for editing labels in KNIME based on Labkit was created.
  • Work is not entirely finish. We plan to finish this work during the Ostrava Hackathon.
  • Labkit was extended, and is now able to handle multiple images.
  • A labeling datatype to store labels, and track modifications was developed.

Simple ImageJ API

  • Discussion between: Deborah, Robert, Curtis, Matthias
  • How can we make the scripting in ImageJ2 easier?
  • Setup a table, of scripting examples in IJ1 and IJ2. Improve the IJ2 API where ever it’s obviously required.
  • Write a SimpleIJ gateway, that provides really simple methods for the most frequent tasks in ImageJ.
  • A ImageJ2 script recorder could improve the IJ2 API, as it clearly shows where the API is to verbos.

Big Data Server

  • Discussion Tobias, Gabriella and Matthias about a mechanism for secure user authentication in Big Data Server (and ImageJ Server).
  • It’s needed by biologists, that want to share there data with specific users.
  • ImageJ Server would also benefit, if the access to the API could be authenticated in a similar way.

Octtree Like, Compressed, Fast, Bitmaps for Imglib2

  • Tobias develops a data structure to store bitmap. For iteration, efficient pixels access and little memory foot print at the same time.
  • Such data structures can be used to better express labels in imglib2. Even instance segmentations that consist of millions of labels, can be accessed efficiently if a cell image like cache is used.

HTTPS (Debo, Curtis, Gaby, Tobi)

  • HTTPS java-version-check
  • move list of update sites to a GitHub repository – off the wiki

Updater/Launcher (Debo, Curtis)

  • Add version to db.xml.gz schema
  • Make the updater smart enough to support serving maven artifacts
  • Migrate “make fiji package” to imagej updater
  • improve “make package” to only zip up non-update-site things (“online mode”)
  • Eliminate native launcher in favor of javafx + java-launches-java scheme

Plot Service (Matthias, Curtis)


  • Merge script editor PRs

add “browse javadoc” and “browse source” options for selected code? e.g. on IOService opens DefaultIOService on GitHub or

  • Finish algorithms branch of imagej-mesh – Move imagej-ops mesh package and algorithms into imagej-mesh – See WIP commit message on algorithms branch – Update imagej-ops to call migrated routines


  • Remove modern mode from GUI (Debo, Curtis)
  • Labkit + KNIME (Matthias, Tim-Oliver, others)
  • KNIME+TensorFlow+Server (Tim-Oliver, Benny)
  • Ilastik tracking (Carsten, Mangal)
  • Scenery + KNIME including BigVolumeViewer (Ulrik, Gabriel)
  • Image metadata (Carsten, Marcel)