ImageJ

From Tuesday, July 5, 2016 through Thursday, July 14, 2016, Christian Dietz of the University of Konstanz 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 supporting technologies such as ImgLib2, ClearVolume and the BigDataViewer.

Timeline

The following chart illustrates when everyone was present:

Gallery

• 

  Hackers!

• 

  Hackers at dinner

• 

  Curtis Rueden

• 

  Kyle Harrington

• 

  Richard Domander

• 

  David Hörl

• 

  Christian Dietz and Curtis Rueden

• 

  Kyle Harrington and Ulrik Günther

• 

  Stefan Helfrich and Tobias Pietzsch

• 

  KNIME 3.2: sushi edition

• 

  The gravity-defying salt shaker!

Hackathon progress

Christian Dietz

• Continued work on KNIME SciJava Nodes and KNIME SciJava Scripting

Richard Domander

• Added first ops from BoneJ legacy code - topology namespace and ops for calculating the Euler characteristic (imagej-ops#413)

Kyle Harrington

• Added 3D Mesh Voxelization to imagej-ops (imagej-ops#419)
• Began ThreeDViewer and reached a moderately usable level
• Refactored Funimage to be more Clojure idiomatic

Stefan Helfrich

• Proof-of-principle implementations of MatrixType and VectorType (matrixType)
• Enable using global thresholds as local thresholds in Ops
• Improve default OOBF handling for filters
  • i.e. do not apply an OOBF if an image already is extended
  • Add defined bounds for RandomAccessibles (imglib2/random-access-defined-bounds)
  • Implement Shape.getBoundingBox() (imglib2#27)

Martin Horn & Alexander Fillbrunn

• Started JavaScript based Image Viewer with BigDataViewer as tile-server

Curtis Rueden

• Made major progress on improved op lookups using Nil (a.k.a. "typed null") objects—work still ongoing on the nil branch of imagej-ops; prep work already on master (1, 2)
• Cleaned up the dependencies of ImageJ Ops; in particular, use SCIFIO for I/O, not ImageJ 1.x and AWT (imagej-ops#413)
• Helped clean up Richard Domander's "Topology namespace and ops" PR (imagej-ops#415)
• Created a (not yet functional) Kotlin SciJava script engine (scijava/scripting-kotlin)

Technical discussions

• The future of ImageJ user interfaces: ImageJFX? KNIME? JavaScript + RESTful image server?
• Languages on the JVM: using Scala, Kotlin and/or Groovy for future SciJava components