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2015-07-27 - Janelia Hackathon

    From Sunday, July 27, 2015 through Friday, July 31, 2015, Stephan Saalfeld at HHMI Janelia in Ashburn, Virginia hosted LOCI’s Curtis Rueden and Mark Hiner for a hackathon to unify SCIFIO/ImgLib2 development efforts (with MPI-CBG’s Tobias Pietzsch ), improve support for the Janelia KLB format (with Janelia’s Burkhard Hoeckendorf), and improve the development tools available for Fiji developers.

    Executive summary

    • SCIFIO is headed in a great direction:
      • Will integrate it better into modern, powerful software tools including ImgLib2 and BigDataViewer.
      • Big step toward breaking the limitations of ImageJ1, in particular the 2GPix plane barrier and limited image types.
      • Will make possible things like more transparent and rapid ability to work with multi-position and multi-angle datasets (mosaics, light sheet, etc.).
    • Stability of ImageJ and Fiji—and other applications built on SciJava components—is now easier to validate.

    Technical discussions

    • Unify BigDataViewer and SCIFIO/SciJava cell caches, and caching in general
    • Unify SCIFIO and ImgLib2 metadata data structures
    • Improve Maven tooling for releases and testing.
    • KLB block-based file format:
      • Generalize SCIFIO’s core API to use N-D blocks instead of planes.
      • Consider pure Java implementation of KLB to avoid native lib issues.
      • Enable multithreaded I/O in SCIFIO as painlessly as possible.

    Progress this week

    Future directions

    • Jenkins automation of melting-pot for Fiji testing.
    • Wiki documentation on how to use the melting-pot for testing your components.
    • Completion of development on the SCIFIO “blockization” and unification of ImgLib2 data structures and caching.
    • Convert KLB native code to a pure Java SCIFIO format implementation.