N5 planning 2020 May 20

Stephan Saalfeld, Davis Bennett, Igor Pisarev, John Bogovic

N5-viewer

Command line tool doesn't currently work on windows.

Is this lower priority if we make Fiji plugins better?

At the Saalfeld lab meeting we talked about:

• scripts don't work because classpath too long (is that right?)
• jgo
• windows powershell
• linking to dependencies in a directory and using wildcard

N5 Opening (Fiji plugin)

• Have a bio-formats like window on open?
• Drag-and-drop would be nice
• File > Import > N5
• Pass an n5 root directory (folder or json?)
  • see what datasets exist, user make choice(s) and open those
• Pass an n5 dataset (folder or json?)
  • Open just that dataset
• Be able to specify bounding box
• Option to force bounding box to conform to block sizes
  • warn if something changes

What happens on "opening"

• As virtual ImagePlus

  • Should be easy to open the whole n5 dataset as imageplus when hardware allows
  • Ensure metadata are preserved

• With bigdataviewer for viewing only

  • maybe not so critical for cosem since neuroglancer exists

• With bigdataviewer with tools

  • such as interactive crop

N5 Saving

• File > Save As.. > N5
• Make saving to new datasets easy
• Make saving a sub-block into an existing dataset hard through the UI
  • but easy (enough) with code.
  • should have examples

Metadata

• Support reasonable specifications.
  • Igor's n5-viewer spec
  • COSEM spec

Distribution

Fiji update site

• n5-zarr (lower priority)
  • needs blosc

N5-explort (long term)

Make something akin to hdf-view

• use eclipse swt! - Stephan