Ticket #45 (closed feature: moved)

Opened 10 years ago

Last modified 5 years ago

Integrate OMERO with ImageJ

Reported by: curtis Owned by: curtis
Priority: major Milestone: imagej-2.0.0
Component: Analysis Plugins Version:
Severity: non-issue Keywords:
Cc: Blocked By:
Blocking: #1003

Description (last modified by curtis) (diff)

We wish to provide a robust  OMERO client as a plugin to ImageJ. Long-term goals include:

  • Download raw and/or rendered images from the OMERO server on demand.
  • Upload derivative images back to the server after performing local image processing.
  • Visualize associated metadata, particularly regions of interest.
  • Store changes as separate revisions, to track data provenance and workflow history.

For now, the OMERO team has released a preliminary  OMERO plugin for ImageJ that works with OMERO Beta 4.1.0. Prior to that, LOCI had a set of  OME plugins that worked with OMERO Beta 3.

We would like to improve the current OMERO plugin to implement the loci.formats.IFormatReader and loci.formats.IFormatWriter interfaces, which will allow smooth operation with the current  Bio-Formats plugins.

Change History

comment:1 Changed 10 years ago by curtis

  • Description modified (diff)

comment:2 Changed 10 years ago by curtis

  • Description modified (diff)

comment:3 Changed 9 years ago by curtis

  • Owner set to curtis
  • Status changed from new to assigned

comment:4 Changed 8 years ago by curtis

  • Type changed from task to feature

comment:5 Changed 8 years ago by curtis

  • Blocking 1003 added

comment:6 Changed 8 years ago by curtis

  • Milestone changed from imagej-2.5 to imagej-2.0-final

comment:7 Changed 5 years ago by curtis

  • Status changed from assigned to closed
  • Resolution set to moved

The  ImageJ-OMERO project is intended to address this work.

Download raw and/or rendered images from the OMERO server on demand.
Upload derivative images back to the server after performing local image processing.

These two are done

Visualize associated metadata, particularly regions of interest.

See ImageJ-OMERO issues  #1 and  #2

Store changes as separate revisions, to track data provenance and workflow history.

OMERO does not yet have a revision system in place; when it does, we can examine what, if anything, needs to be done for ImageJ interoperability to make use of it.

Last edited 5 years ago by curtis (previous) (diff)
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