NOTICE! This is a static HTML version of a legacy ImageJ Trac ticket.

The ImageJ project now uses GitHub Issues for issue tracking.

Please file all new issues there.

Ticket #136 (closed task: fixed)

Opened 2010-07-21T15:17:49-05:00

Last modified 2012-02-24T13:41:36-06:00

OME plugin prep work

Reported by: bdezonia Owned by: bdezonia
Priority: major Milestone: biweekly-2010: Aug-09 to Aug-20
Component: OME Version:
Severity: serious Keywords:
Cc: Blocked By:
Blocking: #1003


LOCI will be participating in writing an IJ plugin to download data from OME servers. Plan is to not develop yet but to have a plan for when and how we'd do this in collaboration with other people.

For now need to setup the latest version of OME on a test server box. Populate with data. Test whether existing plugins even work.

Our student Eric may participate on this project.

Change History

comment:1 Changed 2010-07-21T15:18:02-05:00 by bdezonia

  • Status changed from new to assigned

comment:2 Changed 2010-07-21T15:18:04-05:00 by bdezonia

  • Status changed from assigned to accepted

comment:3 Changed 2010-08-02T17:28:14-05:00 by bdezonia

Got OME updated from 4.1 to 4.2 on
Insight clients can access server.
The ImageJ OME plugin does not get past an authentication screen.
LOCI's ome-io plugin can compile against 4.2. Curtis working to get it working.

Misc. todo:

  • email LOCI users. Let them know we've upgraded to 4.2 and point them to new OME clients
  • coordinate with WiscScan team to setup the omero.fs DropBox
  • create an init.d script on open... that will start up omero after boot

comment:4 Changed 2010-08-03T17:30:00-05:00 by bdezonia

init.d shell script for omero setup on open.mi...

comment:5 Changed 2010-08-09T11:40:45-05:00 by bdezonia

Working with OMERO forum helpers to determine why we can't login using the webclient. We just get redirected to a login screen though authentication passed accoring to logs.

Note this is the same behavior as the ImageJ OME plugin. Did our test of the ImageJ OME plugin throw the server into a bad state? Webclient worked the first time we tried. Then we tried ImageJ plugin. Later noticed webclient not working.

comment:6 Changed 2010-08-16T10:11:10-05:00 by bdezonia

Curtis found solution to web client issues. He also continued work on LOCI's OME plugin. Must determine next steps for this project.

comment:7 Changed 2010-08-16T11:45:24-05:00 by bdezonia

  • Status changed from accepted to closed
  • Resolution set to fixed

ImageJ plugin retested now that our server is correctly upgraded. One can login correctly and download data. The plugin works when interacting with the C & T channels. The Z channel interaction does not work.

comment:8 Changed 2010-08-31T12:04:53-05:00 by curtis

  • Component changed from other to ome

To follow up on the LOCI OME plugin work: never heard back from the OME team on how to access raw pixels from an OMERO server via the Java API. Project shelved for the time being.

comment:9 Changed 2012-02-24T13:41:36-06:00 by curtis

  • Blocking 1003 added