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Ticket #344 (closed task: fixed)

Opened 2011-02-15T16:21:56-06:00

Last modified 2011-09-22T14:05:18-05:00

Create OME-XML to 2D Stitcher conversion utility for Fiji

Reported by: curtis Owned by: curtis
Priority: major Milestone: imagej2-b1-initial
Component: Analysis Plugins Version:
Severity: major Keywords:
Cc: dscho Blocked By:
Blocking:

Description

Johannes Schindelin and I discussed a conversion tool for reading OME-XML metadata and outputting a 2D Stitcher metadata text file. I need to create a simple plugin for reading the OME-XML timestamps and writing to the 2D Stitcher format.

Once complete, I should send it to Johannes and Stephan Preibisch, for integration with Fiji and/or the 2D Stitching plugins.

Change History

comment:1 Changed 2011-03-13T21:35:31-05:00 by curtis

  • Milestone changed from biweekly-2011: Feb-28 to Mar-11 to biweekly-2011: Mar-14 to Mar-25

comment:2 Changed 2011-03-28T10:41:56-05:00 by curtis

  • Milestone changed from biweekly-2011: Mar-14 to Mar-25 to biweekly-2011: Mar-28 to Apr-08

I will prioritize this work in the next week.

comment:3 Changed 2011-05-20T16:47:55-05:00 by curtis

  • Milestone changed from biweekly-2011: May-09 to May-20 to biweekly-2011: May-23 to Jun-03

comment:4 Changed 2011-06-20T14:15:21-05:00 by curtis

  • Priority changed from blocker to major
  • Milestone changed from biweekly-2011: Jun-06 to Jun-17 to biweekly-2011: Aug-29 to Sep-09

Going to wait until Johannes starts at LOCI and we can address this together. There's just too much going on with IJ2 to worry about it right now.

comment:5 Changed 2011-08-01T12:10:55-05:00 by curtis

  • Milestone changed from biweekly-2011: Aug-29 to Sep-09 to imagej-2.0-beta1

Milestone biweekly-2011: Aug-29 to Sep-09 deleted

comment:6 Changed 2011-09-22T14:02:09-05:00 by curtis

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

I created the following plugins to address this issue:

Thanks to Jeremy Bredfeldt and Joe Szulczewski for testing and feedback!

comment:7 Changed 2011-09-22T14:05:18-05:00 by curtis

By the way, the plugins can be obtained from LOCI's Fiji update site:

  1. Download and install Fiji, if you haven't done so.
  2. Help > Update Fiji from the menu.
  3. Perform any needed updates. Restart Fiji, then run Update Fiji again. Repeat until "Your Fiji is up to date!"
  4. Click Advanced Mode.
  5. Click Manage Update Sites.
  6. Click Add.
  7. For Name, specify: LOCI
  8. For URL, specify:  https://sites.imagej.net/LOCI/
  9. Click OK.
  10. Click Close.
  11. You will see a new item "plugins/LOCI/misc_plugins..." with status "Install it"
  12. Click Apply Changes.
  13. When prompted, restart Fiji.
  14. You will see the new plugins in the Plugins > Stitching and Plugins > LOCI menus.