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Ticket #570 (closed enhancement: fixed)

Opened 2010-09-29T20:00:52-05:00

Last modified 2010-10-08T17:15:36-05:00

Populate ImageJ's 'origin' metadata

Reported by: melissa Owned by: melissa
Priority: major Milestone: bio-formats-4.2.1
Component: plugins Severity: cosmetic
Keywords: Cc: curtis, dscho, white@…
Blocked By: Blocking:


The ImageJ import plugin should be populating the '*Origin' fields in ij.measure.Calibration using the values of MetadataRetrieve.getPlanePosition*(...).

This can be tested with tiled LSMs (see data/zeiss-lsm/dan/tiled/), but would also be useful for all the other formats that support multiple tiles and/or stage positions.

Change History

comment:1 Changed 2010-10-02T12:25:07-05:00 by melissa

(In [7018]) Sets the Calibration.*Origin values to equal the stage position (if present). See #570.

comment:2 Changed 2010-10-02T12:35:09-05:00 by melissa

As noted above, r7018 should populate the origin metadata. However, the tiled LSM files are not reporting the correct position information, so this is not completely fixed yet.

Also, we need to decide whether or not the changes in r7018 actually reflect how we want to use Calibration.*Origin. What we are doing now is to set the origin to be the stage position - so when you select "Image > Properties", the "Origin" field shows the stage (or tile) position in pixels.

However, if you mouse over the image, you will notice that the X, Y, and Z coordinates look quite incorrect. The solution would be to set the origin such that the XYZ coordinate of the upper-left-most pixel in the image is the stage or tile position. This would mean that the coordinates would be correct if you mouse over the image, but the "Origin" field in "Image > Properties" would not make much sense.

If anyone has a preference, I would be very glad to hear it.

comment:3 Changed 2010-10-06T18:07:09-05:00 by melissa

(In [7040]) Progress on reading position data from LSM files. See #576, see #570.

comment:4 Changed 2010-10-07T12:03:34-05:00 by curtis

Hmm, it sounds like the "Origin" metadata is not used exactly how I thought. So I'm not actually sure it's the best place to populate the stage positions after all.

Wayne recently added a new macro function to ImageJ called getInfo that returns the value corresponding to a specific field in the Image Info window (Image > Show Info...).

So, perhaps we should simply populate the Info window with some of the key standardized fields according to a standard naming convention (ideally matching the OME schema). Then we can avoid using Origin for something other than its originally intended use.

comment:5 Changed 2010-10-08T16:23:17-05:00 by melissa

(In [7054]) Reverted r7018, see #570.

comment:6 Changed 2010-10-08T17:04:42-05:00 by melissa

(In [7055]) Standardized storage of stage positions in the original metadata hashtable. See #570.

All readers that store stage positions in Plane.PositionX or Plane.PositionY will now also store them in the original metadata hashtable as "X position for position #n" and "Y position for position #n", where n is the series number indexed from 1.

comment:7 Changed 2010-10-08T17:15:36-05:00 by melissa

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

Closing this ticket, as you can now retrieve the stage positions from the original metadata hashtable and the OME-XML window. See #582 for further progress on standardized original metadata keys, or if you don't like the keys introduced in r7055 (they were chosen for compatibility with what NativeND2Reader uses).