Ticket #333 (closed task: fixed)
Opened 2008-12-15T12:02:28-06:00
Last modified 2009-04-07T10:48:46-05:00
Decide how to handle XZ and XT scans
| Reported by: | melissa | Owned by: | melissa |
|---|---|---|---|
| Priority: | major | Milestone: |
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| Component: | bio-formats | Severity: | serious |
| Keywords: | Cc: | sagar.q@…, andrew.vaughan@… | |
| Blocked By: | Blocking: |
Description
Many formats support XZ and XT scans (i.e. Y axis has length 1). Some commercial software displays these scans as X-by-Z images - so if the X axis length is 1024, and the Z axis length is 1024, you would see a single 1024x1024 image. However, Bio-Formats typically returns 1024 1024x1 images.
There have been a few requests to have Bio-Formats display the images as they are shown in the commercial software. We should decide if this is a good idea; if so, we will likely want an option to switch between the two display modes.
Replying to melissa:
This feature can probably be provided by loci.formats.DimensionSwapper. However, DimensionSwapper currently requires that X and Y be the first two dimensions in any order string - we would need to change this so that you could call DimensionSwapper.swapDimensions("XZYCT") to get an XZ scan as a single plane.
The ImageJ plugin would also need to be updated; right now, you can only swap the Z, C and T axes.