Ticket #333 (closed task: fixed)

Opened 11 years ago

Last modified 11 years ago

Decide how to handle XZ and XT scans

Reported by: melissa Owned by: melissa
Priority: major Milestone: bio-formats-4.1
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.

Change History

comment:1 in reply to: ↑ description Changed 11 years ago by melissa

Replying to melissa:

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.

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.

comment:2 Changed 11 years ago by melissa

  • Milestone set to bio-formats-4.1.0

comment:3 Changed 11 years ago by melissa

  • Cc andrew.vaughan@… added

comment:4 Changed 11 years ago by melissa

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

(In [4983]) Swap Y and Z if an XZ scan is encountered, or Y and T if an XT scan is encountered. Closes #333.

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