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User Story #6250 (closed)

Opened 11 years ago

Closed 8 years ago

Tiling support

Reported by: wmoore Owned by: wmoore
Priority: major Milestone: Unscheduled
Component: Specification Keywords: n.a.
Cc: cxallan, ajpatterson, mlinkert, ngdias@… Story Points: n.a.
Sprint: n.a. Importance: n.a.
Total Remaining Time: 2.0d Estimated Remaining Time: n.a.

Description (last modified by wmoore)

Both the data model and OMERO functionality could do a better job of supporting Tiling.

E.g.

http://www.openmicroscopy.org/community/viewtopic.php?f=15&t=722

http://www.openmicroscopy.org.uk/community/viewtopic.php?f=4&t=749&p=2723

Workflows to support:

  • Import a bunch of single plane tiffs or colored jpegs etc each with an X and Y position, either defined in pixels or stage units or microns.
  • Need to be able to stitch them together into a Big image, handling overlap and gaps.

Some questions to resolve:

  • Can we use <Image><StageLabel X=100.2 Y=256.5> or <Plane PositionX=100.2 PositionY=256.5> for tiling if we don't know the units? These are unitless ("microscope reference frame")
  • How do we distinguish from X and Y stored as pixels or stage units or microns or row & column?
  • Do we use StageLabel? or Plane for a bunch of single plane images BEFORE stitching them together? Does it matter? I guess we usually have more than one plane at each Stage position (E.g. rgba from slide scanner).
  • Stitching algorithm should probably check Plane for PositionX etc and if not found, then use StageLabel?
  • Does the "Big Images API" support setting an arbitrary region?

Change History (4)

comment:1 Changed 11 years ago by wmoore

  • Description modified (diff)

comment:2 Changed 11 years ago by wmoore

  • Milestone changed from OMERO-Beta4.3.2 to Unscheduled

comment:3 Changed 8 years ago by mlinkert

  • Cc mlinkert ngdias@… added

It would also be useful to support the workflow of a pre-stitched image having been imported; the original number of X/Y tiles and overlap pixels or percent can then be stored for posterity (or potentially undoing the stitching later). See also http://lists.openmicroscopy.org.uk/pipermail/ome-users/2014-April/004335.html.

comment:4 Changed 8 years ago by wmoore

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

Creation of a Big tiled image by calling setTile() in sequence to cover the whole image is demonstrated here: https://gist.github.com/joshmoore/816cdf461669a7e06d46

Saving of stitching overlap etc will be covered by Original Metadata if this data is available in the imported file. Otherwise need to save it as an annotation or in image description.

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