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Task #6616 (closed)

Opened 13 years ago

Closed 12 years ago

Last modified 12 years ago

Bug: Tiling of large images is not lining up correctly

Reported by: sylittlewood Owned by: mlinkert
Priority: major Milestone: OMERO-4.4
Component: Bio-Formats Version: n.a.
Keywords: n.a. Cc:
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: 0.0d
Sprint: 2012-01-03 (5)

Description

When importing Trestle dataset as part of Phase I testing several images were shown to have bad stitching of images.

Task: #6521

See attachment for an example

Attachments (1)

Screen shot 2011-08-29 at 16.55.40.png (1.9 MB) - added by sylittlewood 13 years ago.
Error in big image rendering

Download all attachments as: .zip

Change History (16)

Changed 13 years ago by sylittlewood

Error in big image rendering

comment:1 Changed 13 years ago by mlinkert

  • Component changed from General to Bio-Formats
  • Remaining Time set to 0.5
  • Sprint set to 2011-09-01 (4)

This is currently expected behavior; it should be fixable by checking and respecting the "OverlapsXY" value in the TIFF comment.

comment:2 Changed 13 years ago by mlinkert

  • Status changed from new to accepted

comment:3 Changed 13 years ago by jburel

  • Sprint changed from 2011-09-01 (4) to 2011-09-15 (5)

Moved from sprint 2011-09-01 (4)

comment:4 Changed 13 years ago by mlinkert

  • Milestone changed from OMERO-Beta4.3.2 to OME-5.0
  • Sprint 2011-09-15 (5) deleted

Pushing to next milestone. This bug has been present since the beginning of Trestle support, and only affects Trestle data (which is an obsolete format anyway).

comment:5 Changed 12 years ago by mlinkert

  • Sprint set to 2011-10-27 (1)

comment:6 Changed 12 years ago by jburel

  • Sprint changed from 2011-10-27 (1) to 2011-11-10 (2)

Moved from sprint 2011-10-27 (1)

comment:7 Changed 12 years ago by jburel

  • Sprint changed from 2011-11-10 (2) to 2011-11-29 (3)

Moved from sprint 2011-11-10 (2)

comment:8 Changed 12 years ago by jmoore

  • Sprint changed from 2011-11-29 (3) to 2011-12-13 (4)

Moved from sprint 2011-11-29 (3)

comment:9 Changed 12 years ago by jburel

  • Sprint changed from 2011-12-13 (4) to 2011-12-27 (5)

Moved from sprint 2011-12-13 (4)

comment:10 Changed 12 years ago by Melissa Linkert <melissa@…>

(In [460513f7c4ffefcb9b57ce3ea5a2d4c99e649c73/bioformats.git]) Allow tile overlaps to be specified

Some TIFF-based formats specify that the tiles in an image should overlap by
some number of pixels. So we now have a getSamples(...) signature that can
accept overlap values in X and Y, though nothing is done with these
values at the moment.

See #6616.

comment:11 Changed 12 years ago by Melissa Linkert <melissa@…>

(In [7297b838daf67ea0028d24f636e851743810bf1c/bioformats.git]) Parse tile overlap values

X and Y overlap values are now parsed, and the image dimensions are
adjusted accordingly.

See #6616.

comment:12 Changed 12 years ago by Melissa Linkert <melissa@…>

  • Remaining Time changed from 0.5 to 0
  • Resolution set to fixed
  • Status changed from accepted to closed

(In [184f604e978db5809087312710d4bffbd7a33233/bioformats.git]) Adjust tile coordinates to account for overlap

Closes #6616.

comment:13 Changed 12 years ago by Melissa Linkert <melissa@…>

(In [460513f7c4ffefcb9b57ce3ea5a2d4c99e649c73/bioformats.git]) Allow tile overlaps to be specified

Some TIFF-based formats specify that the tiles in an image should overlap by
some number of pixels. So we now have a getSamples(...) signature that can
accept overlap values in X and Y, though nothing is done with these
values at the moment.

See #6616.

comment:14 Changed 12 years ago by Melissa Linkert <melissa@…>

(In [7297b838daf67ea0028d24f636e851743810bf1c/bioformats.git]) Parse tile overlap values

X and Y overlap values are now parsed, and the image dimensions are
adjusted accordingly.

See #6616.

comment:15 Changed 12 years ago by Melissa Linkert <melissa@…>

(In [184f604e978db5809087312710d4bffbd7a33233/bioformats.git]) Adjust tile coordinates to account for overlap

Closes #6616.

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