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Task #10356 (closed)

Opened 11 years ago

Closed 11 years ago

Last modified 11 years ago

BUG: Trestle CMU-1 and 2 imports distorted

Reported by:	pwalczysko	Owned by:	mlinkert
Priority:	critical	Milestone:	5.0.0-beta1
Component:	Bio-Formats	Version:	n.a.
Keywords:	n.a.	Cc:	fs@…, ux@…,
Resources:	n.a.	Referenced By:	n.a.
References:	n.a.	Remaining Time:	n.a.
Sprint:	FS Demo 2

Description (last modified by pwalczysko)

Imported
/Volumes/ome/data_repo/test_images_good/trestle/openslide/CMU-1/
/Volumes/ome/data_repo/test_images_good/trestle/openslide/CMU-2/
to Gretzky.
The thumbnails displayed okay in Insight, but the first thumbnail was grey in Web.
The images displayed okay in full viewer Inisght and Web, with the exception of Series 1 image (the first image in these folders) in Web.
The Series-1 in Web displays in such a manner that the tiles are okay, but the birds eye insert in bottom right corner never loads up.(see screenshot)

The images are nevertheless distorted (which is shown in thumbnails as well as in full viewer.
There are black stripes running accross the images Series-1 to Series-3 in both CMU-1 and CMU-2. The images Series 4 to Series 7 are okay.

Imported the CMU-1 set to Howe using today's build - the display is without any black stripes on Series 1 to 3 as expected. This suggests an FS specific import issue

In Web: The display of thumbnail of Series 1 and of the full view of Series 1 on howe is the same as on gretzky (except the black stripes which are only on gretzky) - the thumbnail and bird eye problem in web does not seem to be FS specific.

References

Attachments (8)

trestle CMU-1 first image insight gretzky.png (1.1 MB) - added by pwalczysko 11 years ago.
trestle CMU-1 Series 2 gretzky.png (422.3 KB) - added by pwalczysko 11 years ago.
trestle CMU-1 Series 2 Web gretzky.png (496.0 KB) - added by pwalczysko 11 years ago.
trestle CMU-1 Series 4 Web gretzky okay.png (152.6 KB) - added by pwalczysko 11 years ago.
trestle CMU-2 Series 1 birds eye dows not show up.png (813.6 KB) - added by pwalczysko 11 years ago.
trestle CMU-2 on gretzky insight thumbs.png (83.9 KB) - added by pwalczysko 11 years ago.
trestle CMU-1 on howe web thumbnail display.png (37.0 KB) - added by pwalczysko 11 years ago.
trestle CMU-1 Series 1 on Howe.png (316.4 KB) - added by pwalczysko 11 years ago.

Change History (12)

comment:1 Changed 11 years ago by pwalczysko

Description modified (diff)

comment:2 Changed 11 years ago by mlinkert

Component changed from Import to Bio-Formats
Keywords FS import removed
Owner set to mlinkert

Not FS specific; the problem is in TIFFParser's handling of tiles with non-zero overlap.

showinf -crop 448,352,448,352 test_images_good/trestle/openslide/CMU-1/CMU-1.tif

demonstrates the problem on both develop and dev_4_4.

comment:3 Changed 11 years ago by mlinkert

Resolution set to fixed
Status changed from new to closed

Stable PR opened: https://github.com/openmicroscopy/bioformats/pull/398

comment:4 Changed 11 years ago by mlinkert

Develop PR: https://github.com/openmicroscopy/bioformats/pull/401

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