Task #13233 (closed)
Opened 8 years ago
Closed 8 years ago
Bug: CZI pixel data
| Reported by: | bramalingam | Owned by: | mlinkert |
|---|---|---|---|
| Priority: | minor | Milestone: | Unscheduled |
| Component: | Bio-Formats | Version: | Bio-Formats-5.1.8 |
| Keywords: | external, ZeissCZIReader | Cc: | bf@…, arthur_michaut@… |
| Resources: | n.a. | Referenced By: | https://trello.com/c/y6KpD3sU/4-czi-tickets |
| References: | n.a. | Remaining Time: | n.a. |
| Sprint: | n.a. |
Description
ref : QA 17179
https://www.openmicroscopy.org/community/viewtopic.php?f=13&t=8050
Testing results:
Series 3 seems to have issues with the pixel data when tested with Bio-Formats 5.1.9 (FIJI).
The pixel data was compared with Zen-Lite.
Change History (4)
comment:1 Changed 8 years ago by mtbcarroll
- Cc bf@… arthur_michaut@… added
- Keywords external ZeissCZIReader added
comment:2 Changed 8 years ago by mlinkert
comment:3 Changed 8 years ago by sbesson
- Milestone changed from B-F-5.2.0 to Unscheduled
- Referenced By set to https://trello.com/c/y6KpD3sU/4-czi-tickets
comment:4 Changed 8 years ago by mlinkert
- Resolution set to fixed
- Status changed from new to closed
Confirmed the bug again in 5.1.9, but 5.2.2 now shows the correct dimensions and images for series 3. See https://github.com/openmicroscopy/data_repo_config/pull/133
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You may also have a look at Agilo extensions to the ticket.
See also https://github.com/openmicroscopy/bioformats/issues/2377. The file attached to the GH issue exhibits a similar problem of the detected XY dimensions not matching the actual image dimensions - this is confirmed with Zen.
This is also an example of multi-scene/multi-tile stitching not working quite right; with develop, 16 series (== 4 scenes x 4 tiles) are detected but the SizeX/SizeY are correct for 2x2 stitched tiles, not a single tile. https://github.com/openmicroscopy/bioformats/pull/2330 does not seem to have had an effect, as 5.1.8, 5.1.9, 5.1.10, and develop were all tested and all exhibit the stitched dimensions but unstitched series count.