Task #12556 (closed)
Bug: CZI dimensionality misparsed
| Reported by: | omero-qa | Owned by: | mlinkert |
|---|---|---|---|
| Priority: | minor | Milestone: | 5.0.6 |
| Component: | Bio-Formats | Version: | 5.0.4 |
| Keywords: | n.a. | Cc: | l.maier@…, janosch@… |
| Resources: | n.a. | Referenced By: | n.a. |
| References: | n.a. | Remaining Time: | n.a. |
| Sprint: | n.a. |
Description (last modified by rleigh)
https://www.openmicroscopy.org/qa2/qa2/qa/feedback/9521/
Expected: C=3 Z=11 (T=1)
Actual: C=3 Z=11 T=4
However, the actual file contains entirely different T=18 and S=140 values, plus metadata for all 140 sites. None of these appear when reading into Zen Blue 2012. From the CZI:
<SizeX>512</SizeX>
<SizeY>512</SizeY>
<SizeZ>11</SizeZ>
<SizeT>18</SizeT>
<SizeC>3</SizeC>
<SizeS>140</SizeS>
Change History (6)
comment:1 Changed 10 years ago by rleigh
- Component changed from from QA to Bio-Formats
- Description modified (diff)
comment:2 Changed 10 years ago by rleigh
comment:3 Changed 10 years ago by ejrozbicki
- Cc janosch@… added
comment:4 Changed 10 years ago by mlinkert
See QA 10301.
comment:5 Changed 10 years ago by mlinkert
- Milestone changed from Unscheduled to 5.1.0-m2
- Resolution set to fixed
- Status changed from new to closed
Fixed with: https://github.com/openmicroscopy/bioformats/pull/1386
New builds with this fix are not yet available, though.
comment:6 Changed 9 years ago by Melissa Linkert <melissa@…>
(In [cd26576c220d05cf85d88bb7af55e2e4d7c506b5/bioformats.git] on branch develop) Zeiss CZI: fix dimension calculations when expected planes are missing
See #12556.
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From Lorenz: "The image was acquired with Zen black 2012, using the autosave function. Autosave was configured to split timepoints and positions (series). All generated files together do have T=18 and S=140, but each individual file is only a C=3 Z=11 (T=1) subset of it. Many of the other files are read correctly with T=1, but this is an example of the failing ones."