Task #12977 (closed)
Opened 9 years ago
Closed 8 years ago
BUG: VoxelSizeZ reading in Metamorph
| Reported by: | bramalingam | Owned by: | mlinkert |
|---|---|---|---|
| Priority: | minor | Milestone: | Unscheduled |
| Component: | Bio-Formats | Version: | 5.1.2 |
| Keywords: | MetamorphReader | Cc: | pierre.bourdoncle@… |
| Resources: | n.a. | Referenced By: | n.a. |
| References: | n.a. | Remaining Time: | n.a. |
| Sprint: | n.a. |
Description
ref : https://www.openmicroscopy.org/community/viewtopic.php?f=13&t=7864
And,
1) Although we don't display the voxel sizeZ in the metadata table, the ome-xml contains the voxelSizeZ value. But this value does not correspond with the values mentioned in the forum thread.
Change History (2)
comment:1 Changed 9 years ago by mlinkert
- Keywords MetamorphReader added
comment:2 Changed 8 years ago by sbesson
- Resolution set to fixed
- Status changed from new to closed
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To fix the physical Z size, the difference between the absolute Z positions will need to be used. The absolute Z positions are already parsed by MetamorphHandler? (https://github.com/openmicroscopy/bioformats/blob/develop/components/formats-gpl/src/loci/formats/in/MetamorphHandler.java#L94); you can see the Z values in the file by checking for "z-position" in the output of "tiffinfo" on either of the files. Updating https://github.com/openmicroscopy/bioformats/blob/develop/components/formats-gpl/src/loci/formats/in/MetamorphReader.java#L778 to prefer handler.getZPositions() should work.
Adding the calculated physical Z size to the metadata table should just be a matter of calling addSeriesMeta(...) as is done elsewhere in MetamorphReader?.