Task #8160 (closed)
Opened 7 years ago
Closed 6 years ago
Model: SamplesPerPixel
| Reported by: | wmoore | Owned by: | ajpatterson |
|---|---|---|---|
| Priority: | minor | Milestone: | 5.0.0-beta1 |
| Component: | Specification | Version: | n.a. |
| Keywords: | schema, xsd-2013-1 | Cc: | mlinkert |
| Resources: | n.a. | Referenced By: | n.a. |
| References: | n.a. | Remaining Time: | n.a. |
| Sprint: | n.a. |
Description
For Martin's "sample files.mdb" all the Channels have SamplesPerPixel?="1". The files when displayed in Zeiss viewer have
Average: Frame 2 or Average: Frame 4
I belive it would be appropriate to store this value in SamplesPerPixel? "The number of samples the detector takes to form each pixel value". Although I don't know of a place in the OME model to store "Frame" / "Line" etc and "Average" / "Sum" etc.
Commit that includes these edits to ome.xml: https://github.com/will-moore/openmicroscopy/commit/aff5e1502ffa691ede846a42d06cd5c47090672f
Change History (8)
comment:1 Changed 7 years ago by wmoore
comment:2 Changed 7 years ago by mlinkert
I disagree in this case: changing how SamplesPerPixel? is set will break a lot of things.
The sum of the SamplesPerPixel? values on all Channels in an Image must equal Pixels.SizeC. This allows us to use SamplesPerPixel? > 1 to distinguish between data stored as RGB (SizeC = 3, 1 Channel with SamplesPerPixel? = 3) and multi-channel data stored as separate planes (SizeC = 3, 3 Channels with SamplesPerPixel? = 1). OMERO is spared from having to worry about this because of ChannelSeparator?, but there is a very real need for being able to make this distinction.
In the case of LSM, the channel data is stored as separate planes, which is why SamplesPerPixel? is set to 1. Changing SamplesPerPixel? to 2 means either violating the sum(SamplesPerPixel?) == SizeC rule, or setting SamplesPerPixel? to 0 on all but the first channel.
For my part, I'd much rather see a proper place for this in the schema, so that it's possible to specify the detector sample count, averaging vs. summing, etc. all in one spot that's independent of the metadata describing how the images are actually stored in the file.
comment:3 Changed 7 years ago by wmoore
- Cc mlinkert-x added
- Owner changed from mlinkert-x to ajpatterson
Hmmm - seems like an OME Model issue then.
2011-06.xsd says this on "SamplesPerPixel?"
The number of samples the detector takes to form each pixel value. The SamplesPerPixel attribute is the number of channel components in the logical channel.
It seems that these are two separate parameters. Maybe for now we simply update the docs to state that this is not the same as Frame Average etc.
Also - I didn't see Logical Channel anywhere else in that schema. It's gone now, right?
comment:4 Changed 7 years ago by wmoore
- Component changed from Bio-Formats to Model
- Summary changed from Bug: LSM SamplesPerPixel to Model: SamplesPerPixel
comment:5 Changed 7 years ago by ajpatterson
- Keywords schema added
- Milestone changed from OMERO-4.4 to OMERO-4.5
comment:6 Changed 7 years ago by ajpatterson
- Component changed from Model to Specification
comment:7 Changed 6 years ago by ajpatterson
- Keywords xsd-2013-1 added
- Status changed from new to accepted
comment:8 Changed 6 years ago by ajpatterson
- Resolution set to fixed
- Status changed from accepted to closed
Additional commit: https://github.com/will-moore/openmicroscopy/commit/621b6b5a72da4ae68954a346357580d3b4995e3d
TODO: When making screen-shots of these files in the Zeiss software, I missed some of the Images so I've not been able to verify or update values for these. E.g. SamplesPerPixel?. So they are probably still wrong after these commits.