[ome-devel] Prairie View XML changes for upcoming v5.2 Release

[Andrew Patterson]

Hello Curtis, Jimmy,

On 10 Oct 2014, at 22:53, Curtis Rueden <ctrueden at wisc.edu> wrote:
> == SamplesPerPixel vs. Integration ==
> 
> Jimmy wrote:
> > we often average 3 raw samples together to form 1 pixel value, and
> > only write the single pixel value to Tiff.  We would like our Prairie
> > XML file to still reflect SamplesPerPixel = 3 so users could go back
> > and reference that value.
> 
> The term "SamplesPerPixel" has a very technical meaning in TIFF and OME-XML: it is the number of sample values actually recorded in the file. Since there is only one sample value recorded per pixel, SamplesPerPixel must equal 1 for this data.
> 
> Conversely, what you describe is, I think, what the OME schema refers to as "integration" [1]. It's not exactly "frame" averaging, but seems conceptually equivalent. Andrew, would you agree?

The SamplesPerPixel value is a little odd for historic reasons. It comes from having a specific value for it some years ago when we had separate LogicalChannel and ChannelComponent elements in the model. These were merged to form the current Channel element in September 2009. The value was on LogicalChannel and was the count of ChannelComponent elements (each with their own set of pixels) that the LogicalChannel contained. It was moved to Channel and retained for consistency but it can also be calculated from the structure of other data in the file.
Even if several measurements were taken, if there is only one computed pixel value stored in the file then SamplesPerPixel should equal 1.

From the description of your data I think setting Integration in DetectorSettings is the best fit.

Hope this helps,

Andrew



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