[ome-devel] Recommendation to record spectrums in OME-TIFF

[Munro, Ian]

That would be my understanding as well Curtis.

Ian

On 8 Nov 2013, at 17:33, Curtis Rueden <ctrueden at wisc.edu<mailto:ctrueden at wisc.edu>>
 wrote:

Hi Andrew,

It sounds like Éric simply has one spectra dimension (i.e., C), and thus wouldn't need to use module along C. Instead, for each of his 100 channels, he would add a Channel element with the EmissionWavelength value [1] set matching that channel's wavelength.

Or am I missing something here?

Regards,
Curtis

P.S. I notice the XML documentation for the Channel element says: "An entire spectrum in an FTIR experiment may be stored in a single Logical Channel with each discrete wavenumber of the spectrum constituting a ChannelComponent of the FTIR Logical Channel." This description is out of date and no longer valid, right? We dropped the LogicalChannel/ChannelComponent elements long ago.

[1] https://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2013-06/ome_xsd.html#Channel_EmissionWavelength


On Fri, Nov 8, 2013 at 11:15 AM, Andrew Patterson <ajpatterson at lifesci.dundee.ac.uk<mailto:ajpatterson at lifesci.dundee.ac.uk>> wrote:
Hello Éric,

First, using WaveStart and WaveIncrement is not a good solution. They were dropped completely in 2009 and the upgrade transforms to newer schema used when OMERO or Bio-Formats reads these older files will not preserve the values.

If each of your points is a spectrum from our viewpoint you would be putting an extra dimension into C. To do this you would need to use the Modulo extension:
https://www.openmicroscopy.org/site/support/ome-model/developers/6d-7d-and-8d-storage.html
There are some sample files linked at the bottom of the page.

This places information about how your data is arranged into an annotation attached to the image. The data itself is just stored as usual in C. (or T or Z)

You could define something like:
  <ModuloAlongC Type="other" Start="246.6" Step="1.3" End="376.6" Unit="Hz"/>
to describe evenly spaced values, or:
  <ModuloAlongC Type="other" Unit="Hz">
    <Label>256.6</Label>
    <Label>266.6</Label>
    <Label>273.8</Label>
    <Label>274.2</Label>
    ...
  </ModuloAlongC>
to provide specific value for each point along your spectrum.

If I have not understood your problem right please mail the list again.

I am on holiday next week but I am sure someone else will get back to you. I will check back with you on my return.

Andrew


On 8 Nov 2013, at 08:54, Éric Piel <piel at delmic.com<mailto:piel at delmic.com>> wrote:

> Hello,
>
> I'd like to use OME-TIFF to store our microscope image acquisitions.
> However, after looking at the OME specification, it is not clear how I
> can save all metadata we need, so I'd like ask some advices.
>
> The data contains a (light) spectrum for each spatial point. So it's 3D:
> X, Y, and C. So far, so good. However, I'd like to record the scale
> along C (i.e., the wavelengths). Typically, the C dimension has a length
> of 100 or more points. At least, I'd need to record the minimum and
> maximum wavelength. I cannot find any way to do so. Can anyone suggest a
> way?
>
>
> Note: In old version of the OME schema, I've found WaveStart and
> WaveIncrement as attribute to Pixels. By using floats instead of int,
> this kind of works. But I'd rather follow the latest version of the
> specification.
>
> Thanks,
> Éric Piel
> _______________________________________________
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