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

[Will Moore]

Hi Eric,

If you need to store min and max wavelength for each Channel, you can use a LightPath, with an EmissionFilter that has CutIn and CutOut like:

      <Filter ID="Filter:0:0" Model="SP Mirror Channel 1">
         <TransmittanceRange CutIn="406" CutOut="479"/>
      </Filter>


         <Channel>
            <LightPath>
                <EmissionFilterRef ID="Filter:0:0"/>
            </LightPath>
         </Channel>

Hope that helps,

  Will.

On 8 Nov 2013, at 17:33, Curtis Rueden 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 This description is out of date and no longer valid, right?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> 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> 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
> > _______________________________________________
> > ome-devel mailing list
> > ome-devel at lists.openmicroscopy.org.uk
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
> 
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