<div dir="ltr">Hi Andrew,<div><br></div><div>It sounds like <span style="font-family:arial,sans-serif;font-size:13px">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.</span></div>
<div><br></div><div>Or am I missing something here?</div><div><span style="font-family:arial,sans-serif;font-size:13px"><br></span></div><div><font face="arial, sans-serif">Regards,</font></div><div><font face="arial, sans-serif">Curtis</font></div>
<div><span style="font-family:arial,sans-serif;font-size:13px"><br></span></div><div><span style="font-family:arial,sans-serif;font-size:13px">P.S. I notice the XML documentation for the Channel element says: "</span><span style="background-color:inherit;color:rgb(0,0,0);font-family:arial,helvetica,sans-serif;font-size:12px;white-space:pre-wrap">An entire spectrum in an FTIR experiment may be stored in a single Logical Channel with each discrete wavenumber of the spectrum </span><span style="background-color:inherit;color:rgb(0,0,0);font-family:arial,helvetica,sans-serif;font-size:12px;white-space:pre-wrap">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 This description is out of date and no longer valid, right?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.</span></div>
<div><span style="font-family:arial,sans-serif;font-size:13px"><br></span></div><div><span style="font-family:arial,sans-serif;font-size:13px">[1] </span><font face="arial, sans-serif"><a href="https://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2013-06/ome_xsd.html#Channel_EmissionWavelength">https://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2013-06/ome_xsd.html#Channel_EmissionWavelength</a></font></div>
</div><div class="gmail_extra"><br><br><div class="gmail_quote">On Fri, Nov 8, 2013 at 11:15 AM, Andrew Patterson <span dir="ltr"><<a href="mailto:ajpatterson@lifesci.dundee.ac.uk" target="_blank">ajpatterson@lifesci.dundee.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hello Éric,<br>
<br>
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.<br>
<br>
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:<br>
<a href="https://www.openmicroscopy.org/site/support/ome-model/developers/6d-7d-and-8d-storage.html" target="_blank">https://www.openmicroscopy.org/site/support/ome-model/developers/6d-7d-and-8d-storage.html</a><br>
There are some sample files linked at the bottom of the page.<br>
<br>
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)<br>
<br>
You could define something like:<br>
<ModuloAlongC Type="other" Start="246.6" Step="1.3" End="376.6" Unit="Hz"/><br>
to describe evenly spaced values, or:<br>
<ModuloAlongC Type="other" Unit="Hz"><br>
<Label>256.6</Label><br>
<Label>266.6</Label><br>
<Label>273.8</Label><br>
<Label>274.2</Label><br>
...<br>
</ModuloAlongC><br>
to provide specific value for each point along your spectrum.<br>
<br>
If I have not understood your problem right please mail the list again.<br>
<br>
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.<br>
<span class="HOEnZb"><font color="#888888"><br>
Andrew<br>
</font></span><div class="HOEnZb"><div class="h5"><br>
<br>
On 8 Nov 2013, at 08:54, Éric Piel <<a href="mailto:piel@delmic.com">piel@delmic.com</a>> wrote:<br>
<br>
> Hello,<br>
><br>
> I'd like to use OME-TIFF to store our microscope image acquisitions.<br>
> However, after looking at the OME specification, it is not clear how I<br>
> can save all metadata we need, so I'd like ask some advices.<br>
><br>
> The data contains a (light) spectrum for each spatial point. So it's 3D:<br>
> X, Y, and C. So far, so good. However, I'd like to record the scale<br>
> along C (i.e., the wavelengths). Typically, the C dimension has a length<br>
> of 100 or more points. At least, I'd need to record the minimum and<br>
> maximum wavelength. I cannot find any way to do so. Can anyone suggest a<br>
> way?<br>
><br>
><br>
> Note: In old version of the OME schema, I've found WaveStart and<br>
> WaveIncrement as attribute to Pixels. By using floats instead of int,<br>
> this kind of works. But I'd rather follow the latest version of the<br>
> specification.<br>
><br>
> Thanks,<br>
> Éric Piel<br>
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