[ome-devel] Question about LogicalChannel

[Curtis Rueden]

Hi Nick,

On Tue, Sep 8, 2009 at 4:22 AM, Nick Perry <nperry at stanford.edu> wrote:

> >From
> http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_LogicalChannel
> :
>
> "There must be one per channel in the Image, even for a single-plane
> image."
>
> In my head, this translated to:  # LogicalChannels == SizeC. But later -
>
> "The total number of ChannelComponents for a set of pixels must equal
> SizeC."
>
> So...which is it?
>

At the moment, it is the latter. That is, LogicalChannel can encompass
either one or multiple related channels. But if a LogicalChannel covers more
than one, it should have multiple ChannelComponents (one per channel
covered).

I believe this is changing in the next version of the schema. LogicalChannel
is being renamed to Channel, and ChannelComponent is going away. I am not
sure how the new schema will allow modeling of groups of related channels;
perhaps Andrew can comment further.

Also, what if channel in the image file type I'm converting isn't actually a
> 'color?' What if it's some sort of calculated value (for example, a
> lifetime)? Is LogicalChannel the appropriate place to put that?
>

Yeah, it's still a "channel," just doesn't have any particular emission
wavelength. For example, at LOCI we record a "transmitted" channel collected
with a regular grayscale camera, in addition to specific emission spectra
resulting from laser excitation.

-Curtis

On Tue, Sep 8, 2009 at 4:22 AM, Nick Perry <nperry at stanford.edu> wrote:

> >From
> http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_LogicalChannel
> :
>
> "There must be one per channel in the Image, even for a single-plane
> image."
>
> In my head, this translated to:  # LogicalChannels == SizeC. But later -
>
> "The total number of ChannelComponents for a set of pixels must equal
> SizeC."
>
> So...which is it?
>
> Also, what if channel in the image file type I'm converting isn't actually
> a 'color?' What if it's some sort of calculated value (for example, a
> lifetime)? Is LogicalChannel the appropriate place to put that?
>
> Thanks,
> Nick
>
> _______________________________________________
> ome-devel mailing list
> ome-devel at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>
>
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