[ome-users] OME format

[Jason Swedlow]

Hi Jose-

Following our discussion, I am forwarding your email to our ome-users  
and ome-devel mailing lists.  They are some interesting issues here  
that i am sure the list will want to see.

Cheers,

Jason

On 21 Feb 2007, at 11:53, Jose Viña wrote:

> Dear Dr. Swedlow,
>
> I've seen that Gitta already wrote you an email about the fact that
> our Huygens software supports the OME-XML file format. I am very
> interested in its evolution, in order to keep our software up to date.
>
> These days I am particularly interested in how the refractive indexes
> involved in the image formation are recorded in the file.
>
> At http://cvs.openmicroscopy.org.uk/tiki/tiki-index.php?page=OME-XML 
> %20Evolution
> I've seen a suggested (but apparently not yet accepted)
> RefractiveIndex attribute linked to the <ObjectiveRef> which our
> software currently (correctly?) interprets as the refractive index of
> the medium in which the sample is embedded, not the one in which the
> lens is immersed.
>
> About the latter, I've noticed an ImmersionType attribute of the
> <Objective> that is a word (like "air" or "water"), not a numerical
> value.
>
> I am willing to make sure that we read and interpret these parameters
> correctly. From our point of view, to properly generate a PSF both
> refractive indexes must be known as precisely as possible. It is
> therefore also important for us to store them in the file as well. I
> have some questions:
>
> 1) Would it be possible to store not only the name of the immersion
> medium, but also its numerical refractive index, along with the
> <Objective>?
>
> 2) Am I correct in thinking that the RefractiveIndex attribute of
> <ObjectiveRef> refers to the embedding medium for the sample?
>
> 2-a) If so, are you sure this is the best place to store it? (I would
> expect <ObjectiveRef> to be a reference to the used objective,
> described in the <Instrument>, and nothing about the sample
> preparation).
>
> 2-b) If not (if this is the value of the r.i. of the lens immersion
> medium), why not simply put it in <Objective> instead of
> <ObjectiveRef>?
>
> 3) In your email to Gitta you mention some "levels" suggested by Hans.
> What are those?
>
> I'm looking forward to having this great file format fully stablished!
>
> Yours faithfully,
>
> Jose V.
>
> ------------------------------------------------------------
> Dr. Jose Viña                                +31 35 642 1626
> Scientific Volume Imaging BV               http://www.svi.nl
> Laapersveld, 63. 1213 VB Hilversum           The Netherlands


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