[ome-devel] Questions of a newbie

[Ilya Goldberg]

Hi Phillip

On Feb 21, 2005, at 12:15 PM, phillip ryan ganir wrote:

> Sir/Ma'am,
>
>      I'm just new to studying microscopy and image processing. I just 
> want to
> clarify if saying OME image format is identical to saying OME-XML.

Yes they are the same.

>  Moreover, I
> explored your site and found the OME image format in the link XML 
> schemata -->
> image (Am I correct?).

Yes, the OME image format is specified in XML Schema - a language (from 
the W3C) for specifying XML structure.

>  I've found some symbols (?, <>, *, etc.) in the boxes
> that I don't understand, and unfortunately, there's no provided legend 
> for
> those symbols. Could someone explain these to me?

Sorry -
? Means zero or 1 (optional)
* Means zero or more (also optional, but may be more than one)
+ Means 1 or more (not optional, but may be more than one)
Absence of a symbol means that exactly one is required.
Not sure what you mean by <>.
In most browsers, holding the mouse still over a block ("hovering") in 
the diagrams will display additional information in a little pop-up 
window.  Clicking on a block will take you to the XML Schema document 
that has more detailed information.

> Also the organization of the
> chart, like for example why the image environment feature, thumbnail, 
> channel
> info are not linked to the image unlike the block containing the image 
> ID,  the
> creation date, etc.

These blocks are elements that are nested inside the Image element.  
The block that is connected to the Image element is describing the 
element attributes.  Its much clearer if you look at an actual example 
document:
http://www.openmicroscopy.org/XMLschemas/OME/latest/Sample.ome
Make sure you download the file and open it in a text editor of some 
kind - most browsers will not display it correctly because they will be 
confused by the XML.

>  Also, what's the difference in the pixel size
> (pixelsizeX,Y,Z) in the upper part and the feature size for the 
> separate object
> "pixel" (size X,Y,Z)?

The PixelSize attributes are the physical dimensions of a pixel in 
microns.  The SizeX, etc are the number of pixels in the image in each 
of its 5 dimensions.

>  Is the latter really a separate object (that has features)
> from the image, and the image just uses features of this object, which 
> makes the
> two sets of sizes really the same except in the datatype? Well, this 
> is just my
> interpratation, but please comment on this.

XML has elements and attributes.  An element is in angle brackets and 
the attributes of an element go inside the brackets: <Image 
PixelSizeX="0.2">.  In XML-speak, this is an Image element with a 
PixelSizeX attribute.  In the diagrams, the round-cornered block at the 
top that's connected to an element with a red line specifies the 
attributes of the element.  The square-cornered blocks to the right of 
the element are other elements nested inside that one.  Hopefully 
looking at the example will make this clearer than trying to describe 
it verbally.

>
>      I'm hoping for your response. It would greatly be appreciated. A 
> million
> thanks in advance!!!

Thanks for your interest!

>
> Phillip

Ilya

>
>
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