[ome-users] incell import and plate ids

[Melissa Linkert]

Hi Rajarshi,

> Hi, I had a question about the incell importer (I've been using the OMERO
> Importer GUI on Windows). I pointed it to the XDCE file in a folder that is
> named by the plate barcode. The XDCE file itself is named as H1050234.xdce
> 
> On import when I go to view my project in the web client I see a hierarchy
> like
> 
> Project Name
>   H1050234
>     Plate 2
> 
> (this happened to be the second plate I imported in this project).
> 
> I have two questions
> 
> 1. In the hierarchy,what does H1050234 refer to? is this plate identifier?
> I'm particularly interested in programmatic access to images via the Java
> API and so I'd need to know whether this is the actual plate identifier.

That is the plate name ("label" in InCell terms), and not a unique plate
identifier.

> 2. What does 'Plate 2' refer to? is it simply the second plate imported? Is
> it possible to have another entry under the 'H1050234' level?

I believe that "Plate 2" would be a user-chosen name at import time, but
someone else can correct me if I am mistaken.

> Looking at the XDCE file itself I see
> 
> <SpecimenHolder type = "Plate" label = "H1050234"/>
> 
> Is this what is read during the import process?

The plate name/label is taken from the name of the .xdce file, which in
practice is equivalent to the "label" attribute of the "SpecimenHolder"
node in the .xdce file.

Regards,
-Melissa

On Wed, Jun 13, 2012 at 01:56:38PM -0400, Rajarshi Guha wrote:
> Hi, I had a question about the incell importer (I've been using the OMERO
> Importer GUI on Windows). I pointed it to the XDCE file in a folder that is
> named by the plate barcode. The XDCE file itself is named as H1050234.xdce
> 
> On import when I go to view my project in the web client I see a hierarchy
> like
> 
> Project Name
>   H1050234
>     Plate 2
> 
> (this happened to be the second plate I imported in this project).
> 
> I have two questions
> 
> 1. In the hierarchy,what does H1050234 refer to? is this plate identifier?
> I'm particularly interested in programmatic access to images via the Java
> API and so I'd need to know whether this is the actual plate identifier.
> 2. What does 'Plate 2' refer to? is it simply the second plate imported? Is
> it possible to have another entry under the 'H1050234' level?
> 
> Looking at the XDCE file itself I see
> 
> <SpecimenHolder type = "Plate" label = "H1050234"/>
> 
> Is this what is read during the import process?
> 
> Any pointers would be appreciated
> 
> -- 
> Rajarshi Guha | http://blog.rguha.net
> NIH Center for Advancing Translational Science

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