[ome-devel] ScanR

[Melissa Linkert]

Hi Ruben,

I'm moving this discussion to the ome-devel list, as it may be of
interest to others.

> Please consider my ScanrReader.java as possible help.

Thank you very much for the patch.  I've committed a modified version
of it to the LOCI SVN repository; you can view the changes here:

https://skyking.microscopy.wisc.edu/trac/java/changeset/5652

The only major difference between the committed changes and your patch
is that the committed changes do not have hard-coded well, position,
Z, T, and channel counts.  The number of wells is currently being
calculated from the well names in the "well selection table + cDNA"
table.  The number of channels (core[0].sizeC) is equivalent to the
number of channels defined in experiment_description.xml that have the
"idle" flag set to 0.

The latest revision of ScanrReader does correctly detect the
dimensions for all of the datasets that I have.  If you continue to
experience problems, though, please let me know.

Regards,
-Melissa

On Fri, Oct 23, 2009 at 5:53 PM, Rubén Muñoz <ruben.munoz at embl.de> wrote:
> Hi Melissa, thanks for your reply.
>
> I'd be happy to fix this, but first would like to clarify that an
> assumption is correct.
>
> core[0].sizeC (the number of channels) is taken from a block like this:
>
> <Name>multiple_channel_typedef</Name>
> <Dimsize>3</Dimsize>
>
> Yes, but not all the channels are finally used.
> While the experiment_descriptor.xml reads:
> <Name>multiple_channel_typedef</Name>
> <Dimsize>12</Dimsize>
> The directory only has two channel Cherry and eGFP.
>
> My understanding is that Dimsize is used in multiple places, and its
> usage is determined by the value in in the "Name" element.  Is this
> correct?  If so, do you know what the correct Name values are for
> channels and positions?
>
> That's how it should be...
> ... but the new set only gets converted for me when I fix all the next
> values:
> wellColumns = 2;
> wellRows = 3;
> core[0].sizeC = 2;
> core[0].sizeT = 6;
> core[0].sizeZ = 3;
> Im sorry to do that now but a colleague is going to offer me details about
>  experiment_descriptor.xml.
> Additionally I introduced some code to handle different positions in a well,
> P00001, P00002 and so on.
> Please consider my ScanrReader.java as possible help. It is working well for
> the set and generates an OME.TIF with 1.7G that imports to OMERO and
> displays Z, T, and C data in the correct way
> .
> Regards,
> Ruben
>
>
>
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