[ome-devel] BD Pathway

[Melissa Linkert]

Hi Shawn,

I apologize for not getting back to you sooner.

> In using the BD Pathway importer I wrote I've noticed a few improvements that would really help our lab. First of all, the
> http://trac.openmicroscopy.org.uk/omero/wiki/WorkPlan/HCSData plan, shows these nice plate formats. Do I need to update
> the importer code to include this information?

To my knowledge, no, you don't need to update anything.  The fact that
the BD reader populates Well and WellSample metadata should be
sufficient.

> Also in the importer, I copied over a line: 'MetadataTools.setDefaultCreationDate(store, id, i)' when saving each image in a
> stack. Does this pull the file creation date and store it in the metadata?

'MetadataTools.setDefaultCreationDate(store, id, i)' will set the
creation date for Image #i to the creation date of the file whose path
is 'id'.  If no such file exists, then the creation date is set to the
current time.

Note that in the BD reader, all images will have the same creation
date, as the same file name is passed to
MetadataTools.setDefaultCreationDate.  If you would like, it would be
easy to change the reader so that the image creation date is
equivalent to the creation date of the first TIFF file in the stack;
essentially:

MetadataTools.setDefaultCreationDate(store, tiffs[i * getImageCount()], i);

instead of:

MetadataTools.setDefaultCreationDate(store, id, i);

Regards,
-Melissa

On Fri, Feb 19, 2010 at 9:57 AM, Shawn Garbett
<shawn.p.garbett at vanderbilt.edu> wrote:
> In using the BD Pathway importer I wrote I've noticed a few improvements that would really help our lab. First of all, the http://trac.openmicroscopy.org.uk/omero/wiki/WorkPlan/HCSData plan, shows these nice plate formats. Do I need to update the importer code to include this information? If so, what's a good example?
>
> Also in the importer, I copied over a line: 'MetadataTools.setDefaultCreationDate(store, id, i)' when saving each image in a stack. Does this pull the file creation date and store it in the metadata? This is the best indicator of the time of an image for us.
>
> Shawn Garbett <shawn.p.garbett at vanderbilt.edu>
> Vanderbilt Cancer Biology
> 220 Pierce Ave, PRB 715AA
> Nashville, TN 37232
> Office: 615.936.1975
> Cell: 615.397.8737
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>
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