[ome-users] Creation date?

[Curtis Rueden]

Hi Susan,

Sorry for the delay in my reply. I am not sure why CreationDate isn't
showing up in OMERO. In the course of investigating it, though, we have
fixed a bug in the DateTime parsing for TIFF files that caused some
datestamps to be parsed incorrectly. The latest trunk build of Bio-Formats,
available from the web site at
http://www.loci.wisc.edu/ome/formats-download.html, contains the fix.

Unfortunately, OMERO will not contain the bugfix until its next release, but
you can at least verify that the datestamps are being parsed and
standardized properly with your TIFF files.

If you use the Bio-Formats command line tools (
http://www.loci.wisc.edu/ome/formats-tools.html), you can verify it using
the showinf tool:

showinf myFile.tif -nopix -omexml

This will parse your TIFF, dump the metadata key/value pairs (including
"DateTime" if present) to the console, and then dump the standardized block
of OME-XML, which should contain a CreationDate element beneath the Image
element. OMERO is supposed to be using the value of this element -- if not,
it's likely a bug in OMERO.

As I mentioned before, you can also check your TIFFs using ImageJ. The
latest trunk build contains a new "Display OME-XML metadata" option as part
of the Bio-Formats Importer plugin, which will show the OME-XML tree in its
own window.

If you don't see CreationDate being populated properly, let us know and we
will fix it. However, if the problem is OMERO-specific, I'll have to defer
to the OMERO guys on possible causes.

-Curtis

On Wed, Oct 1, 2008 at 4:05 PM, Susan Wilson <smwilson at hpc.unm.edu> wrote:

> Curt, I am using the LOCI Plugin with ImageJ and that's where I see the
> DateTime value.  My question is why isn't CreationDate showing up as a
> Property in either OME or OMERO.insight for that same image.  That would be
> an important piece of annotation to be shown by default in your servers, so
> that researchers could use it to distinguish between many similar images.
> I am going on vacation now until Tuesday and so will not be able to respond
> or iterate with you until then.  Just so you know I'm not ignoring you.  :>)
>
> Susan
>
> On Oct 1, 2008, at 1:42 PM, Curtis Rueden wrote:
>
> Hi Susan,
>
> Where exactly are you are seeing the metadata?
>
> Are you using Bio-Formats in ImageJ? If so, are you checking the "Display
> metadata in results window" option? Please note that the metadata displayed
> there is in the file's original format, and not standardized to OME.
>
> The "DateTime" key is a TIFF-specific piece of metadata corresponding to
> the TIFF's DateTime field (value 306). It will only be displayed if a
> DateTime IFD entry was present in the TIFF file.
>
> However, CreationDate is a required field under Image in OME, and
> Bio-Formats guarantees that it will be populated one way or another. In the
> case of TIFF, any given DateTime will be saved as the CreationDate. If no
> DateTime is present, the system's current date and time is used to populate
> the CreationDate (this is actually the default for all supported file
> formats).
>
> Right now, you can view the standardized OME metadata in ImageJ by choosing
> "Data Browser" for "View stack with" in the Bio-Formats Importer Options,
> and then clicking the Metadata button when the window pops up. You should
> see another window containing a colored XML tree structure, with a
> <CreationDate> node beneath the <Image> node in the tree.
>
> -Curtis
>
> On Wed, Oct 1, 2008 at 1:20 PM, Susan Wilson <smwilson at hpc.unm.edu> wrote:
>
>> Hi,
>>
>> I'm surprised that Creation Date is not a piece of metadata about an
>> imported image (they're using tif images because their zvi images are
>> not working properly at this time).  It seems that ImageJ knows
>> _something_ about a DateTime (although the units of such is a mystery
>> to me).  Any comments on that, since it is a very important property
>> of images for my users.
>>
>> Thanks.
>> Susan
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>
>
>
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