[ome-users] Creation date?

[Susan Wilson]

Thanks Curtis.
I am in the middle of a server crisis right now and will get to this  
next week.
Susan

On Oct 22, 2008, at 2:44 PM, Curtis Rueden wrote:

> 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
>>
>
>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20081022/2826da57/attachment.html>