[ome-users] time stamp in tiff from nd2

[Melissa Linkert]

Hi Karin,

> I have one big ND2 file, with many shots. Each shot has a timestamp, that both Bio-Formats reads without problems. I am using the ImageJ/Fiji plugin, options "Bio-Formats Importer / Exporter".
> 
> My question is: is it possible to extract each frame as a TIFF file that contains, in its EXIF metadata, the corresponding image acquisition timestamp?
> 

There isn't a way for the timestamp to be automatically saved to EXIF
metadata using Bio-Formats.  However, if you export to OME-TIFF then all of
the metadata including timestamps should be preserved in the OME-XML that is
stored in the TIFF Description field (see
http://www.openmicroscopy.org/site/support/ome-model/ome-tiff/).

To export to OME-TIFF, just use the ".ome.tiff" extension instead of ".tiff"
when saving files in ImageJ or on the command line.  Any software that
can read TIFF files can also read the images from OME-TIFFs.

Regards,
-Melissa

On Mon, May 13, 2013 at 10:14:12PM +0200, Karin MITOSCH wrote:
> Hello everybody,
> 
> I have one big ND2 file, with many shots. Each shot has a timestamp, that both Bio-Formats reads without problems. I am using the ImageJ/Fiji plugin, options "Bio-Formats Importer / Exporter".
> 
> My question is: is it possible to extract each frame as a TIFF file that contains, in its EXIF metadata, the corresponding image acquisition timestamp?
> 
> So far I've been able to extract the images, but that metadata was missing.
> 
> Curiously, if I extract the images from the command-line using e.g.:
> 
>   bfconvert -series 0 bleach_mCherry.nd2 out/bleach_%A.tiff
> 
> then the information I'm looking for is part of the file-name, but still not "inside" as EXIF metadata.
> 
> Many thanks in advance,
> Karin
> 

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