[ome-devel] accessing ome-metadata from matlab.

[Melissa Linkert]

Hi Heinrich,

> I am building a LabView-controlled fluorescence microscope. As a data format for saving the acquired images, I chose ome.tif, and therefore wrote a dll putting the image and metadata into a tif file. It all seems to be working out quite fine by now, the command line tool tells me I have a valid ome.tif, and using the loci plugin for imageJ, I can display everything OK.
> There are some issues left, though. I have written some matlab code for image evaluation, and some of that access metadata. Lately, I cannot access that any more, though. I have made some minor changes to the OME-xml, and updated to a new loci_tools.jar and bio-formats.jar, but changing back does not help which confuses me. So I wouldlike to ask you guys whether you might find anything wrong in my ome-xml that the command line tool does not, and whether you can access metadata via matlab with the script I wrote to check.
> The script returns sensible values only for getPixelsSizeX, it returns the current date and time when asking for the acquiredDate, always returns one for getImageCount and getChannelCount and otherwise, it returns nothing.
> 
> I attach the metadata checking matlab script and a sample image
> Any help is highly appreciated

Thank you for the report.  Just so that you know, we do have a fix in
the works, it just hasn't quite made it into the trunk builds yet.  If
you're interested, you can see the discussion of the fix here:

https://github.com/openmicroscopy/openmicroscopy/pull/21

In short, the problem was that the OME-XML failed to be parsed, which
caused the OME-TIFF file to be read as a plain TIFF file - that's why
the metadata looked completely wrong.  The fix proposed above will
prevent the XML parsing from failing, allowing the file to be properly
read as an OME-TIFF.

We'll let you know once a new trunk build is available with the fix.

Regards,
-Melissa

On Wed, Nov 02, 2011 at 04:33:41PM +0000, Grabmayr, Heinrich wrote:
> Hey everyone,
> 
> I am building a LabView-controlled fluorescence microscope. As a data format for saving the acquired images, I chose ome.tif, and therefore wrote a dll putting the image and metadata into a tif file. It all seems to be working out quite fine by now, the command line tool tells me I have a valid ome.tif, and using the loci plugin for imageJ, I can display everything OK.
> There are some issues left, though. I have written some matlab code for image evaluation, and some of that access metadata. Lately, I cannot access that any more, though. I have made some minor changes to the OME-xml, and updated to a new loci_tools.jar and bio-formats.jar, but changing back does not help which confuses me. So I wouldlike to ask you guys whether you might find anything wrong in my ome-xml that the command line tool does not, and whether you can access metadata via matlab with the script I wrote to check.
> The script returns sensible values only for getPixelsSizeX, it returns the current date and time when asking for the acquiredDate, always returns one for getImageCount and getChannelCount and otherwise, it returns nothing.
> 
> I attach the metadata checking matlab script and a sample image
> Any help is highly appreciated
> 
> Best
>    Heinrich



> _______________________________________________
> ome-devel mailing list
> ome-devel at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel