Open Microscopy Environment

We want to transfer Lab data to Omero routinely, mostly from our plate readers, - in which case Omero images are created by specific procedure. It is called from our "importer" utility written in Matlab.
"importer" opens list of data directories and transfers these directories to Omero, one after another.

We also have lot of data in Becker&Hickl sdt format and it would be convenient to import them in the same process.
"importer" can transfer sdt files, however there is one part that isn't transferred.
If sdt image is imported by Omero-client like Insight, the imported Image has an annotation file "original_metadata.txt" (aliased as ORIGINALMETADATA I believe). This annotation contains many B&H acquisition settings, which are meaningful. So I would like to keep this annotation file, and the problem is how to get that text string that is written there.

I looked at Java code in "bioformats" - the getInfo() function in "SDTReader" class looked promising.
I tried in Matlab, naively, just javaMethod('getInfo','SDTReader',sdtfilename) but result was error message "No class SDTReader can be located on Java class path".

I'm not sure if what I want to get is achievable form Matlab, but if it is, - please send your advice.

Best regards everybody,
Y.

Hi Yuriy,

OMERO creates original_metadata.txt from a hashtable of metadata stored by Bio-Formats. This hashtable is accessible from Matlab as shown here:

http://www.openmicroscopy.org/site/supp ... l-metadata

If that doesn't work, please let us know.

Regards,
-Melissa

Thanks Melissa,

I expected to find something like

loci.formats.MetadataTools.getOriginalMetadata() ???

it looks like, close, but not exactly..

Best,
Y.

OK now I got what You've meant -

Code: Select all

data = bfopen('/path/to/data/file');
metadata = data{1, 2};

I was fixed on Java function calls, and forgot about this option.
If I don't come back with more questions tomorrow, - it means it worked, and the case closed!

Many, many thanks,
Y.