Open Microscopy Environment

Hi All,

We work with Bioformats and Matlab, and want to create OME-tiffs with Modulo specifications.

Modulo is the OME XML annotation specifying additional XY-plane indexing attribute (e.g. the lifetime in FLIM, agreed to be ModuloAlongT).

Bioformats provides mechanism for adding ModuloAlong to metadata, and I now want to use it, as it should result in desired effect in corresponding OME.tiff files and Omero-imports made of them.
To pass metadata to the writer, I copy the code from "bfsave" function:

Code: Select all

OMEXMLService = loci.formats.services.OMEXMLServiceImpl();
metadata = OMEXMLService.createOMEXMLMetadata();
...
writer = loci.formats.ImageWriter();
...
writer.setMetadataRetrieve(metadata);
...


"OMEXMLService" object there contains "addModuloAlong" functions, "getModuloAlongZ"(C,T), and likely this is the place where one can add Modulo annotation to metadata.

Will be grateful for any hint.

Best,
Y.

Something like this should work:

Code: Select all

OMEXMLService = loci.formats.services.OMEXMLServiceImpl();
metadata = OMEXMLService.createOMEXMLMetadata();

% set all of the other metadata fields

% define the Modulo annotations

coreMetadata = loci.formats.CoreMetadata();

% see the loci.formats.Modulo javadoc for details of what fields can be set
% this will be turned into a Modulo XML annotation later
coreMetadata.moduloC.step = 3;
coreMetadata.moduloC.end = 12;
coreMetadata.moduloC.type = loci.formats.FormatTools.LIFETIME;
coreMetadata.moduloC.unit = 'ns';

% moduloZ and moduloT in coreMetadata can be set in the same way if desired

% adds each of the Modulo annotations defined by coreMetadata to the OME-XML
% the '0' argument specifies the Image to which the annotations should be attached;
% for multi-Image datasets (multi-series in Bio-Formats terms) you will need to call this method
% in a loop over the number of Images
OMEXMLService.addModuloAlong(metadata, coreMetadata, 0);

writer = loci.formats.ImageWriter();
writer.setMetadataRetrieve(metadata);


...
Many thanks Melissa,

It looks really good, almost everything is working.

The only thing that remains, - I should use "public String[] labels" field in Modulo, and wasn't able to adjust the assignment syntax.

I tried this (and similar) constructions but all result in errors

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for i=1:length(delays)
   modlo.moduloT.labels(i)= java.lang.String(num2str(delays(i)));
end

Just wonder how to get this puzzle solved..

Best wishes, thanks again,
Y.

...
Actually I found that pre-allocating helps in this case.
The following code is working:

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modlo.moduloT.labels = javaArray('java.lang.String',length(delays));                                 
for i=1:length(delays)
   modlo.moduloT.labels(i)= java.lang.String(num2str(delays(i)));
end

now need to fix my other stuff to make it practical..

Thanks All,
Y.