Open Microscopy Environment

From webclient, using General > Download > Export as OME-TIFF, one can generate a OME-TIFF file on the server and then download it. Using command line tools etc, one can then extract the embedded OME-XML metadata.

I wonder if there is a way to directly extract OME-XML from an image in OMERO using Java API. But I could not find relevant Java class in API. Is there any way to achieve this by programming?

Hi Kouichi

You are correct, neither insight nor web expose the option to export the Image as OME-XML.
You can do it using the Exporter service
Follow some pseudo-code using the Java Gateway

Code: Select all

final int INC = 262144 //Maximum size of pixels read at once
SecurityContext ctx;
File f;
ExporterPrx store = gateway.getExporterService(ctx)
long size = store.generateXml();
FileOutputStream stream = new FileOutputStream(f);
for (offset = 0; (offset+INC) < size;) {
    stream.write(store.read(offset, INC));
    offset += INC;
}
stream.write(store.read(offset, (int) (size-offset)));
stream.close();


I hope it is helpful

Cheers

Jmarie

Thank you for the code snippet.

I've translated it into MATLAB code without understanding what's happening.

Code: Select all

userName = '********';

password = input('password:','s');

host = 'demo.openmicroscopy.org';

INC = 262144; % //Maximum size of pixels read at once



[gateway,user,cred] = loadOmeroGateway(userName, password, host);

ctx = omero.gateway.SecurityContext(user.getGroupId()); % 'omero.gateway.SecurityContext'
store = gateway.getExporterService(ctx); % 'omero.api.ExporterPrxHelper'

SIZE = store.generateXml(); %102

f = java.io.File('out.xml');

stream = java.io.FileOutputStream(f);

offset = 0;
while offset+INC < SIZE
    stream.write(store.read(offset, INC));
    offset = offset + INC;
end

stream.write(store.read(offset, int32(SIZE-offset)));
stream.close();

using loadOmeroGateway.m of mine:
https://gist.github.com/kouichi-c-nakam ... ogateway-m

This resulted in

Code: Select all

<?xml version="1.0" encoding="UTF-8"?><OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06"/>

I need to specify an image before retrieving XML. How could I do that?

Hi Kouichi

Sorry I forgot a line
You need to add the following after creating the Exporter Service

Code: Select all

store.addImage(imageID);


WORKED LIKE A MAGIC! Thank you so much, Jmarie.

Best,
Kouichi

Code: Select all

imageID = 56134;

[gateway,user,cred] = loadOmeroGateway(userName, password, host);

ctx = omero.gateway.SecurityContext(user.getGroupId()); % 'omero.gateway.SecurityContext'
store = gateway.getExporterService(ctx); % 'omero.api.ExporterPrxHelper'

store.addImage(imageID);

SIZE = store.generateXml(); %102

f = java.io.File('out.xml');

stream = java.io.FileOutputStream(f);

offset = 0;
while offset+INC < SIZE
    stream.write(store.read(offset, INC));
    offset = offset + INC;
end

stream.write(store.read(offset, int32(SIZE-offset)));
stream.close();

gateway.close();

bfTiffComment('out.xml','Indent','on','outxmlfile','auto')


bfTiffComment.m is here:
https://gist.github.com/kouichi-c-nakam ... fcomment-m

Hi Kouichi

Great that it works
Thanks for letting us know
We will add an example to our documentation.

Cheers

Jmarie