Matlab import of Aperio .svs file not retrieving XML data

[epaulw]

I have gotten Matlab to import Aperio .svs files. However, the data I get back seem a little odd. It comes as a cell array that replicates the original image in smaller and smaller thumbnails (if you can call a 6500x5500 image a thumbnail).

Further, it only grabs some of the ancillary information, but it does not retrieve the XML data. The XML is my whole reason for using bio-formats. Otherwise, just renaming the image file to tiff or jpeg makes it importable (without all the extra baggage showing up). The XML data contains the overlays, hand drawn outlines of the pathologist's regions of interest.

Should I be expecting that XML to show up as data? Or should I assume that I need to import the XML data separately, and program my way through it?

Paul

[mlinkert]

I have gotten Matlab to import Aperio .svs files. However, the data I get back seem a little odd. It comes as a cell array that replicates the original image in smaller and smaller thumbnails (if you can call a 6500x5500 image a thumbnail).

Further, it only grabs some of the ancillary information, but it does not retrieve the XML data. The XML is my whole reason for using bio-formats. Otherwise, just renaming the image file to tiff or jpeg makes it importable (without all the extra baggage showing up). The XML data contains the overlays, hand drawn outlines of the pathologist's regions of interest.

Should I be expecting that XML to show up as data? Or should I assume that I need to import the XML data separately, and program my way through it?

If you're referring to the OME-XML that Bio-Formats creates, then you should be able to retrieve it like so:

Code: Select all

reader = bfGetReader('/path/to/file');
omexml = loci.formats.MetadataTools.getOMEXML(reader.getMetadataStore());


I've never seen an .svs file that contained actual XML, so if your files do contain extra XML data (or have an associated XML file) then it's likely that Bio-Formats does not read this. The best thing to do then would be to send at least one dataset so that we can verify the problem and test any changes. If you need a place to upload data, let me know and I will send instructions in a private message.

Regards,
-Melissa

[epaulw]

Melissa-

If you are still there and listening, I'd like to take you up on the offer to look at the Aperio .svs files and accompanying .xml files.

Paul

[mlinkert]

Thank you for offering to send files. Instructions on how to upload files have been sent in a private message.

-Melissa

[mlinkert]

Thank you for uploading data. I have filed a ticket on our issue tracking system to add support for these XML files:

http://trac.openmicroscopy.org.uk/ome/ticket/10504

-Melissa

[epaulw]

Melissa-

Did you ever follow up on import of the Aperio XML accessory files?

Thanks

Paul

[mlinkert]

No, this feature has not yet been completed. The above ticket will be marked as "closed" when it is finished.