Open Microscopy Environment

Hi,

A colleague of mine has written some code to extract the xml metadata header from ome-tiff files. He is able to parse the xml and get the data that he needs.

He would like to store the images in omero and be able to just grab the ome-xml metadata from the server (returned as a String). I haven't found a way to get this - does anyone know if this is a possible?

Thanks,
Chris

Hi Chris,

sorry, but I think at the moment this isn't possible directly via the API. The possibilities that exist include:

• Download the whole image via the API and extract
• Use the API to obtain the OME-XML that the server sees (varies from what's in the file)
• Write a script to extract remotely.

Let us know if we can help with any of the three.

In addition, I think adding an API method to obtain the original OME-XML would make sense. Thanks for the suggestion!

Cheers,
~Josh.

Hi Josh,

Thanks for the reply.
What part of the API should I look at to get the OME-XML the server sees?

Also, I noticed that if exporting an OME-TIFF of an image (original is a Zeiss lsm) that the original metadata is not included in the OME-TIFF (it's not shown in the BioFormats window when opening in Fiji). Is that something I could request an enhancement for.

Thanks
Chris

Hi Chris,

chriswood wrote:Thanks for the reply.
What part of the API should I look at to get the OME-XML the server sees?

One starting point would be the CLI:

Code: Select all

bin/omero export --file - --type XML Image:38884


which eventually uses the Exporter service.

Also, I noticed that if exporting an OME-TIFF of an image (original is a Zeiss lsm) that the original metadata is not included in the OME-TIFF (it's not shown in the BioFormats window when opening in Fiji). Is that something I could request an enhancement for.

Definitely. Export is something that we hope to have improved for the next major release (5.1.0).

Cheers,
~Josh