Open Microscopy Environment

Hi,

After importing some Gatan .dm4 files with Fiji we couldn't find a couple of metadata fields (acceleration voltage and magnification) that are present in Gatan's proprietary software. Are these fields not supported yet or am I just looking in the wrong place? There were also a couple of error messages saying that 'correction' and 'immersion' are unknown.

Thanks,

Matt.

Dear Matt,

The underlying metadata model should be able to store these settings, and I see that the GatanReader does do so:

https://github.com/openmicroscopy/biofo ... .java#L309
https://github.com/openmicroscopy/biofo ... .java#L301

When you import into Fiji, if you select the OME-XML metadata option, these settings should be visible in the XML data on the detector settings and the objective.

If you wanted to upload a sample image with these metadata fields present, I could take a look at it to see what's going on. You can upload here: https://www.openmicroscopy.org/qa2/qa/upload/


Regards,
Roger

Hi,

thanks for replying Roger and apologies for the delay in getting back to you. I've uploaded an example to the qa site.

We've been uploading a few .dm4 files in the past couple of weeks and noticed another odd behaviour: when we have used the Gatan software to add measurement metadata to the files that seems to cause problems when we try and import them. It either gives a file format error or keeps them pending indefinitely.

Thanks again,

Matt.

Hi Matt,

I was able to debug through the sample file you uploaded, the 2 expected fields (acceleration voltage and magnification) are expected by Bio-Formats to be labelled as "Voltage" and Indicated "Magnification". I was unable to find reference to either label within the file, however there are a number of tags which Bio-Formats was unable to recognise. None of them contained a label which would obviously apply to either setting but they may be listed there.

Do you know what the expected values of voltage and magnification are supposed to be for that uploaded sample file?

David Gault