Open Microscopy Environment

I measured a mouse tibia which according to the measurement tool was
55.1um, however I imagine that it would be in the order of mm (difficult
to say exactly how much without going back to check which mouse / age it
was, probably 10-15mm). Can you please advise if I have missed anything or wrong in process?
Thank you in advance

Thanks for reporting the problem.
It could be that we did not display correctly the value in the client or misread some information while reading the original image file. We will need the file to track down the issue.
Could you upload the file via our QA system http://qa.openmicroscopy.org.uk/qa/upload/
Which version of OMERO are you using?

Thanks
Jmarie

Hi Jmarie, I am using OMERO 5. I am also double checking to make sure the image metadata is in the correct scale. once I confirm the settings on the machine are accurate I will upload the file to the QA system.

Thank you again for your help

Hi Jmarie, I have uploaded 2 DCM files to QA link. ID 9219. measurements are off in both in about a 1000. i.e. - 0.008mm instead of 8mm. additionally, this is xray image, why does it appear all black?

any help will be highly appreciated.
Thank you

Thanks for uploading the file.
We will look at it asap.

Cheers
jmarie

Hi Jmarie,

I was wondering if you have managed to have a look at the dcm file?

Please let me know if additional information is required.
Thanks
Hilla

Hi Hilla

I did not have a chance yet, I will do that this week

Thanks

Jmarie

Hi Hilla

I checked your images. In both cases, the values stored for the pixels size X and size Y are 0.049 microns. This will explain the measurement you see when you draw lines in the Measurement tools.
There is probably an error while reading the metadata.
I checked using another tool and the distance should be in mm so we are not correctly reading the metadata, ticket opened see https://trac.openmicroscopy.org.uk/ome/ticket/12307

Regards
Jmarie

If we're out by a factor of 1000 (as suggested above) are the real pixel sizes 0.049 mm (instead of microns)?
Is that metadata in the file anywhere?
If so, I guess it's just a Bio-Formats issue to convert to microns.

Thank you for looking at the files, great help!
I hope it will be planned for resolution soon.

Do you know why the image is completely black and not an x-ray?
if I export the DCM to TIFF it will appear as x-ray, and on the machine itself it is X-ray as well.

Thank you again for any feedback/input.
Hilla