Open Microscopy Environment

upgrade Omero5.02 to 5.0.4 resulted in silhouettes for dicom images? I didn't notice these on 5.0.2 so there is a bug or misconfiguration on my end? when opening these dicoms in osirix results in X-rays as I would expect them to look. I downloaded the new 5.04 insight and it still displays these images as silhouettes.

On the up side the performance is better with 5.0.4 with the new configuration option set. So thanks for that

I don't suppose you have any that are non-identifying that you'd be able to send us?

If you can, please do via: https://www.openmicroscopy.org/qa2/qa/upload/

Best,

Kenny

Just uploaded 1 image. bug id=9532

If you adjust the rendering settings so that the maximum pixel value is ~4000, that should result in a better looking image. Was this file imported with 5.0.2, or after upgrading to 5.0.4?

mlinkert wrote:If you adjust the rendering settings so that the maximum pixel value is ~4000, that should result in a better looking image. Was this file imported with 5.0.2, or after upgrading to 5.0.4?

Thanks -Where do I set the maximum pixel value ~4000 - googling and searching docs I didn't find anything? Obviously I can give this a go - but i'm doubtful as to whether it would fix the display of these images..as it looks like more than an adjustment is needed...

Imported using 0.2.

Hi,

jwarren wrote:Thanks -Where do I set the maximum pixel value ~4000 - googling and searching docs I didn't find anything?

See http://help.openmicroscopy.org/viewing-data.html for how to adjust the rendering settings. The max pixel value 4000 can be entered into the textbox at the right of the slider.

So when you imported with 5.0.2 they used to look more like Osirix displays them without having to manually change the rendering settings?

Thanks,

Kenny

I'm 90% sure they were displaying ok previously as all our dicom images are now completely reversed - like a negative. I think I would have noticed before.

I can twiddle with the settings as you suggest on a per image basis - it did get something more like an xray imags should look - but one of the main reasons we use omero is to make thumbnails etc without having to fiddle with this kind of thing. We are talking thousands of dicom images with slightly different dicom settings here. So I can't expect users or me to do this for every one...

I'll experiment with uploading again using the new server.

jwarren wrote:all our dicom images are now completely reversed - like a negative. I think I would have noticed before.

We are talking thousands of dicom images with slightly different dicom settings here. So I can't expect users or me to do this for every one...

Totally understandable - thank you for your patience, and for providing all the details that we need to try and diagnose the issue.

All the best,

Kenny

So the image I uploaded displays ok for you? Not completely black and white?

For what it's worth, for me, when I update the rendering settings as Melissa has mentioned, I can start to see skeleton appear in the x-ray, but if you think this an issue with our reading of the format, it's likely Melissa that needs to deal with this, who will be on-line later.

We need to do more work here to determine if this is a bug specifically with OMERO and not the Bio-Formats reader, which we will continue to do here.

As you say, if these were all fine before the upgrade, and are unusable now, we need to work out why, and how to fix.

Best,

Kenny