Open Microscopy Environment

I have just upgraded from 5.0.3 to 5.1.2.
I had no problems starting OMERO and all the data is in place as it was before.
However, the rendering settings are not working properly:

* I am viewing a DeltaVision image imported as floating-point

* If I set the rendering scale to "Min/Max", it looks relatively fine.

* However, if I *increase* the "Min" level (slider or manually), the smallest-valued areas in the image start to become the brightest. They should be zero/black, since the "Min" level is now above those pixel values, but it looks instead is as if a LUT is being applied setting those pixels to full intensity.

* If I *continue to increase* the "Min" level, the pixel values start to go back down, and with continued increasing, the pixel intensities get stranger and eventually become noise (see attachments).

* Under "Advanced" (in the Rendering Settings in Insight), the Bit Depth is set as 255 — probably not right? Does that mean 8-bit? These should be floating-point images.

So, something strangely specific is wrong…

EDIT 02015-06-02: This scaling/rendering problem does not occur with a UInt16 image which I just imported. So this is specific to floating-point images after the 5.0.3→5.1.2 upgrade (before the upgrade, there were no problems with either floating-point or UInt16).

Thanks,
Pete Carlton

Images and `omero admin diagnostics` here: https://dl.dropboxusercontent.com/u/458 ... arlton.zip

Hi Pete,

thanks for reporting this rendering issue. Would it be possible for you to upload a sample DeltaVision file allowing us to reproduce the problem at https://www.openmicroscopy.org/qa2/qa/upload/?

Best,
Sebastien

Hi Sebastien,
Thanks for the reply; I uploaded a dataset (ID: 11111).

Some image info:

Image Size (X,Y,Sections)............... 1024 1024 204
Data Organization (NZ,NW,NT)............ 51 4 1
Image Sequence.......................... Z -> T -> W
Multi-Resolution Settings............... 1 1
Data Type............................... Floating-point
Start Pixel / Grid Spacing (X,Y,Z)...... 0 0 0 1 1 1
Pixel Size.............................. 0.06402 0.06402 0.2000

Best,
Pete

Hi Pete,

many thanks for the sample file upload. I was able to duplicate the problem using OMERO 5.1.2 and the OMERO.web client. This hints towards a regression in 5.1.x for this kind of data and/or this format as I was not able to reproduce the issue with OMERO 5.0.8. I opened a ticket corresponding to this issue. Let us know if you would like to be cc'ed on it.

Best,
Sebastien

Thanks a lot for checking it, and yes, please cc me on the ticket.
In the meantime I can work around by reimporting any needed images as UInt16.
—Pete

As you've hopefully seen, I've CC'd you on the ticket, Pete.

Cheers,
~Josh.

Thanks for fixing this in 5.1.4, everything works for us now.

Hi Pete, do you mind if we post your most recent comment on Twitter? Thanks,

Kelli
OME Social Media Assistant