[ome-users] Display rendering problems with big images

[Jean-Marie Burel (Staff)]

Hi Peter

Thanks for reporting the problems.
I have created a card https://trello.com/c/r4cINtil/105-32-bit-images-issue
It looks like the clients are not correctly handling the min/max value for
that pixels

The preview pane is disabled for pyramid images and the images can only be
viewed in the main viewer.
When a pyramid is not available, omero will generate one if the size of a
plane is above a given value.
This can be configured. In order to do so, you will need to modify in
omero.properties the following values
omero.pixeldata.max_plane_width
omero.pixeldata.max_plane_height

For example in your case, set them to 4096 and 4096

Cheers

Jmarie


On 04/08/2017 14:46, "ome-users on behalf of Peter Zentis"
<ome-users-bounces at lists.openmicroscopy.org.uk on behalf of
Peter.Zentis at uni-koeln.de> wrote:

>Hi all,
>
>We are experiencing problems with "big" 32bit floating point images on
>our Omero server.
>When we import such images by default they just look uniformly gray,
>because by default the images are rendered with a lookup table ranging
>from -2147483648.000 to 2147483647.000 as can be seen in the preview
>pane. In the insight-client the Min/Max-button has no effect, in the
>web-client the Min/Max-button sets the values to a range from -32768 to
>32767 (completely independent of the image histogram). Interestingly, in
>the acquisition pane one can find correct min- and max-values in the
>metadata table, which manually copied to the preview pane allow for a
>useful display of the image.
>Originally we noted the problem with dm4-files from our 4K Gatan camera.
>However, we can reproduce the problem also with other images e.g.
>generated with this ImageJ script:
>
>run("Lena (68K)");
>run("32-bit");
>saveAs("Tiff", "noProblem.tif");
>selectWindow("noProblem.tif");
>run("Scale...", "x=- y=- width=3617 height=3617 interpolation=Bilinear
>average create");
>saveAs("Tiff", "bigProblem.tif");
>
>We do not have the problem with an image of 3616x3616 pixels, but with
>every image which is 3617x3617 pixels and bigger.
>Moreover, there occurs another problem (only in the insight-client, but
>not in the web-client), when the images have been converted to a 16bit
>integer format before, apparently connected to the image dimensions in
>the same way: Images of 3617x3617 pixels have the preview pane completely
>disabled. However, in the Full Viewer via the rendering controls the
>settings pane is available and works well.
>
>Do you think there is any possibility to fix this behaviour by adjusting
>our configuration? For now just pushing the limit for everything to work
>to 4096x4096 images would already be sufficient :)
>
>Cheers,
>Peter
>
>
>--
>Peter Zentis
>CECAD Imaging Facility
>CECAD Cluster of Excellence | University of Cologne
>Joseph-Stelzmann-Str. 26 | 50931 Cologne | Germany
>
>phone:(+)49-221-478-84028
>
>email: Peter.Zentis at uni-koeln.de
>


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