[ome-users] Rendering image view settings on the OMERO web application

[Will Moore]

Hi Moran,

 You are right, you'll need to apply rendering settings to each "Dataset" in turn.
You can do this by right-clicking on an image thumbnail or on an image in the 'tree' on the left, then "Copy Settings".
Then you can right-click on each 'Dataset' in the tree and "Paste Settings".
You can also do this on the parent "Project" to apply settings to several Datasets at once.

I'm afraid I don't know of any documentation on how OMERO sets rendering settings on import.
In general, the min & max values are set just within the min & max pixel intensities for the image.
Channel colours can be read directly from the imported image metadata if they are specified in the file.
Let us know if you think we're missing this for a particular format.
Otherwise channel colours are chosen based on a bunch of channel metadata
Channel wavelength, emission filter wavelength etc.

Unfortunately the ranges are not read from the imported file into the OMERO metadata on import
so there's no way to "reset" to that original range.
However, we have started to look at fixing this limitation.

 Regards,

  Will.



On 13 Mar 2014, at 14:41, Moran Cabili-Kalmar wrote:

> Hi Ola,
> 
> so I did manage to run a version of insight that let me update the setting and do apply all- It seems like I would need to do that for each directory , correct?
> Can you please point me to a documentation that explains how omero decides on the def setting of RGB, if one such exist?  I am actually not sure how to set the ranges such that it which match my original image exactly.
> 
> thanks!
> 
> Moran
> 
> 
> 
> On Thu, Mar 13, 2014 at 8:47 AM, Moran Cabili-Kalmar <nmcabili at broad.mit.edu> wrote:
> Dear Ola,
> 
> 
> Thanks so much for the quick response!
> the version is OMERO.web 4.4.9-ice34-b98
> I attach the image I uploaded and a snapshot of how it appears on the web server .
>  I am currently having some security problem with running insight on my computer but will try to solve this and write you back. 
> either way I attach the image as it was uploded (this is an overlay), and provide a snapshoot for how it is displayed on the web application , which is different from the original image.
> if I set the red and green channel to display the max value as the maximal value in the range then I can see the correct image, but that is not seen by default, nor I was able to save this.  
> I will need to save and apply this setting to all my images and I have a few hunderds f those.
> please let me know if I can provide more info.
> thanks so much!!!
> 
> moran
> 
> 
> On Thu, Mar 13, 2014 at 6:03 AM, Aleksandra Tarkowska <A.Tarkowska at dundee.ac.uk> wrote:
> Dear Moran
> 
> Which version of OMERO software do you use?
> 
> Could you send us a screenshots showing the difference between Insight and Web. Both clients uses the same resources and should display images exactly in the same way.
> 
> If you feel your image is imported incorrectly by default please submit original file to us and we will investigate it. You can upload it via our support system http://qa.openmicroscopy.org.uk/qa/upload/
> 
> Kind regards
> Ola
> 
> 
> The University of Dundee is a registered Scottish Charity, No: SC015096
> 
> 
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20140319/39bbea9f/attachment.html>