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

[Moran Cabili-Kalmar]

Will,
thanks so much for the detailed answer, I'll use the copy settings as
suggested and be in touch if I have more questions.
Thanks Again!

Moran


On Tue, Mar 18, 2014 at 8:13 PM, Will Moore <will at lifesci.dundee.ac.uk>wrote:

> 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
>>>
>>
>>
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