Apply Rendering Settings for HCS data

[albot]

Hi all,

One of our OMERO users reported that she could not apply the rendering settings for a screen as it works same way it works for the usual datasets.
The button does not seem to work for screens (stays greyed-out).

Maybe, we have overlooked something. But could you give any feedback on how to get this to work?

Thanks.

Best regards,
Alex

OMERO version: 4.1.3

[mlinkert]

Hi Alex,

One of our OMERO users reported that she could not apply the rendering settings for a screen as it works same way it works for the usual datasets.
The button does not seem to work for screens (stays greyed-out).

Maybe, we have overlooked something. But could you give any feedback on how to get this to work?

As you're using OMERO 4.1.3, this problem should be fixed by upgrading to the most recent version of OMERO (currently 4.3.4).

Regards,
-Melissa

[albot]

Hi Melissa,

We have verified the versions - so we seem to use OMERO 4.3.4 (server). It was a typo in my previous post.
The current client version is 4.3.3 as has been confirmed by my colleague.

She told me that the rendering button stays greyed-out when she would like to apply the rendering to a number of images on the plate.

Could you please verify - maybe we are doing something wrong? Or do you have a new client version (4.3.4) to test ?

Thanks.
Best,
Alex

[wmoore]

I'm not sure which button you mean. Maybe a screen-shot would help?

If you right-click on the thumbnail, you should have an option to "Copy Settings". Then right-click on the plate in the left-hand hierarchy and "Paste Settings".

The other option is to use the "Apply to All" button in the preview right-hand tab when you're looking at the image with rendering settings you want to use. Is this the button that's greyed out? It isn't greyed out for me when I just tried it.

Will.

[elauwers]

Hi Melissa,

I am the user Alexander was mentioning in his previous post. I was able to adjust the brightness and contrast for a batch of 768 screen pictures by copy-pasting the settings the way you just described.
Thanks a lot for your help and your prompt answer.

Elsa

[dsudar]

Hi Will,

Sorry to bring this old topic back but I have a followup question:
Currently, when viewing a screen, a copied rendering setting CAN be pasted to the whole plate but CANNOT be pasted to a selected subset of wells. When viewing images in the "projects" view, you CAN paste rendering settings to a selected subset of images in that collection. Can that functionality be extended to screen data as well?

Just to explain why: we regularly run 2 (or more) different cell lines in the same plate and would like to set rendering settings to be the same for the wells for one single cell line but different for the other wells.

I understand the added complexity of doing this since one would like the new settings to be pasted to all fields in the same well.

Thanks,
- Damir

[bramalingam]

Hi,

The clients do not allow for copy/pasting rendering settings between a specific set of wells (as of now).
This is definitely a use case worth adding to our clients,
and I have added a ticket on this regard,

https://trac.openmicroscopy.org.uk/ome/ticket/12441

We will definitely keep you posted, once this gets resolved.

For the time being,
You can definitely achieve this using a script (python/Matlab/Java,etc).
Our documentation pages should help you on this regard.

Best,
Balaji

[Dominik]

This issue has been addressed within this PR: https://github.com/openmicroscopy/openmicroscopy/pull/3311; copy/paste between a subset of wells will be available with version 5.1

Cheers,
Dominik

[dsudar]

Hi Dominik,

Sorry I hadn't replied to this earlier but thanks a bunch. Copying/Pasting rendering settings between subsets of wells now works great. Extremely useful, thanks!!

I have another question related to this topic:
One of our main uses for applying rendering settings to all in a plate is to change the default channel color assignment (the ScanR files do not encode what the appropriate channel colors should be and thus our images all are assigned in the order red, green, blue, which makes the DAPI red and people don't like that). However, using the apply-all functionality also changes the color ranges for all channels which in some cases is not desired. Is there a way to "apply-all" the channel assignment but leave the ranges as they are? Alternatively, is there a way to "force" a different default channel color assignment order upon import?

Thanks,
- Damir

[Dominik]

Hi Damir,

unfortunately there's no way to perform an "apply-all" with just a subset of the rendering settings at the moment, "apply-all" will always apply all rendering settings incl color ranges to all images. It's also not possible to specify any rendering settings on the import level. But these are certainly useful features; I'll add your ideas as RFEs to the particular cards on our trello board.

Regards,
Dominik