Open Microscopy Environment

Hi,

Our biology team is currently undertaking a screen optimization project.
They are trying lots of different probes to compare which are the most informative.

Currently when previewing an image the microscope channels are displayed (DAPI, FITC, Cy5 etc.), but not the probes (Hoescht etc.).
Is there any way I can insert this data somewhere, so it is displayed in the preview tab?

The current workaround I have in mind is to create a well or image annotation with something like:
DAPI: Hoescht
However, it would not be available from the preview tab...

Thank you for your time,

Etienne

Hi Etienne,

if having the data in the previous is your goal, then you can update the channel names to also include the probe information. If you can install the render plugin we can provide you examples for how to do that.

Otherwise, your best bet is an annotation.

Cheers,
~Josh

Hi Josh,

The render plugin solution seems more attractive, do you have some examples?

Thanks,

Etienne

Hi Etienne

The OMERO CLI render takes a target OMERO object and the YAML or JSON file containing your desired rendering settings. You can see a couple of examples here:

• https://github.com/IDR/idr-metadata/blob/master/idr0015-UNKNOWN-taraoceans/screenA/idr0015-screenA-renderdef.yml
• https://github.com/IDR/idr0045-reichmann-zygotespindle/blob/3b5af72b862775d508c8c4c6414dec6a0a6966cf/experimentA/rendering_settings/SupplementaryFigure01.json

You can define settings such as the channel name, min/max. If you omit a field it'll be unchanged.

Apply the settings to all images in Dataset:123 by running:

Code: Select all

omero render Dataset:123 render-settings.yml

You can also apply settings in individual images (Image:123) projects, plates, etc.

Hi,

Thanks, that helps a lot. But, I am unclear what the min/max parameters do and I could have a use case for something like that.

We use a classic method for finding the image saturation parameters (but those are in uint16, not in uint8 as in your examples). Can we include those by default? Ideally, it would be an option in "User Settings" under the Preview tab of an image.

Regards,

Etienne

The min/max should set the default range used for auto-scaling the display in the image viewer and preview pane, and it should work for all integer types. Is this what you wanted?

I think it could. I will need to test it and then I will get back to you.

I have a last question, it seems in your examples, you set channel names and saturation parameters for an entire screen. However, in our use case, we have different probes in a single screen. Does the render plugin handles this use case?

You can pass any omero target to the command, for example Dataset:123, Plate:123, Well:123, Image:123. You'll have to create separate definition files for each though.

Hi all,

Thanks for the detailed instructions! Have you guys run into memory issues when executing the "omero render set" command? I am running into serious memory problems when applying the render settings for a screen. The server seems to be consuming increasing amounts of memory per plate without releasing the memory. Closing the connection, terminating the session etc. does not seem to free up more memory.

We are running a 8 core machine with 32G of memory (Blitz configured to use 70%)
OMERO.server version: 5.4.9

Is there any configuration that we have missed causing this memory leak?

Regards,
Frank

Hi Frank,

the 'render set' command triggers the regeneration of the image pyramid (for large images > 3192 x 3192px) and the thumbnails. This can use up a lot of memory. This process also detaches from the cli connection and the OMERO session and runs in a background thread. That's why the memory isn't released immediately, but only after the process is finished.

If you run into memory issues, you could try to decrease the maximum number of these background threads:
https://docs.openmicroscopy.org/omero/5 ... nd-threads

Kind Regards,
Dominik