Open Microscopy Environment

Hello everyone,

I have a puzzling situation regarding rendering settings and their effects on the behavior of the image viewer for public data.

I refer here to this public project: https://images.jax.org/webclient/?show=project-1

The data in this project were bulk imported and passed through a couple of "users" before making it to the current state, in which they are owned by a service account (an admin user) and are in the Public group with the Public User.

For some of the datasets/images therein, everything looks fine. For example: https://images.jax.org/webclient/?show=dataset-178

There, all of the images have thumbnails, and when you open the preview pane you can see that the image renders, the 'navigation thumbnail' looks fine, and there are three sets of rendering settings reflecting the past owners of the data.

For other datasets/images, something weird is happening. For example: https://images.jax.org/webclient/?show=dataset-379

In that dataset, there were no thumbnails present for most of the images until I opened them as the public user for the first time. The images have rendering settings for the original user ('Dave Mellert') and, once opened by the Public User, got rendering settings for the Public User as well. These rendering settings look fine except for the fact that the aspect ratio of the navigation thumbnail is stretched and the red field-of-view rectangle no longer functions correctly.

I have tried deleting the rendering settings for an image/dataset, and I still see the same weird behavior for the Public User--the thumbnails start out unrendered and the navigation thumbnail in the image viewer does not work correctly.

What is really confusing is that if I log in as the owner of the data, everything looks totally fine across the board.

Any insight into what I am experiencing here? I don't care so much about the lack of thumbnails when browsing the data, but I would hate for the Public User to have a broken experience trying to navigate around a slide view using the little navigation thumbnail.

Hi Dave,

Thanks for the detailed post and examples!

I have been able to reproduce some of the issue you have discovered on a clean setup and have created a github issue.

In my use case, the usage scenario was slightly different in that there were no user settings present for an image before my public user previewed it. Also, if the user who imported the image browses it, the public user sees the correct aspect ratio in the web client.

Does the error persist on OMERO.insight when viewing the preview pane as a public user?

Also, could you let us know what version of OMERO you are using?

Many thanks,

Riad

I am using 5.4.9.

Does the error persist on OMERO.insight when viewing the preview pane as a public user?

You mean log in with the password I created when I created the Public User (insight doesn't seem to have a "Log in Public User" option the way that the web client does). The following info is assuming that this is the case:

So this is interesting. Insight shows the same preview thumbnails (or lack thereof) available to the Public User through the web client. When I open an image for the first time with Insight, the thumbnail is generated and will show up in both the Insight and web client views. When I open an image in the web client for the first time, the thumbnail will become available in both the web client and Insight views as well. So there is clearly something happening server-side with the thumbnails (which remember are all immediately viewable when logged in as the data owner regardless of whether I am using Insight or the web client).

I am not able to use the Preview pane for these data in Insight regardless of how I am logged in. Maybe that is because preview in Insight doesn't handle very large pyramid data well?

As I mentioned before, I can open the images in the default web client viewer as the Public User and I get the distorted aspect ratio on the navigation thumbnail and the corresponding problem with the red area indicator window. However, when I open these same data while logged-in as the Public User with Insight, I do not see this error.

Does this information help?

I did some more testing and updated the github issue above.

To fix the problem, you need to delete the Rendering Defs for the Images in that Dataset and then make sure that the Owner of the images is the first to browse them in the webclient.
Then, when the public user views these images, they will simply use the Owner's settings and thumbnails and not be able to create their own.
In a Read-Only group (such as a public group), users do not normally have permissions to create rendering settings on other users' images. But, if there are NO existing rendering settings when a public user tries to view the images, OMERO does allow creation of settings belonging to the public user. This is best avoided.

You can delete RenderingDefs for a single image using the command line with Image ID or for a whole Dataset with Dataset ID;

Code: Select all

$ bin/omero delete Image/RenderingDef:79953
$ bin/omero delete Dataset/Image/RenderingDef:25951


Hope that helps,

Will.

Will,

Thanks, that indeed fixed the problem!

Is there a way I can programmatically create RenderingDefs for the data owner following the deletion step? Previewing each of the 5000+ images in that Project could be a bit of a time sink

-Dave

Hi Dave,

There is a command-line tool for batch setting of rendering defs to some known values,
(https://github.com/ome/omero-cli-render) but unfortunately it doesn't support regeneration of new rendering defs.

I wrote a Python script to do this job:
https://gist.github.com/will-moore/7a37 ... c2d876c79c

Simply edit username and password (to the data owner) and set Project, Dataset or Image IDs.

This resets the rendering defs to defaults, then generates thumbnails belonging to the owner (which are needed in the Preview panel).

If this script is useful, we may port the functionality into the cli-render plugin.

You might also want to install the newer image viewer which is a bit nicer than the default one https://www.openmicroscopy.org/omero/iviewer/

Regards,

Will.

Will,

Thanks, this worked like a charm. Although I did make a minor modification.

This line was giving me some trouble when I tried to run the script for a single large project:

Code: Select all

rv = rss.resetDefaultsInSet(obj_type, obj_ids, conn.SERVICE_OPTS)

Things got hung up on that step and it was tough to gauge progress. I rewrote the script to call that method once for every dataset rather than across the whole project. It worked well and I was able to work in a progress indicator. I think this would be an excellent addition to the CLI, although you might think about reworking along the lines I described, as it can be disconcerting to wait a long time (>40 min in my case) with no feedback.

Regarding iViewer -- yes I have installed that on our Dev server and it's great! It is scheduled to be installed for our Prod server, we're just not there yet.

Thanks for the feedback and glad you managed to improve the performance.

I created an issue at https://github.com/ome/omero-cli-render/issues/30 to add this to the cli-render plugin.

Cheers,

Will.