A couple of queries about OMERO.web (iviewer and search by key-value pairs)

Dear OME Team,

Users at our institution (EPFL) are asking for two different features in OMERO.web:

  1. In the iviewer, timepoints are updated after sliding the time slider. Is it possible to have a “live” view of the different timepoints while sliding the time slider?
  2. Several users would like to search for values using a drop-down menu when filtering images by key-value pairs, in the same way as they can choose between existing keys. Is there a way to change that?
    Drop-down_menu_key-value_pairs

Many thanks,
Claire

HI Claire,

The “live” view of timepoints would be a nice feature but it’s a big change since we don’t have all the data “in hand” in the client and we can’t load the whole image (all Z/T planes) when you open the image since this could be a large amount of data. So we can only try caching the planes that are loaded, so that they are quickly available after that. But this would still be a large piece of work. See Update image while sliding Z/T (cache planes) · Issue #364 · ome/omero-iviewer · GitHub

For the filtering, are you wanting to choose Values for a particular Key (e.g. choose Key first, then select from dropdown of Values for that Key)? The filter field does support auto-complete (when you start typing a Value - see screenshot), but I guess you have to know at least the first letter of an existing Value.
If the drop-down list were to show as soon as you choose a Key, I assume that would be sufficient?

Or do you want to search for a Value from Any Key? I guess we could look at adding a Choose Key > Any option?

Screenshot 2021-01-12 at 08.49.12

Cheers,

Will

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Hi Will,

Thank you very much for your answer and for having created an issue regarding the updated view of timepoints.
For the key-value filtering, displaying a drop-down list of existing values as soon as a specific key is selected would indeed be sufficient!

Best,
Claire

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Hi Claire,

Thanks for the reply and sorry for the delayed response. I was trying to implement the fix straight away but it’s taking longer than expected so I created an issue for it for now: Filter by Key-Value: show auto-complete immediately · Issue #247 · ome/omero-web · GitHub

Cheers,
Will

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UPDATE: I’ve opened a PR to fix this at Show autocomplete for KV filter when Key selected by will-moore · Pull Request #250 · ome/omero-web · GitHub

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Hi Will,

Thank you very much for your reactivity and for the pull request redarding the search by key-value pairs!

I have a couple more questions/queries from my users regarding OMERO.web:

  • Is it possible to display the filesize of a selected image, dataset or even project in OMERO.web (for example under the general tab from the right panel)? For now, I am only able to retrieve the size of raw images by downloading them, like shown here:
    image
  • We would like to allow public users to download public data. It is already possible to create .zip files after selecting multiple images and hitting the download image as.. arrow button, but this is not really convenient for datasets that contains a lot of images (more than one page in OMERO.web).
    Would it be possible to have the opportunity to download entire datasets or even entire projects as .zip, with a similar download button?

Cheers,
Claire

Hi Claire,

It’s not very obvious I’m afraid, but you can see the size of the original files for all selected images in the Download menu tool-tip:

Screenshot 2021-01-21 at 11.03.26

The webclient will struggle to generate .zip files on-demand for large amounts of data. I’m surprised if it even works well for a whole ‘page’ of images. One option is for you to create a zip manually, with (for example) all the images for a Project. You could attach this zip file to the Project as a File Annotation (and could also link this same annotation to the Datasets or Images within the Project, without adding to the data on disk). This would allow users to download without having to generate a zip on the fly.
This manual approach might not scale well if you are making a lot of data public, and you may find that the webclient still doesn’t handle downloading of very large Files very well, but it’s worth trying to see how it works for you.

For downloading larger amounts of data as scale, OMERO is probably not the right tool for the job. For the IDR, we use Aspera www.ibm.com/products/aspera.
If you have another tool for handling downloads, it could be possible to configure webclient’s Open-with… menu to direct users to a download URL for a particular Project etc, or simply add a download URL to the description of a Project or Dataset.

Hope that helps,
Will.