Filter only main image

Dear all,

quick question regarding viewing WSI (ndpi) images in OMERO web client:

How can I view only the “main” images and hide the macro and ROI image?
(by default I can see three images per “main” image - the image itself, a macro and a ROI image).
Technically it probably means view only series=0/1 and filter out the rest.

Thanks for any help in advance!

Regards,
Manuel

Dear Manuel

OMERO.web is very customisable, the macro and ROI images could be hidden in the orphaned_images folders. This is the strategy used in Dundee on our server used for teaching University students.

We had a similar problem for an IDR study about to be released, in that case, the images have been “hidden” in a dataset.

One problem of that approach is that if, for example, the user wants to move the data to another group. In that case, in the current version of OMERO.web the images will not be “visible”, preventing the selection in OMERO.web and so preventing the move.

We have been reworking the move workflow in OMERO.web to avoid such confusion.
The improvement is currently under review and test.

We are also considering allowing the deletion of such images i.e. macro, ROI. This is something we have been hesitant to do since it breaks the fileset. We have created a design issue [1]. Feel free to add comments and/or suggestions

Cheers

Jmarie

[1] https://github.com/ome/design/issues/107

Dear @j.burel,

thanks a lot for your input.
I thought about an approach by simply filter by image.series==0 somehow.
Unfortunately the series attribute is nowhere visible.
Maybe one option is to write a script which exposes the series number as key-value pair or tag and then filter by key-value or tag?

Regards,
Manuel

For most formats, OMERO will add e.g. [0] or something to the name for the first image in the series?
But a script would certainly work if the metadata is more hidden.
You could also add a rating and filter by that.

Another option is to use the Table layout in centre panel of webclient. This shows you the X and Y sizes in columns and you can sort by these, which will show you all the Big images first.

Cheers,
Will.

Dear @will-moore and @j.burel,
thanks a lot for your comments on this. Indeed a name filter “[0]” works.

However, I guess this is more a work-around, also moving macro images into e.g. another dataset is probably not the way to go (moving image issues…).

To make OMERO-WEB the user-friendly client for e.g. Pathologists it would be great to only see the main images by default, and then have the option to visualize e.g. the macro optionally. Do you think this could be handled as a feature-request for future OMERO-WEB versions?

Cheers,
Manuel

Hi Manuel,

It’s actually not that bad when you keep the ‘macro’ images in a different Dataset.
When you want to move the images to a new group, the webclient will ask if you want to move all the images from the fileset (since you can’t split the fileset between groups). The images will get moved into one Dataset in the new group, but that’s not too painful.

Similarly, if you try to Delete just 1 image from a fileset, the webclient won’t allow it and this time will ask you to actually select ALL the images to delete, in order that you don’t accidentally “Delete All”.

One of the options considered at https://github.com/ome/design/issues/107 is to allow partial deleting of a fileset, to permanently remove the images you don’t want.

The advantage of using separate Datasets compared to a custom filter is that other clients will show the same Images in the Dataset (without needing to implement the same filtering). For example Insight or even Orbit.

Because we have to deal with hundreds of different file formats, it’s unlikely we’d support behaviour that is specific to one or two formats.
It’s certainly possible that we’d support the ability to save a filter on a Dataset. We’d need some ‘standard’ way of storing the filter, possibly as some sort of annotation on the Dataset.

However, even in that case, we would likely ask the user to choose which images are filtered, since making that decision is very dependent on the types of images, the file format and personal workflow preference. So, it may not have that many advantages over the existing option of moving images to a different Dataset.

If you wish to ‘automate’ the hiding of images in a different Dataset, you could consider scripting this move after images have imported (run the script over a recently-imported Project or Dataset). Or if you are importing the images via a client-side script (CLI, Python or Java) then that could hide some images in a different Dataset as part of the import workflow.

Let us know how that approach works and what are the ‘pain points’ that need addressing,

Cheers,

Will.

Dear @will-moore,

thanks for this details input. We’ll try the different approches and come back to you.
Let’s continue on https://github.com/ome/design/issues/107

Manuel

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