Open Microscopy Environment

Hi team,
I finally upgraded one of my production servers to 5.3.3 (from 5.2.8) and bumped into an unexpected issue with viewing Tables-held metadata in the regular web image viewer. In 5.2.x the "Image Information" button would show the metadata in the Table that annotated the Well from which the viewed image came. Now that Annotations from the Well are no longer directly associated with the Image, such info does not show up in the viewer. You have provided a nice script to transfer back Annotations from the Image to the Well which works fine. Is there an equivalent facility to move Table Annotations of the Well over to the Images in the Well? Or is there a plan to show e.g. MapAnnotations in that viewer (and/or in the new iviewer)? The latter would probably be preferable to me.
Thanks,
- Damir

Hi Damir,

Apologies for that 'unexpected issue'. The breaking of that workflow was not anticipated simply because in the main webclient you can easily see the parent Well for an Image (so it's easier to access table data for the Well). However, we'll look at adding that functionality back for the main image viewer where it clearly makes sense to keep it.

Moving table data to images wouldn't be easy (you'd need to create a new table and copy each Well row from the old table into multiple identical Image rows in the new table).

However, we certainly plan to display all types of annotations in the iViewer in the not-too-distant future.

Regards,

Will.

Hi Will,

Thanks. We use the webgateway to pull up the main image viewer for selected images from our web-deployed analysis/visualization packages so being able to easily pull up the tabular metadata/results inside that viewer window has been very useful. In such cases the main webclient isn't there.

I'll look whether the "omero metadata" cli routine can be used to populate the table on a per-image basis. I still have all the files that I had used to populate the per-well info using that approach.

Great that iviewer is rapidly evolving and getting all the desirable features. What is the best way to suggest additional feature requests, report bugs, etc. in iviewer? Here in the forum or directly in a Trello card?

Cheers,
- Damir

Hi Damir,

It looks like I've fixed the display of Well table data in the main image viewer: https://github.com/openmicroscopy/openm ... /pull/5441 (pending testing and review)...

You can add iViewer suggestions on trello or the forum, but if you want a response then the forum might be best (can link to a trello card) and it is more 'visible' to us in the forums over and above all the other trello notifications we get.

I started a card for annotations in iViewer at https://trello.com/c/Ogx4zfoJ/21-annota ... splay-edit

Cheers,

Will.

Hi Will,

With 5.4.0 I'm glad to see the table data show up again in the main image viewer. Thanks!!

However, with another new feature in 5.4.0 that I'm starting to use, I would like to propose to go a step further.
That new feature is the ability with Populate_Metadata to annotate individual images with Table data. So now I can use that to annotate images in wells with measurement results and other info that is specific to the image and not to the entire well. So the proposal is: can the table data shown with the image in the main image viewer be pulled from the Image itself if such data is present and from the Well if it is not present? Or, if that is too clunky, I'm happy with always pulling it just from the Image and I'll just have to make sure to always annotate the images with whatever table data I want to have show up.

I'm sure the IDR team has some thoughts on this so I'll be happy to go with whatever approach works for IDR as well.

Thanks,
- Damir

Hi Damir,

That should be possible. I've created a card here: https://trello.com/c/BvrQELe8/20-image- ... ge-or-well
The only issue is that we have to check for potentially 4 queries each time we open the image viewer
(query Table on Screen OR Plate with rows corresponding to Well OR Image).
But that shouldn't be too bad.

Regards,

Will.

Hi Will,

Thanks. If the multiple queries turns out to be problematic, I'm perfectly fine with a purist approach where you only get the Table attached to the Image in the Image Viewer.

For a future version of the iviewer, where you have more conveniently available real estate, it would be nice to show both the Well-associated Tables and KeyValue metadata AND the Image-associated metadata. I've been using the logic that more global info on cells, treatments, etc. are stored on a Well basis while measurements which are per-image, are stored on an Image basis.

Cheers,
- Damir

Hi,

I added note to the iviewer card at https://trello.com/c/Ogx4zfoJ/1-annotat ... splay-edit.
Cheers,

Will.