OMERO.figures linked to Image-of-a-Figure

[will-moore]

We want to be able organise figures in much the same way we can organise Images https://trello.com/c/LwAVYUjm/165-save-figures-in-folders

Adding File-Annotation support to Tagging, Project/Dataset (folders), and even OMERO.parade would be a lot of work and would also not provide a thumbnail / preview of the figures you are working with.

However, if we were to save the Figure as an OMERO Image and keep the Image-of-a-Figure linked to the figure FileAnnotation, then we can use all the existing functionality for organising Images.

We can already 'export' a Figure as a new Image in OMERO (currently this has no link back to the original figure file), but several changes are needed to make this workflow visible and easy to use. In particular, we need to keep the Figure and Image-of-a-Figure in sync as one entity.

• Instead of simply adding a Figure URL in the image description, we need to maintain the link between the exported Image and the figure itself. We could link the figure-FileAnnotation to the Image. This would make figures searchable since the JSON file would be indexed (need to test): TODO:
  • First need to ensure that the figure wouldn't get accidentally deleted by a user in webclient or Insight. See https://github.com/openmicroscopy/openmicroscopy/pull/5774
• Also, if the figure is also linked to the images that are IN the figure, we need to be able to distinguish between these and the figure-exported Image, possibly via an annotation on the Image or even its description.
• Open-with support should be extended to Files. Figure files (namespace) should open in Figure.
• For OMERO.figure users to know that this workflow is supported, we’d need these options to be more visible, such as in the figure Save dialog. E.g. option to also save as Image in OMERO, in a chosen Dataset. This will form the main entry point for this workflow. Needs some thought to design this UI.
• Update of the Image when the figure is updated (saved). This could happen automatically or after user confirmation. If it’s not possible to update the Pixels of an image, we’d need to replace it with a new image (copy all links etc) and delete the older one.
  • If using a script to e.g. export all Figures in a certain Tag, need to iterate through all the figure-Images under the Tag and get the figure linked to each.

Potential issues:

• If we don't provide any features for organising Figure files, users will need to save as an Image before they can Tag, put in Dataset etc.
• Updating the Image-of-a-Figure when changes are saved to the Figure: Currently OMERO does not allow the pixels values to change once an image has been created. Can we work around this, or do we need to create a new Image, copy links & annotations to the new Image then delete the old one each time?

[jstitlow]

Re: the first Potential issue: Tagging, Dataset specification, KV, etc. could be added in either the File dropdown menu (Add Figure Annotation...) or/and in the Info panel when no images are selected.

[jstitlow]

Is it possible to increase resolution of thumbnails in the OMERO web client center panel? Thumbnails at the current res are not interpretable, e.g., compare thumbnail to preview:

[mtbc]

There is a omero.client.browser.thumb_default_size configuration property which may help?

[will-moore]

So https://github.com/openmicroscopy/design/issues/96#issuecomment-394691601 gets to the crux of this solution: The idea is that we can avoid re-building a Project/Dataset & Tagging workflow in figure itself (and the browse by Project/Dataset/Tag too). I guess the way this would work is File > Tag this figure in OMERO which would open the corresponding Image-of-a-Figure in webclient. However, this wouldn't be enabled until you had saved the Figure (including creation of the Image). So you'd have to disable the "Tag this figure in OMERO" option, with a tooltip "Save the figure to enable Tagging". I know this is a little clunky, but if we are going to support the whole "Figures linked to Image-of-a-Figure" workflow, then we have the whole structure for organising & browsing Figures, without having to build it again from scratch.

[jstitlow]

Thank you Mark!

[will-moore]

Unfortunately, with the way we now load thumbnails in bulk in webclient (and parade), the omero.client.browser.thumb_default_size won't be taken into account. But I'd be reluctant to suggest changing it anyway, since OMERO itself caches thumbnails at size 96 so trying to use a different size from the clients would hit performance. However, I understand the need for better resolution. A long time ago I played with the idea of loading a high-resolution thumbnail (full plane) when you clicked on an image https://www.youtube.com/watch?v=1ijH9cw2GsM - Loading the full plane is not a good idea for big images, but we could think about loading a larger thumbnail in some situations if this is important (and the Preview panel won't do)?