Smoother multilabel annotation of multiple 3D images and metric generation

[thanushipeiris]

Hi @Karol-G ,

This PR improves the 3D annotation workflow for multilabelling of multiple images.

Main changes are:

• When user clicks on a labels layer, the SAM output layer is changed to that label (enables smoother multilabel imaging instead of having to press the Activate/Deactivate buttons each time).
• Allows for reading in precomputed embeddings which speeds up annotation time and makes using this plugin feasible for large 3D images. (I plan to add bash scripts that I've been using to generate these embeddings from IMARIS files to the readme as an example).
• Saves annotations, generates an excel spreadsheet of metrics (area, percentage area based on a selected label's area, minimum distance to a particular label type) and clears viewer ready for next image in one click
• Option to read in image metadata from an excel spreadsheet so can add experimental information to the metrics output file.

I've made these changes to the plugin after feedback from my lab group who wanted a better workflow for annotating slices of 3D images with multiple label layers. We're now using it routinely in the lab and I think that these improvements will likely also be useful to other users.

I've made a lot of changes and some of my commits are not very piecemeal so am very happy to respond to feedback on this!

[Karol-G]

Hey @thanushipeiris,

Thank you for your extensive work. The added features appear to be quite substantial! I am currently in a crunch time phase and won't be able to review this PR for a couple of weeks, as other projects have a higher priority right now. I will definitely take a look at it though and will set a reminder so I don't forget. I hope this is okay with you :)

Best regards,
Karol