ImagingDataCommons / slim

Interoperable web-based slide microscopy viewer and annotation tool

https://imagingdatacommons.github.io/slim/

Apache License 2.0

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Improvements to ROI presentation and UI support #184

Open fedorov opened 11 months ago

fedorov commented 11 months ago

Right now, on this example, same color is applied, and it is impossible for the user to tell different kinds of ROI one from another

https://andrey-slim-test.web.app/studies/2.25.155017484756498730492136597238994838876/series/1.3.6.1.4.1.5962.99.1.3434988325.342625608.1687062201125.4.0

fedorov commented 11 months ago

Additional ideas related to visualization of the individual regions:

allow applying the same color all regions of the same semantics and allow toggling them all at the same time
show ROI number/details in a tooltip as an option on mouse-over

fedorov commented 10 months ago

Related suggestions from Javed Khan group communicated by @curtislisle:

Each SR object belongs to a class (e.g. ERMS, ARMS, connective tissue, etc). Could it someday be added to have a way to enable or disable all the annotations of only a particular class simultaneously?
it would be great to have the option of hovering over an object and having the class or a class nickname displayed.
when selecting a particular object (by clicking on the right column), it would be nice to also be able to select by clicking a contour and seeing the corresponding entry in the column highlight.
when an object is highlighted, it displays lighter than the rest. I think it would be more intuitive to make all non-selected objects become lighter instead.
could we have different classes be displayed in different colors (or give a per color selector so the user could change colors at the class level.

fedorov commented 10 months ago

Feedback from Tom G:

being able switch on ALL the ROI’s for a given class would be nice, eg, a button to just turn on all the stroma. Also, it seems like all the ROI’s are the same blue color. Differentiating by class would be helpful, ie necrosis = red; stroma = blue, etc.

fedorov commented 8 months ago

Example of how contours are shown in Aperio ImageScope (just to take into account while deciding what to do in Slim):

pedrokohler commented 1 month ago

@fedorov can this be closed? We had created other tickets to address these changes:

https://github.com/ImagingDataCommons/slim/issues/193 https://github.com/ImagingDataCommons/slim/issues/194 https://github.com/ImagingDataCommons/slim/issues/195

These have all been addressed and their PRs have been merged already.

pedrokohler commented 1 month ago

@fedorov my mistake, we actually still have 2 tickets that haven't been addressed about this issue, namely:

192

196

fedorov commented 4 weeks ago

@pedrokohler I tested in the IDC test tier, and I do not understand why the color of the large annotation in the top part of the image changes color when I select regions for the annotations in the bottom part. I do not understand the logic for highlighting that is implemented right now, it is not intuitive. I suggest we have a quick meeting sometime next week to discuss this.

curtislisle commented 4 weeks ago

Thank you for looking into multiple colors for different annotation types. This will be popular with our scientists. On Nov 1, 2024, at 5:29 PM, Andrey Fedorov @.***> wrote: @pedrokohler I tested in the IDC test tier, and I do not understand why the color of the large annotation in the top part of the image changes color when I select regions for the annotations in the bottom part. I do not understand the logic for highlighting that is implemented right now, it is not intuitive. I suggest we have a quick meeting sometime next week to discuss this. 2024-11-01_17-24-52.1.gif (view on web)

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you were mentioned.Message ID: @.***>

pedrokohler commented 3 weeks ago

@pedrokohler I tested in the IDC test tier, and I do not understand why the color of the large annotation in the top part of the image changes color when I select regions for the annotations in the bottom part. I do not understand the logic for highlighting that is implemented right now, it is not intuitive. I suggest we have a quick meeting sometime next week to discuss this.

Can you provide the URL?

fedorov commented 2 weeks ago

Sent via slack.

I think it would also be helpful to allow user to choose if regions should be shown as outlines or filled regions.

Also, the choice of the default colors should be revisited to make them more prominent over H&E. The current colors are very hard to see.

fedorov commented 2 weeks ago

Also, I just realized, for overlapping ROIs, only one label is shown, which can be confusing - in the example below, the same label overlay is provided for what appears as different ROI (probably because they are overlapping). It might be better to show information for all overlapping ROIs under the mouse pointer.