Can you expand on why the screen icon doesn’t work for you ?
That’s a cool project… however Blender is really not made for “presenting” content, so if you want your atlas to be accessible to Blender-illiterate people, maybe the best is to offer it online (webGL) or through a dedicated application.
If I understand correctly you are using annotations for labels right now ? and this annotation system is supplied by the addon “measureIt” ? text objects are not super flexible but they can have materials, just like any other object, and you can control your visibility through there. My suggestion would be to create an interface, in the form of an armature with control sliders (or simply as custom properties in the sidebar) that control visibility of the different structures. You can then link those to a group node that turns your material into a transparent shader when it’s off, and reverts to the regular material when it’s on.
What would you think of this ? how are users supposed to interact with the atlas ? would you rather have everything in one place, or let the user navigate the scene and click on structures to show them ?
I don’t have time to download and check for myself, maybe later