Thank you @lassoan for your awesome reply!
Lots to digest, so it may take me some time to come back with some significant progress, but I’ll let you know how this progresses. I’m happy to develop any plugins in the open.
At least, 3D Slicer seems well suited for working with these types of microscopy images. I really like the fine tuning of the renderer look-up tables (both colour and opacity) which is not something I’m used to from the usual microscopy oriented tools I use (e.g. Imaris). And you’re absolutely right, adding colours makes the image way more interesting 
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Kind regards,
Egor