Non-negative fluorescence output? about waveorder HOT 2 OPEN

I think it sense to have clipping as a default-off option clip=False. My rough experience is that downstream consumers (people and algorithms) often expect smooth reconstructions on the scale of a few pixels, and clipping like this creates sharp edges that can create problems downstream.

Shifting the histogram avoids the sharp edges, but I think it will lead to different kinds of confusion---should the maximum value shift based on distant regions in the image?

from waveorder.

@talonchandler @ziw-liu I agree that clipping should be avoided to avoid texture or high-spatial frequency artifacts. I would add a constant offset, just like we adjust the black level for a camera. It can be a parameter to apply inverse and we can default it to a small value that avoids negative output in most cases.

from waveorder.