Current CP illum pipeline is not automated + saves images as different bit depth

[jenna-tomkinson]

For both CP and DP, the corrected images are saved as different bit depth than the original image during the IC step. I am not 100% sure why in the PyBaSiC method we rescaled and converted to 8-bit (which is reflected in CellProfiler) but it might be for good reason.

Based on research, bit-depth is important if you convert and go down bit-depth like we do, we do it in the correct way (see https://bioimagebook.github.io/chapters/1-concepts/3-bit_depths/python.html) by rescaling then converting, but do we need to actually do this or not?

As well, the CP illumination correction pipeline is not automated like the CellProfiler analysis.

[jenna-tomkinson]

Looking back at this issue now, I see that when I implemented the methodology of PyBaSiC from Roshan in IDR_stream, I overlooked the part of the code was directly converting the images into 8-bit, which is why this occurred here.

This can easily be corrected for, but note this is why this occurred.