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WayScience / Benchmarking_NF1_data

Benchmarking data processing strategies for Cell Painting data of NF1 Schwann cells. See analysis repository (https://github.com/WayScience/NF1_SchwannCell_data_analysis) for information on how the data was interpreted.
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Current CP illum pipeline is not automated + saves images as different bit depth #44

Open jenna-tomkinson opened 1 year ago

jenna-tomkinson commented 1 year ago

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 commented 1 year ago

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.