Hi Chris 
Thanks, so the step 1 to step 4 are the pipeline how you implement the "remove haze and smooth edges" function. right?
So level means the threshold for the image. 
follow the https://scikit-image.org/docs/dev/auto_examples/segmentation/plot_multiotsu.html, I should first use the 1.5 as the threshold. the do the following computation? 
sorry I did not get  the  abcde part. do you mean use Level 1 step 1?  So in a, I compute the Otsu 4 levels (use 4 thresholds and set the darkest as air) b. step 2: use Otsu 3 levels (3 thresholds and set the darkest as air etc.) could you explain more detailed?

I think calling MRIcroGL scripts from Python or BASH scripts will also help me in some sense.
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