Some of the items I noticed, which are hopefully not too difficult to fix:
instead of commenting out installation of prerequisites, it is better to put those into an if clause, which would check whether papermill-initialized variable (say, "interactive") is reset
if the notebook is executed in the "colab" (interactive) mode, it would be good to make it possible to run it without assuming that manifest file is present, and instead generate it on the fly, or use pre-defined SeriesInstanceUIDs, so that the notebook is completely self-contained
I noticed that in some cases global variables are used - it would be good to get rid of those and instead use function parameters for passing these variables
things such as SeriesNumber may be easiest to fetch from the input CT series instead of relying on the manifest or query
Some of the items I noticed, which are hopefully not too difficult to fix:
globalvariables are used - it would be good to get rid of those and instead use function parameters for passing these variablesSeriesNumbermay be easiest to fetch from the input CT series instead of relying on the manifest or query