Closed mgeplf closed 6 months ago
I have a counter proposal for this pull request. The issue happened because the outside of the Nissl used is set to 0. Why not solving the issue in the function normalize_intensity in utils.py? I can provide a simple implementation.
@drodarie why would you like to still apply thenormalize_intensity
function when all the processings applied in it are already applied to the input volume?
Then the function will not do anything and that's fine. This way, we don't have an extra user option which would make the pipeline even more difficult to use.
See my proposal here
If that's what you want, that works for me. I very much prefer fewer options that modify the behavior (ie: I agree with what you on we don't have an extra user option...
)
Ok let's try
I ran the code using @drodarie's branch and this gave the same cell density file than on the main branch. So this is okay for me.
Done better in #74
@lecriste and @Sebastien-PILUSO can you try this, and see if it solves the problem you were running into?