Closed Helveg closed 4 years ago
@alberto-antonietti we had decided to put back the clustering method? I can't find notes on this, so I don't remember if I should have put it back or not (very poor memory......)
If I remember correctly, we decided to leave out the clustering because it was causing problems with the labelling (positive and negative microzones). We wanted to be sure that positive PCs were connected to positive IOs. In addition, we decided to cut out the clustering of PCs since it did not have a specific biological counterpart.
So, conclusion, the current algorithm that selects 1 random IO per PC is fine?
Yes, 1 random PC within the same microzone, to have the right divergence value
There was a note in the docstring of the
ConnectomeIOPurkinje
class:But the algorithm doesn't do any sort of clustering at all: it just did
len(purkinje_cells)
shuffles ofio_cells
and picked the first shuffled IO cell and matched it with thei
th purkinje cell. (An expensive way of picking a random IO cell to connect to each Purkinje cell)So I went looking and found this other implementation for this strategy:
This code does include these clusters. It seems to be mostly your commits @AliceGem, do you remember the story here? Is there a reason that the clusters were removed or is this by accident?