On a dataset with 160 images and 42,000 ROIs, the density calculation ballooned out of memory.
The heart of this is using from scipy.spatial.distance.squareform, which reasonably could be expected to be pretty optimised, but it might be that this function hasn't been tested on so many cells.
More investigation is needed.
On a dataset with 160 images and 42,000 ROIs, the density calculation ballooned out of memory.
The heart of this is using from
scipy.spatial.distance.squareform, which reasonably could be expected to be pretty optimised, but it might be that this function hasn't been tested on so many cells.More investigation is needed.