Acceleration #14
Description
Hello,
thank you for the software. The cell segmentation look good to us.
We currently are using your software together with sopa, which works well. Still, the duration of a segmentation on one patch, even when having small patches like in your tutorial, is burdensome. Currently, we're facing wall-times per patch of up to 3d and an overall segmentation duration of close to 7d.
Is there a way to increase the speed of the segmentation? I've tried increasing the number of cpus, as I saw that you're using scanpy within your code. Still, that barely accelerated the segmentation. Are there other things worth trying?
Best,
Jonas