Currently, to create ROIs, cggnn calculates the distance between every pair of cells in a specimen that exhibits a certain phenotype in order to determine where to place ROIs such that they're located where cells are densest. This accounts for the bulk of runtime when running the cggnn pipeline and most of the calculation results are barely used, making it an excellent candidate for a speedup refactor.
Currently, to create ROIs, cggnn calculates the distance between every pair of cells in a specimen that exhibits a certain phenotype in order to determine where to place ROIs such that they're located where cells are densest. This accounts for the bulk of runtime when running the cggnn pipeline and most of the calculation results are barely used, making it an excellent candidate for a speedup refactor.