Sparse-SIM-python

I modified the SIM project from @Tlambert03 to get a simple Python version of sparse hessian denoise

Sparse-SIM has two steps, the first is sparse denoising and the second is RL deconvolution

Tlambert03's SIM project

https://github.com/tlambert03/pycudasirecon

Sparse-SIM official project address:

https://github.com/WeisongZhao/Sparse-SIM

Usage

from sparse_deconv import sparse_hessian_denoise
from tifffile import imread

img = imread('raw.tif')
g = sparse_hessian_denoise(img,mu=100,sparsity=5,iters=70,sigma=0.8)

RL deconvolution can be done by gputools.deconv

Requirements

numpy or cupy(CUDA needs to be installed)

tifffile

matplotlib

Tips

The code under 'Matlab style implementation' folder is my own implementation according to the Sparse-SIM author's Matlab version