filtering

pysmFISH.filtering.nuclei_filtering(img_stack)

This function remove the background from the nuclei For the sigma I seleced a value quite bigger than the nuclei size in order to remove them from the image. I used what showed on the gaussian filter code page and on this link on stackoverflow: http://stackoverflow.com/questions/25216382/gaussian-filter-in-scipy

img_stack: np.array float64

3D numpy array with the image

filtered_image: np.array float64

2D flattened image

pysmFISH.filtering.smFISH_filtering(img_stack)

This function remove the background from the smFISH and enhance the dots.

img_stack: np.array float64

3D numpy array with the image

filtered_image: np.array float64

2D flattened image