Yes, as you say and as suggested by Brian, I think using the background from the watershed would be the proper way. You could also find the mean intensity of each label and set to background those with a mean intensity below some threshold. The ndimage.labeled_comprehension function should be able to do this: https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.labeled_c... as well as our own regionprops. On 26 Apr 2017, 8:01 AM +1000, Cedric Espenel <espenel@stanford.edu>, wrote:

Hi,

Sorry, I guess I can just mask the result with the watershed segmentation. I guess I wonder if it is the proper way to do it? And also, from your point of view, if it's the way to go to segment these cells or if you think of a better way?

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