Hi Jeremy, Thank you for your answer, it makes a lot of sense to mask the intensity image with the label region before measuring the mean intensity, which is exactly what is in the source code:
> np.mean(self.intensity_image[self.image]) I guess I should have check before sending an email but the thank you for your help! Best, Cedric 2017-07-14 6:49 GMT-07:00 Jeremy Chacon <chaco...@umn.edu>: > Hi Cedric, > > I'm just a user but my interpretation is that mean_intensity is the mean > intensity of the pixels in that labeled region, whereas intensity_image is > the region within its bounding box. So intensity_image can contain zeros > where the label isn't present. > > See this: > > from skimage import measure > import numpy as np > a = np.array([[2,3,4,5],[6,5,4,3]]) > b = np.array([[0,1,1,0],[0,1,0,0]]) > > rp = measure.regionprops(b, a) > > rp[0].mean_intensity # 4 > rp[0].intensity_image # contains a zero, making the mean of this < 4 > > > > On Fri, Jul 14, 2017 at 12:23 AM, Cedric Espenel <cedric.espe...@gmail.com > > wrote: > >> Hi scikit-image users/devs, >> >> I'm using skimage.measure.regionprops and I'm little bit confused about a >> result I get with it. >> >> I'm working with a zstack of a microscopy image that I have >> segmented/label and I'm trying to get the mean intensity of the labeled >> region: >> >> region_props = measure.regionprops(label_image, intensity_image) >>> >> >> If now I do: >> >> for prop in region_prop: >> >> print('x', prop.mean_intensity) >>>> >>> print('y', np.mean(prop.intensity_image)) >>>> >>> >> prop.mean_intensity and np.mean(prop.intensity_image) give me different >> value, which confuse me. Can someone help me understand why I'm getting >> something different? >> >> Thank you in advance for your help. >> >> Sincerely, >> >> Cedric >> >> >> _______________________________________________ >> scikit-image mailing list >> scikit-image@python.org >> https://mail.python.org/mailman/listinfo/scikit-image >> >> > > > -- > > *___________________________________________________________________________Jeremy > M. Chacon, Ph.D.* > > *Post-Doctoral Associate, Harcombe Lab* > *University of Minnesota* > *Ecology, Evolution and Behavior* > > > _______________________________________________ > scikit-image mailing list > scikit-image@python.org > https://mail.python.org/mailman/listinfo/scikit-image > >
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