Water-shedding non-circular particles
Claiborne Morton
claiborne.morton at gmail.com
Tue Mar 24 16:42:36 EDT 2015
Hey sorry for getting back to you so late. Here is the code I am using as
well as the segmentation (attached). Im a little new to this, so do not
know what you mean by "selecting the markers and elevation function". Do
you see any reason why I am getting these errors?
import skimage.morphology as morphology
from skimage.segmentation import random_walker
from skimage.morphology import watershed
from skimage.feature import peak_local_max
image = binary_filled
# Now we want to separate the two objects in image
# Generate the markers as local maxima of the distance
# to the background
from scipy import ndimage
distance = ndimage.distance_transform_edt(image)
local_maxi = peak_local_max(distance, indices=False,
footprint=np.ones((20, 20)), labels=image)
markers = morphology.label(local_maxi)
labels_ws = watershed(-distance, markers, mask=image)
Thanks again!
Clay
On Thursday, March 19, 2015 at 6:24:10 PM UTC-4, Emmanuelle Gouillart wrote:
>
> Hi Clay,
>
> how do you select the markers and the elevation function used in the
> watershed algorithm? Could you include the code that results in the
> segmentation you attached?
>
> Cheers,
> Emmanuelle
>
> On Thu, Mar 19, 2015 at 06:07:57PM -0400, Claiborne Morton wrote:
> > Hey guys, Im still having trouble finding ways to separate touching
> particles
> > if the are not both circular. Further when dealing with elliptical
> shapes, a
> > single particle tends to incorrectly get cut in half. Any ideas how I
> could
> > change parameters in the water-shedding function to correct for this?
> Attached
> > are a few problem cases so you can see examples.
>
> > Thanks,
> > Clay
> > Inline image 1
>
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