Re: Equivalent of watershed for cutting connected components of an image of particles?
Hey guys, Im following up on Adam's behalf, but this is an example of an image we are working with in trying to separate cells that are touching each other. Also you can see the top middle particle has a crescent shape, but is actually a healthy red blood cell that has been segmented incorrectly because of glare. Is that a way to connect the two tips of the shape so that I could then run "binary_fill_holes()" to correctly segment the cell. Thanks! On Wednesday, February 18, 2015 at 7:04:10 PM UTC-5, Adam Hughes wrote:
Hi,
In ImageJ, one can select watershedding to break up connected regions of particles. Are there any examples of using watershed in this capacity in scikit image? All of the examples I see seem to use watershedding to do segmentation, not to break connected particles in an already-segmented black and white image.
Also, is there a straightforward way to remove particles on a the edge of an image? Sorry, googling is failing me, but I know this is possible.
Thanks
You could do a morphology.closing. That's kind of why it's called that. =D Obviously you don't want to run it on the whole image, but I presume you're doing classification on the regionprops objects, so you could do the closing on each object individually. On Wed, Mar 11, 2015 at 5:12 AM, Claiborne Morton <claiborne.morton@gmail.com> wrote:
Hey guys, Im following up on Adam's behalf, but this is an example of an image we are working with in trying to separate cells that are touching each other. Also you can see the top middle particle has a crescent shape, but is actually a healthy red blood cell that has been segmented incorrectly because of glare. Is that a way to connect the two tips of the shape so that I could then run "binary_fill_holes()" to correctly segment the cell. Thanks! On Wednesday, February 18, 2015 at 7:04:10 PM UTC-5, Adam Hughes wrote:
Hi,
In ImageJ, one can select watershedding to break up connected regions of particles. Are there any examples of using watershed in this capacity in scikit image? All of the examples I see seem to use watershedding to do segmentation, not to break connected particles in an already-segmented black and white image.
Also, is there a straightforward way to remove particles on a the edge of an image? Sorry, googling is failing me, but I know this is possible.
Thanks
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Hey thanks for the help, here are a few other issues we are running into. When a sickle cell is in contact with a regular cell, we cannot find a way to separate the two. Also bottom-middle circle is of a healthy blood cell that is on its side. The watershed function tends to break these cells into two or more partitions when the should not be separated. Any idea on how to fix these problems? On Tue, Mar 10, 2015 at 2:12 PM, Claiborne Morton < claiborne.morton@gmail.com> wrote:
Hey guys, Im following up on Adam's behalf, but this is an example of an image we are working with in trying to separate cells that are touching each other. Also you can see the top middle particle has a crescent shape, but is actually a healthy red blood cell that has been segmented incorrectly because of glare. Is that a way to connect the two tips of the shape so that I could then run "binary_fill_holes()" to correctly segment the cell. Thanks!
On Wednesday, February 18, 2015 at 7:04:10 PM UTC-5, Adam Hughes wrote:
Hi,
In ImageJ, one can select watershedding to break up connected regions of particles. Are there any examples of using watershed in this capacity in scikit image? All of the examples I see seem to use watershedding to do segmentation, not to break connected particles in an already-segmented black and white image.
Also, is there a straightforward way to remove particles on a the edge of an image? Sorry, googling is failing me, but I know this is possible.
Thanks
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participants (2)
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Claiborne Morton -
Juan Nunez-Iglesias