Pixel-boundary contours for segmentation visualisation

[Juan Nunez-Iglesias]

Hi Robin!




Well, the easy workaround is to zoom your image a lot using ndi.zoom or skimage.transform.rescale, and then use mpl's contour. =)




The potentially slower way is to use scikit-image.segmentation.mark_boundary with mode=subpixel. =)




Juan.

On Mon, Oct 26, 2015 at 7:25 PM, Robin Wilson
<r.t.wilson.bak at googlemail.com> wrote:

> Hi,
> I'm struggling with a problem that I'm sure has been solved before - and 
> probably by some users of this mailing list! I have a segmentation image 
> and I want to extract the edges of the segments and show them on the 
> original image. This sounds nice and easy, so I had a go using the 
> matplotlib contour function and got the following:
> <https://lh3.googleusercontent.com/-S2zawy2Wsq0/Vi3i9tFMwbI/AAAAAAADLj0/2Gt222-V4EE/s1600/ExampleContour.png>
> From my perspective, there are two issues with this: one is that the two 
> segments (which are separate by pixels with the value zero) are actually 
> joined, and the other is that the segment outlines don't follow the pixel 
> boundaries: they are offset by around half a pixel, and 'cut the corners'. 
> What I'd really like to produce is the following:
> <https://lh3.googleusercontent.com/-UUwZAEhue8I/Vi3jQewKW-I/AAAAAAADLj8/gh66GU9-2yY/s1600/ExampleOutline.png>
> (if you look carefully you can see the blue outline around the edge of the 
> segment)
> Does anyone know how to do this easily (and, ideally, reasonably quickly) 
> in Python? From my investigations it seems that the contour function won't 
> do what I want - but I can't find anything else that will do this, and I'd 
> rather not implement something from scratch.
> Any thoughts?
> Robin
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