Produce overlay between original image and labelled objects

[Tony Yu]

On Thu, Nov 8, 2012 at 4:30 AM, Frank <pennekampster at googlemail.com> wrote:

> Hi,
>
> I want to use Python and scikit image for detection, counting and
> measuring cells from digital pictures. So far most of the things I want to
> do work fine: I just use a global threshold which separates my cells well
> from the background. After labelling the thresholded objects the
> regionprops function provides many of the features I am interested in
> (area, centroid *etc*).
> To be completely satisfied, I would like to produce an overlay between the
> original image and the identified objects after thresholding for error
> checking. I searched a while to find the proper function to do so and then
> encountered the mark_boundaries function. However, that one is not working,
> because the function is not found after importing the skimage.segmentation
> module (ImportError: cannot import name mark_boundaries). Do you have any
> suggestions, why it is not working? Or maybe you know a better way to
> achieve my goal?
>
> Many thanks,
>
>     Frank


Hi Frank,

Are you using the latest release (0.7) or the development version on
github? It's a bit unfortunate, but the documentation link on the website
goes directly to the dev docs instead of the latest release.

I believe `mark_boundaries` is only in the development version of
scikit-image, but really that was just a slight modification of
`visualize_boundaries`, which should be available in 0.7. Note:
`visualize_boundaries` doesn't work with grayscale images, so you may need
to call `skimage.color.gray2rgb`.

Hope that helps.

-Tony
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