On Thu, Nov 8, 2012 at 4:30 AM, Frank <pennekampster@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