Thanks Juan, I will followup and get a NB or two returned to the list. On Thu, Nov 21, 2013 at 8:29 AM, Guillaume Gay < guillaume@mitotic-machine.org> wrote:

Hi,

This: http://damcb.com/posts/segmenting-nuclei-with-skimage.html

links to a notebook where I expose what I'm doing for the segmentation. It won't be too much work to turn it into an example if needed. Also feel free to comment on the post... As you'll see I kind of go around the 3D part by clustering strategies, more that by doing real 3D stuff...

Cheers.

Guillaume

PS: I'll try to have syntax highlighting in nikola soon, so that this code is more readable.

On 20/11/2013 13:55, Juan Nunez-Iglesias wrote:

@Guillaume, please contribute the example ASAP because I'm struggling with the exact same problem! =D In particular, the nuclei example from pythonvision is not ideal because they gloss over a lot of parameter tuning that is much easier to deal with in 2D than 3D. I'll be happy to hear about your experience!

Juan.

On Wed, Nov 20, 2013 at 9:50 PM, Brickle Macho wrote:

...

I can always adapt this example (http://pythonvision.org/basic-tutorial) which uses pymorph and mahotaos to counting nuceli and segments the image as a gallery example for skimage (obviously acknowledging the original tutorial). Or is it bad form to copy/use another example.

Michael. --

On 20/11/2013 2:13 pm, Stéfan van der Walt wrote:

On 20 Nov 2013 07:33, "Juan Nunez-Iglesias" wrote:

...

I'm guessing you are applying label() directly to your image, which is

not the right way to use it.

Looks like isolating objects is a common problem. Time for another gallery example? We already have the coins, but perhaps something more realistic with some biological data.

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