Advice on improving a analysis on images of nanoparticles

[Adam Hughes]

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 at 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 <bricklemacho at gmail.com>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" <jni.soma at gmail.com> 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.
>>
>> Stéfan
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