Weka Segmentation probability maps

[Niko Ehrenfeuchter]

Dear all,

is there a quick way (or code snippet) to transform the probability maps
resulting from a Weka run into the other result format (segmentation map)?

Thanks,
~Niko
--
Niko Ehrenfeuchter | Image Analysis Specialist | Biozentrum, University
of Basel | Klingelbergstr. 50/70 | CH-4056 Basel
Phone: [phone] | [hidden email] |
www.biozentrum.unibas.ch | www.microscopynetwork.unibas.ch

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Ignacio Arganda-Carreras]

Hello Niko,

How many classes do you have? In principle, you should assign to each pixel
the class with higher probability. This is what happens when you click in
the GUI on "Create result".

I just made a short Beanshell script that does exactly that:

https://gist.github.com/iarganda/c7fc0a88b8d2737c9d3d

Let me know if you need help with it.

ignacio

On Tue, Nov 4, 2014 at 4:26 PM, Niko Ehrenfeuchter <
[hidden email]> wrote:

> Dear all,
>
> is there a quick way (or code snippet) to transform the probability maps
> resulting from a Weka run into the other result format (segmentation map)?
>
> Thanks,
> ~Niko
> --
> Niko Ehrenfeuchter | Image Analysis Specialist | Biozentrum, University of
> Basel | Klingelbergstr. 50/70 | CH-4056 Basel
> Phone: [phone] | [hidden email] |
> www.biozentrum.unibas.ch | www.microscopynetwork.unibas.ch
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
Ignacio Arganda-Carreras, Ph.D.
Seung's lab, 46-5065
Department of Brain and Cognitive Sciences
Massachusetts Institute of Technology
43 Vassar St.
Cambridge, MA 02139
USA

Phone: [phone]
Website: http://bioweb.cnb.csic.es/~iarganda/index_EN.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Niko Ehrenfeuchter]

Hi Ignacio,

thanks a lot, this is exactly what I've been looking for!

Cheers
~Niko

On 04.11.2014 18:50, Ignacio Arganda-Carreras wrote:

> Hello Niko,
>
> How many classes do you have? In principle, you should assign to each pixel
> the class with higher probability. This is what happens when you click in
> the GUI on "Create result".
>
> I just made a short Beanshell script that does exactly that:
>
> https://gist.github.com/iarganda/c7fc0a88b8d2737c9d3d
>
> Let me know if you need help with it.
>
> ignacio
>
> On Tue, Nov 4, 2014 at 4:26 PM, Niko Ehrenfeuchter <
> [hidden email]> wrote:
>
>> Dear all,
>>
>> is there a quick way (or code snippet) to transform the probability maps
>> resulting from a Weka run into the other result format (segmentation map)?
>>
>> Thanks,
>> ~Niko
>> --
>> Niko Ehrenfeuchter | Image Analysis Specialist | Biozentrum, University of
>> Basel | Klingelbergstr. 50/70 | CH-4056 Basel
>> Phone: [phone] | [hidden email] |
>> www.biozentrum.unibas.ch | www.microscopynetwork.unibas.ch
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
>
>

--
Niko Ehrenfeuchter | Image Analysis Specialist | Biozentrum, University
of Basel | Klingelbergstr. 50/70 | CH-4056 Basel
Phone: [phone] | [hidden email] |
www.biozentrum.unibas.ch | www.microscopynetwork.unibas.ch

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html