Re: Manually seeded nuclei segmentation/ Marker controlled watershed plugin

Posted by Ignacio Arganda-Carreras-2 on
URL: http://imagej.273.s1.nabble.com/Manually-seeded-nuclei-segmentation-Marker-controlled-watershed-plugin-tp5014479p5014481.html

Hello Anders,

Regarding the marker-controlled watershed plugin, you need to introduce the
following images:

- Input image: usually the gradient version of the image you want to
segment (because the watershed floods from the low intensity values).
- Marker image: this is the seeds image. It needs to be of the same size as
the input image and containing the labeled seeds to start the flooding
from. For example, if you have a 512x512 grayscale input image, you can use
a 512x512 16-bit image with dots on each seed, where each dot needs to have
a different integer intensity value.

I'm attaching an example of the images so you can see what I mean (input
image = nuclei-Gradient.png, marker image = seeds-lbl.png, result =
nuclei-Gradient-watershed.png). Let me know if you need further help.

Best regards,

ignacio



On Sun, Sep 27, 2015 at 9:53 PM, Anders Lunde <[hidden email]>
wrote:

> Hi all,
>
>
> Here is what I am looking for:
>
>
> I want to manually or semi-automatically mark the aproximate center of
> cell nuclei in 2D grey-scale images, then I want to find a plugin that
> could generate a segmentation of these nuclei, for example as ROIs in the
> ROI manager. Attached is an example image of nuclei that is similar to what
> I will be using. The end-goal is to measure the intensity of different
> antibody staining colors in individual nuclei (extra channels not in
> attached image).
>
>
> It seems so hard to find a working plugin that takes MANUAL seed input!
>
>
> Some options I've tried:
>
>
> http://fiji.sc/Marker-controlled_Watershed
>
> This plugin also claims to be fit for my problem, but I don't understand
> how it works. How should the marker input image be? Should it contain ROIs,
> 255-value pixels on a 0-value background, some RGB input markers or
> something else? It's really frustrating. Whatever I'm trying its just
> outputting a totally black image as the result.
>
>
>
> http://imagej.nih.gov/ij/plugins/inserm514/Documentation/Watersheds_514_V2/Watersheds_514_V2.html
>
> This plugin by Cutrona J. and Bonnet Noel seems to do excately what I
> want, but for some reason it doesnt work on my computer/ImageJ/FIJI. Is it
> due to not working on newer Javas or something?
>
>
> Best wishes,
>
> Anders
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
Ignacio Arganda-Carreras, Ph.D.
Ikerbasque Research Fellow
Departamento de Ciencias de la Computacion e Inteligencia Artificial
Facultad de Informatica, Universidad del Pais Vasco
Paseo de Manuel Lardizabal, 1
20018 Donostia-San Sebastian
Guipuzcoa, Spain

Phone : [phone]
Website: http://sites.google.com/site/iargandacarreras/
<http://biocomp.cnb.csic.es/~iarganda/index_EN.html>

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