Re: Does IMAGEJ have a watershed segmentation function similar with the marker based watershed segmentation in Avizo

Posted by Ignacio Arganda-Carreras-2 on Nov 26, 2019; 12:57pm
URL: http://imagej.273.s1.nabble.com/Does-IMAGEJ-have-a-watershed-segmentation-function-similar-with-the-marker-based-watershed-segmentato-tp5022707p5022714.html

Hello again, Yongqiang,

In the Morphological Segmentation plugin the markers are automatically
found using extended minima (you can select how extended using a tolerance
value). In the rest of marker-based plugins, you need to introduce yourself
the markers either as ROIs or as a separate marker image.

Cheers!

On Tue, Nov 26, 2019 at 1:16 PM Yongqiang Chen <
[hidden email]> wrote:

> Hi Ignacio,
>
> Thank you for your information.
> It may be that I am unfamiliar with the library. I want to select seeds
> based on CT intensity and then do the watershed based on these seeds. I
> don't know how to put the marker on the image in MorphoLibJ. I tried to use
> the select points in ImageJ to put the marker on images. But the results
> are not perfect. I want to know if there is a way to select seeds globally
> rather than manually put the markers on the images.
> Do you know if any detailed tutorials are available for MorphoLibJ?
>
> Regards,
> Yongqiang
>
>
>
> -----Original Message-----
> From: Ignacio Arganda-Carreras <[hidden email]>
> Sent: Tuesday, November 26, 2019 11:15 AM
> To: [hidden email]
> Subject: Re: Does IMAGEJ have a watershed segmentation function similar
> with the marker based watershed segmentation in Avizo
>
> Dear Yongqiang,
>
> MorphoLibJ's marker-controlled watershed methods is as good as your makers.
> What is the difference you notice with respect to Avizo's method?
>
> Have you tried the Interactive Marker-controlled Watershed plugin <
> https://imagej.net/Interactive_Marker-controlled_Watershed> or the
> Morphological Segmentation plugin <
> https://imagej.net/Morphological_Segmentation> as well?
>
> Best,
>
> On Tue, Nov 26, 2019 at 11:49 AM Yongqiang Chen <
> [hidden email]> wrote:
>
> > Hi ImageJ experts,
> >
> > I want to know that if ImageJ has a watershed segmentation function
> > similar with the marker-based watershed segmentation in Avizo?
> >
> > I tried the watershed segmentation in the MorphoLibJ, but the results
> > are not as good as the watershed in Avizo.
> >
> > Please give me some guidance.
> >
> > Regards,
> > Yongqiang
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
>
> --
> Ignacio Arganda-Carreras, Ph.D.
> Ikerbasque Research Fellow
> Departamento de Ciencia 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/
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
Ignacio Arganda-Carreras, Ph.D.
Ikerbasque Research Fellow
Departamento de Ciencia 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/

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