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

classic Classic list List threaded Threaded
6 messages Options
Reply | Threaded
Open this post in threaded view
|

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

Yongqiang Chen
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
Reply | Threaded
Open this post in threaded view
|

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

Ignacio Arganda-Carreras-2
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 : +34 943 01 73 25
Website: http://sites.google.com/site/iargandacarreras/

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Reply | Threaded
Open this post in threaded view
|

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

Yongqiang Chen
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 : +34 943 01 73 25
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
Reply | Threaded
Open this post in threaded view
|

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

Ignacio Arganda-Carreras-2
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 : +34 943 01 73 25
> 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 : +34 943 01 73 25
Website: http://sites.google.com/site/iargandacarreras/

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Reply | Threaded
Open this post in threaded view
|

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

Michael Schmid-3
In reply to this post by Yongqiang Chen
Hi Yongqiang,

The Process>Find Maxima command also has an option for "Segmented
particles", which is a very basic watershed.

So, if the seeds you need for the watershed can be obtained with "Find
Maxima", you can try this function. You will need to adjust the
"prominence" (named "tolerance in older ImageJ versions) to suppress
small maxima.


Michael
________________________________________________________________
On 26.11.19 11:48, Yongqiang Chen 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
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Reply | Threaded
Open this post in threaded view
|

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

Yongqiang Chen
Hi Michael,

Thank you for your help. Really appreciate it.

Regards,
Yongqiang

-----Original Message-----
From: Michael Schmid <[hidden email]>
Sent: Tuesday, November 26, 2019 1:54 PM
To: [hidden email]
Subject: Re: Does IMAGEJ have a watershed segmentation function similar with the marker based watershed segmentation in Avizo

Hi Yongqiang,

The Process>Find Maxima command also has an option for "Segmented particles", which is a very basic watershed.

So, if the seeds you need for the watershed can be obtained with "Find Maxima", you can try this function. You will need to adjust the "prominence" (named "tolerance in older ImageJ versions) to suppress small maxima.


Michael
________________________________________________________________
On 26.11.19 11:48, Yongqiang Chen 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
>

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

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