Grayscale watershed

[LMAnovitz]

Does anyone have a good grayscale watershed plugin or macro ?
--Larry

[Michael Schmid]

Hi Larry,

the built-in 'Find Maxima' command can doe grayscale watershed, taking the maxima (or minima) found as seeds. It is not really perfect, e.g. it has a preference for segmentation lines running in horizontal, vertical or 45-degree directions.

I have tried to improve this, but this results in rather awful code. If this is a limitation and you find nothing better, I could try to dig out that code and publish it somewhere.

Michael
______________________________________________________________

On 2011-Aug-29, at 23:28, Anovitz, Lawrence {Larry} M. wrote:

> Does anyone have a good grayscale watershed plugin or macro ?
> --Larry

[Krs5]

Dear list members

In a macro we would like to capture the thresholding method the user has chosen for thresholding. We can get the threshold levels by using getThreshold(lower, upper) and we can get the different thresholding methods via getList("threshold.methods"), but I cannot find a way to record the actual method chosen for thresholding. Any suggestions?

Thanks

Kees


Dr Ir K.R. Straatman
Senior Experimental Officer
Centre for Core Biotechnology Services
College of Medicine, Biological Sciences and Psychology
University of Leicester
http://www.le.ac.uk/biochem/microscopy/home.html

[Ignacio Arganda-Carreras]

http://bigwww.epfl.ch/sage/soft/watershed/index.html

ignacio

On Tue, Aug 30, 2011 at 12:01 PM, Michael Schmid <[hidden email]>wrote:

> Hi Larry,
>
> the built-in 'Find Maxima' command can doe grayscale watershed, taking the
> maxima (or minima) found as seeds. It is not really perfect, e.g. it has a
> preference for segmentation lines running in horizontal, vertical or
> 45-degree directions.
>
> I have tried to improve this, but this results in rather awful code. If
> this is a limitation and you find nothing better, I could try to dig out
> that code and publish it somewhere.
>
> Michael
> ______________________________________________________________
>
> On 2011-Aug-29, at 23:28, Anovitz, Lawrence {Larry} M. wrote:
>
> > Does anyone have a good grayscale watershed plugin or macro ?
> > --Larry
>

--
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

[David Webster]

Did you check the ImageJ/Plugins page? I hgave a greyscale plugin so it must
come from there.

David Webster

On Mon, Aug 29, 2011 at 2:28 PM, Anovitz, Lawrence {Larry} M. <
[hidden email]> wrote:

> Does anyone have a good grayscale watershed plugin or macro ?
> --Larry
>

[Rasband, Wayne (NIH/NIMH) [E]]

On Aug 30, 2011, at 12:45 PM, Straatman, Kees R. (Dr.) wrote:

> Dear list members
>
> In a macro we would like to capture the thresholding method the user has chosen for thresholding. We can get the threshold levels by using getThreshold(lower, upper) and we can get the different thresholding methods via getList("threshold.methods"), but I cannot find a way to record the actual method chosen for thresholding. Any suggestions?

Upgrade to the 1.45n daily build and use

   method = getInfo("threshold.method");

-wayne

[Krs5]

Dear Wayne,

Fantastic. That will do the trick. Thanks for the fast response.

Kees

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Rasband, Wayne (NIH/NIMH) [E]
Sent: 30 August 2011 22:21
To: [hidden email]
Subject: Re: Capture thresholding method

On Aug 30, 2011, at 12:45 PM, Straatman, Kees R. (Dr.) wrote:

> Dear list members
>
> In a macro we would like to capture the thresholding method the user has chosen for thresholding. We can get the threshold levels by using getThreshold(lower, upper) and we can get the different thresholding methods via getList("threshold.methods"), but I cannot find a way to record the actual method chosen for thresholding. Any suggestions?

Upgrade to the 1.45n daily build and use

   method = getInfo("threshold.method");

-wayne

[JosephPreston]

There is LabIris Pro software - the basic version is free and includes most of the features needed.  You can download it from V-Brane Labs web site http://www.v-brane.com