Is there really no answer to this question?

[Philip Ershler]

I sent out the question below last week. Is there really no answer to this problem?

Thanks Again, Phil

This is probably a dumb question but when using the Spot Enhancing 2D... plugin in a macro, how do automatically select the "Enhance" button in the dialog box? Or suppress the dialog box altogether? As in this short macro

run("SpotEnhancingFilter2D...","Diameter=4.0");
selectWindow("S.E.F. (4.0) of Untitled");
run("Find Maxima...", "noise=95 output=[Point Selection]");
run("Measure");

Thanks, Phil

[David Webster]

Where is SpotEnhancingFilter2D...? I can't find it in ImageJ

On Mon, Aug 15, 2011 at 12:00 PM, Philip Ershler <[hidden email]>wrote:

> I sent out the question below last week. Is there really no answer to this
> problem?
>
> Thanks Again, Phil
>
> This is probably a dumb question but when using the Spot Enhancing 2D...
> plugin in a macro, how do automatically select the "Enhance" button in the
> dialog box? Or suppress the dialog box altogether? As in this short macro
>
> run("SpotEnhancingFilter2D...","Diameter=4.0");
> selectWindow("S.E.F. (4.0) of Untitled");
> run("Find Maxima...", "noise=95 output=[Point Selection]");
> run("Measure");
>
> Thanks, Phil

[Michael Schmid]

Hi Phil,

according to Google, it seems that this filter is not available on  
any free website? If its website has disappeared and the license of  
the plugin allows it, it would be good to publish it somewhere again!

Anyhow, you can try Plugins>Macros>Record. If the command gets  
recorded, the plugin probably uses the standard ImageJ dialog  
("GenericDialog" class) and you will see how options are recorded.  
Then, if there is a checkbox named "enhance", recording will show you  
that you have to add "enhance" to your argument string, separated by  
a space, e.g.,

   run("SpotEnhancingFilter2D...","Diameter=4.0 enhance");

If 'enhance' is not a checkbox but a button, your chances to run it  
in a macro are worse. Either analyze the plugin's source code or  
maybe Gabriel Landini's IJ_robot plugin can help.
   http://www.dentistry.bham.ac.uk/landinig/software/software.html

Michael
________________________________________________________________

On 15 Aug 2011, at 21:00, Philip Ershler wrote:

> This is probably a dumb question but when using the Spot Enhancing  
> 2D... plugin in a macro, how do automatically select the "Enhance"  
> button in the dialog box? Or suppress the dialog box altogether? As  
> in this short macro
>
> run("SpotEnhancingFilter2D...","Diameter=4.0");
> selectWindow("S.E.F. (4.0) of Untitled");
> run("Find Maxima...", "noise=95 output=[Point Selection]");
> run("Measure");
>
> Thanks, Phil

[jchanson]

>Does anyone know of an ImageJ plug-in that can carry out positive pixel
count...
Michael -
        To the best of my knowledge, nobody's created a plugin or macro
that mimic's Aperio's Positive Pixel algorithm.  But, you can mimic all of
operations by converting your color image to a Hue/Saturation/Brightness
stack (Image -> Type -> HSB Stack).
        Also, if you are going to be assessing stain intensity in
brightfield images, you ought to check out Landini's Colour
Deconvolution** plugin (
http://www.dentistry.bham.ac.uk/landinig/software/cdeconv/cdeconv.html) --
.

good luck,
Jeff Hanson
Senior Imaging Analyst

** - Also, please read Ruifrok & Johnston's paper on the colour
deconvolution, to understand what it's doing.

[Philip Ershler]

On Aug 16, 2011, at 9:47 AM, Michael Schmid wrote:

> Hi Phil,
>
> according to Google, it seems that this filter is not available on any free website? If its website has disappeared and the license of the plugin allows it, it would be good to publish it somewhere again!
>
> Anyhow, you can try Plugins>Macros>Record. If the command gets recorded, the plugin probably uses the standard ImageJ dialog ("GenericDialog" class) and you will see how options are recorded. Then, if there is a checkbox named "enhance", recording will show you that you have to add "enhance" to your argument string, separated by a space, e.g.,
>
>  run("SpotEnhancingFilter2D...","Diameter=4.0 enhance");
>
> If 'enhance' is not a checkbox but a button, your chances to run it in a macro are worse. Either analyze the plugin's source code or maybe Gabriel Landini's IJ_robot plugin can help.
>  http://www.dentistry.bham.ac.uk/landinig/software/software.html
>
> Michael

Hi Michael,
        This  plugin comes with the distribution of ImageJ that comes with Micro-Manager. I'll try to attach a small screen shot. It may or may not make it through.

[Christine Labno]

I think this plugin is part of the SpotTracker2D distribution from the Biomedical Imaging Group:

http://bigwww.epfl.ch/sage/soft/spottracker/

Their website is pretty up to date, so I would try contacting the group directly.  Maybe they could tell you how to pass an argument to their plugin, or give you source code to modify for your needs:  http://bigwww.epfl.ch/sage/index.html

>On Aug 16, 2011, at 9:47 AM, Michael Schmid wrote:
>
>> Hi Phil,
>>
>> according to Google, it seems that this filter is not available on any free website? If its website has disappeared and the license of the plugin allows it, it would be good to publish it somewhere again!
>>
>> Anyhow, you can try Plugins>Macros>Record. If the command gets recorded, the plugin probably uses the standard ImageJ dialog ("GenericDialog" class) and you will see how options are recorded. Then, if there is a checkbox named "enhance", recording will show you that you have to add "enhance" to your argument string, separated by a space, e.g.,
>>
>>  run("SpotEnhancingFilter2D...","Diameter=4.0 enhance");
>>
>> If 'enhance' is not a checkbox but a button, your chances to run it in a macro are worse. Either analyze the plugin's source code or maybe Gabriel Landini's IJ_robot plugin can help.
>>  http://www.dentistry.bham.ac.uk/landinig/software/software.html
>>
>> Michael
>
>Hi Michael,
> This  plugin comes with the distribution of ImageJ that comes with Micro-Manager. I'll try to attach a small screen shot. It may or may not make it through.
>
>________________
>Screen shot 2011-08-16 at 11.00.08 AM.jpeg (83k bytes)
>________________
>
>
> However,  enhance is a button. I'll try your suggestion.
>
>Thanks so much,
>
>Phil
>
>
>> ________________________________________________________________
>>
>> On 15 Aug 2011, at 21:00, Philip Ershler wrote:
>>
>>> This is probably a dumb question but when using the Spot Enhancing 2D... plugin in a macro, how do automatically select the "Enhance" button in the dialog box? Or suppress the dialog box altogether? As in this short macro
>>>
>>> run("SpotEnhancingFilter2D...","Diameter=4.0");
>>> selectWindow("S.E.F. (4.0) of Untitled");
>>> run("Find Maxima...", "noise=95 output=[Point Selection]");
>>> run("Measure");
>>>
>>> Thanks, Phil
>