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Bring up threshold menu

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Himanish Ghosh

Bring up threshold menu

Hello All,

From my macro I would like to call the threshold image menu and show it and
wait for the user to adjust parameters in the threshold dialog and then
resume the macro.

How can this be done

thank you

Jerome Mutterer-3

Re: Bring up threshold menu

Himanish, you could use:

run("Threshold...");
waitForUser("Adjsut Threshold and click OK to continue");

Sincerely,
Jerome

On Thu, Mar 17, 2011 at 2:29 PM, Himanish Ghosh <[hidden email]>wrote:

> Hello All,
>
> From my macro I would like to call the threshold image menu and show it
> and
> wait for the user to adjust parameters in the threshold dialog and then
> resume the macro.
>
> How can this be done
>
> thank you
>

Himanish Ghosh

Re: Bring up threshold menu

Hello

Jerome,

Thank you very much, it worked just right.

I tried all sorts of combinations before i sent the email.

cheers

On Thu, Mar 17, 2011 at 3:09 PM, Jerome Mutterer <
[hidden email]> wrote:

> Himanish, you could use:
>
> run("Threshold...");
> waitForUser("Adjsut Threshold and click OK to continue");
>
> Sincerely,
> Jerome
>
> On Thu, Mar 17, 2011 at 2:29 PM, Himanish Ghosh <[hidden email]
> >wrote:
>
> > Hello All,
> >
> > From my macro I would like to call the threshold image menu and show it
> > and
> > wait for the user to adjust parameters in the threshold dialog and then
> > resume the macro.
> >
> > How can this be done
> >
> > thank you
> >
>

--
Himanish Ghosh

http://www.jaxtr.com/himanishghosh
the journey has begun

chenyanpei

Re: Bring up threshold menu

How I can get a "threshold" image automaticly. I running
run("8-bit");
run("Threshold...");
setThreshold(255, 255);
run("Convert to Mask");
saveAs("Jpeg", dir2+list[i]);
close();
but I still get the image
Title: 00002.jpg
Width: 738 pixels
Height: 495 pixels
Pixel size: 1x1 pixel
ID: -2
Coordinate origin: 0,0
Bits per pixel: 8 (grayscale LUT)
Display range: 0-255
No Threshold
Uncalibrated
Path: K:\R1\00002.jpg
No Selection

Thank you very much!

2011/3/17 Himanish Ghosh <[hidden email]>

> Hello
>
> Jerome,
>
>
> Thank you very much, it worked just right.
>
> I tried all sorts of combinations before i sent the email.
>
> cheers
>
>
>
> On Thu, Mar 17, 2011 at 3:09 PM, Jerome Mutterer <
> [hidden email]> wrote:
>
> > Himanish, you could use:
> >
> > run("Threshold...");
> > waitForUser("Adjsut Threshold and click OK to continue");
> >
> > Sincerely,
> > Jerome
> >
> > On Thu, Mar 17, 2011 at 2:29 PM, Himanish Ghosh <[hidden email]
> > >wrote:
> >
> > > Hello All,
> > >
> > > From my macro I would like to call the threshold image menu and show
> it
> > > and
> > > wait for the user to adjust parameters in the threshold dialog and then
> > > resume the macro.
> > >
> > > How can this be done
> > >
> > > thank you
> > >
> >
>
>
>
> --
> Himanish Ghosh
>
> http://www.jaxtr.com/himanishghosh
> the journey has begun
>

--
Chen Yanpei, phD
MssMat
Ecole Centrale Paris
Grande voie des vignes
92295 Châtenay Malabry
Paris, France

Jerome Mutterer-3

Re: Bring up threshold menu

>
> How I can get a "threshold" image automaticly. I running...

Chen,
run("Threshold..."); is optionnal, it will just open the threshold tool
window. You don't need that if you want an automated thresholding.

setThreshold(255, 255); this will retain only pixels with value 255 in your
threshold.

If you want an automatically computed threshold, you could try:

setAutoThreshold(method);

'method' should be one of the available methods described at :
http://imagej.nih.gov/ij/docs/guide/userguide-25.html#toc-Subsubsection-25.2.4
and http://pacific.mpi-cbg.de/wiki/index.php/Auto_Threshold

saveAs("Jpeg", dir2+list[i]);
it looks that you only pasted part of the faulty macro. This makes it
difficult to guess why it doesn't behave as expected.

Sincerely,
Jerome.

On Thu, Mar 17, 2011 at 5:04 PM, Yanpei Chen <[hidden email]> wrote:

> How I can get a "threshold" image automaticly. I running
> run("8-bit");
> run("Threshold...");
> setThreshold(255, 255);
> run("Convert to Mask");
> saveAs("Jpeg", dir2+list[i]);
> close();
> but I still get the image
> Title: 00002.jpg
> Width: 738 pixels
> Height: 495 pixels
> Pixel size: 1x1 pixel
> ID: -2
> Coordinate origin: 0,0
> Bits per pixel: 8 (grayscale LUT)
> Display range: 0-255
> No Threshold
> Uncalibrated
> Path: K:\R1\00002.jpg
> No Selection
>
>
>
> Thank you very much!
>
>
> 2011/3/17 Himanish Ghosh <[hidden email]>
>
> > Hello
> >
> > Jerome,
> >
> >
> > Thank you very much, it worked just right.
> >
> > I tried all sorts of combinations before i sent the email.
> >
> > cheers
> >
> >
> >
> > On Thu, Mar 17, 2011 at 3:09 PM, Jerome Mutterer <
> > [hidden email]> wrote:
> >
> > > Himanish, you could use:
> > >
> > > run("Threshold...");
> > > waitForUser("Adjsut Threshold and click OK to continue");
> > >
> > > Sincerely,
> > > Jerome
> > >
> > > On Thu, Mar 17, 2011 at 2:29 PM, Himanish Ghosh <
> [hidden email]
> > > >wrote:
> > >
> > > > Hello All,
> > > >
> > > > From my macro I would like to call the threshold image menu and show
> > it
> > > > and
> > > > wait for the user to adjust parameters in the threshold dialog and
> then
> > > > resume the macro.
> > > >
> > > > How can this be done
> > > >
> > > > thank you
> > > >
> > >
> >
> >
> >
> > --
> > Himanish Ghosh
> >
> > http://www.jaxtr.com/himanishghosh
> > the journey has begun
> >
>
>
>
> --
> Chen Yanpei, phD
> MssMat
> Ecole Centrale Paris
> Grande voie des vignes
> 92295 Châtenay Malabry
> Paris, France
>

chenyanpei

Re: Bring up threshold menu

Thank you very much. I already tried. but after I saved the images,they
change to not the threshold image again. I want to use the Mtraker2, so i
need the threshold image . it need the stack to threshold image.
the rest parts of my macro is here:

makeRectangle(90, 16, 697, 493);//
run("Crop");
//run("Invert");
run("Subtract Background...", "rolling=50 light");
//run("Watershed");
//run("Invert");
setAutoThreshold("Default");
setThreshold(0, 128);
run("Convert to Mask");
run("Set Measurements...", "area mean centroid center");
//run("Analyze Particles...","clear record");
run("Analyze Particles...", "size=0-Infinity circularity=0.00-1.00
show=Nothing display record");
setForegroundColor(0,0,0);
setBackgroundColor(255,255,255);
j=0;
x=0;
y=0;
for(j=0;j<nResults;j++){
x=getResult('X',j);
y=getResult('Y',j);
doWand(x, y);
getStatistics(area);
if(area<200)
//run("Clear","slice");
run("Fill", "slice");
}
run("Clear Results");

run("8-bit");

run("Threshold...");
setThreshold(255, 255);
run("Convert to Mask");
saveAs("Jpeg", dir2+list[i]);
close();

2011/3/17 Jerome Mutterer <[hidden email]>

> >
> > How I can get a "threshold" image automaticly. I running...
>
>
> Chen,
> run("Threshold..."); is optionnal, it will just open the threshold tool
> window. You don't need that if you want an automated thresholding.
>
> setThreshold(255, 255); this will retain only pixels with value 255 in your
> threshold.
>
> If you want an automatically computed threshold, you could try:
>
> setAutoThreshold(method);
>
> 'method' should be one of the available methods described at :
>
> http://imagej.nih.gov/ij/docs/guide/userguide-25.html#toc-Subsubsection-25.2.4
> and http://pacific.mpi-cbg.de/wiki/index.php/Auto_Threshold
>
> saveAs("Jpeg", dir2+list[i]);
> it looks that you only pasted part of the faulty macro. This makes it
> difficult to guess why it doesn't behave as expected.
>
> Sincerely,
> Jerome.
>
>
>
> On Thu, Mar 17, 2011 at 5:04 PM, Yanpei Chen <[hidden email]> wrote:
>
> > How I can get a "threshold" image automaticly. I running
> > run("8-bit");
> > run("Threshold...");
> > setThreshold(255, 255);
> > run("Convert to Mask");
> > saveAs("Jpeg", dir2+list[i]);
> > close();
> > but I still get the image
> > Title: 00002.jpg
> > Width: 738 pixels
> > Height: 495 pixels
> > Pixel size: 1x1 pixel
> > ID: -2
> > Coordinate origin: 0,0
> > Bits per pixel: 8 (grayscale LUT)
> > Display range: 0-255
> > No Threshold
> > Uncalibrated
> > Path: K:\R1\00002.jpg
> > No Selection
> >
> >
> >
> > Thank you very much!
> >
> >
> > 2011/3/17 Himanish Ghosh <[hidden email]>
> >
> > > Hello
> > >
> > > Jerome,
> > >
> > >
> > > Thank you very much, it worked just right.
> > >
> > > I tried all sorts of combinations before i sent the email.
> > >
> > > cheers
> > >
> > >
> > >
> > > On Thu, Mar 17, 2011 at 3:09 PM, Jerome Mutterer <
> > > [hidden email]> wrote:
> > >
> > > > Himanish, you could use:
> > > >
> > > > run("Threshold...");
> > > > waitForUser("Adjsut Threshold and click OK to continue");
> > > >
> > > > Sincerely,
> > > > Jerome
> > > >
> > > > On Thu, Mar 17, 2011 at 2:29 PM, Himanish Ghosh <
> > [hidden email]
> > > > >wrote:
> > > >
> > > > > Hello All,
> > > > >
> > > > > From my macro I would like to call the threshold image menu and
> show
> > > it
> > > > > and
> > > > > wait for the user to adjust parameters in the threshold dialog and
> > then
> > > > > resume the macro.
> > > > >
> > > > > How can this be done
> > > > >
> > > > > thank you
> > > > >
> > > >
> > >
> > >
> > >
> > > --
> > > Himanish Ghosh
> > >
> > > http://www.jaxtr.com/himanishghosh
> > > the journey has begun
> > >
> >
> >
> >
> > --
> > Chen Yanpei, phD
> > MssMat
> > Ecole Centrale Paris
> > Grande voie des vignes
> > 92295 Châtenay Malabry
> > Paris, France
> >
>

--
Chen Yanpei, phD
MssMat
Ecole Centrale Paris
Grande voie des vignes
92295 Châtenay Malabry
Paris, France

chenyanpei

Re: Bring up threshold menu

In reply to this post by Jerome Mutterer-3

I already try these two plugin. it can not work.Mtrack2 still said it is not
thresold.

2011/3/17 Jerome Mutterer <[hidden email]>

--
Chen Yanpei, phD
MssMat
Ecole Centrale Paris
Grande voie des vignes
92295 Châtenay Malabry
Paris, France