draw circles with defined diameter according to scale bar

[Daniyard]

Dear all,

I am using imagej to analyse EM pictures. Now I would like to count particles within a defined circular region. This would require that in the simpliest case I can overlay circles on the picture by clicking at a certain point of the picture and thereby define the middle of the circle and it then draws a circle with defined radius.

Is there a workaround with the normal imagej functions or does anybody know a plugin that would make the job?

Thanks and best wishes,

daniyard

[carlo bianco]

Hi
in my opinion, I think you can manually select the area of interest,
delete the outer area, then apply the command "analyze particles" choosing your parameters (min area- max area...and so on)
You can try to use the batch command recording the handmade circle
and then choosing process.
In   a while I'll sentd u a macro that could work
bye
 

________________________________
 Da: Daniyard <[hidden email]>
A: [hidden email]
Inviato: Lunedì 10 Giugno 2013 16:20
Oggetto: draw circles with defined diameter according to scale bar
 

Dear all,

I am using imagej to analyse EM pictures. Now I would like to count
particles within a defined circular region. This would require that in the
simpliest case I can overlay circles on the picture by clicking at a certain
point of the picture and thereby define the middle of the circle and it then
draws a circle with defined radius.

Is there a workaround with the normal imagej functions or does anybody know
a plugin that would make the job?

Thanks and best wishes,

daniyard



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[Herbie-3]

Daniyard,

actually the subject of your mail and the text body seem to be somehow
different...

If you should like to draw defined circles as selections you may use a
macro. For example:

getCursorLoc(x, y, z, modifiers);
d = getNumber( "Diameter", 32 );
run("Specify...", "width=[d] height=[d] x=[x] y=[y] oval centered");

Click on the desired circle center in your image, then start the macro.

HTH

Herbie

__________________________________
On 10.06.13 16:20, Daniyard wrote:

> Dear all,
>
> I am using imagej to analyse EM pictures. Now I would like to count
> particles within a defined circular region. This would require that in the
> simpliest case I can overlay circles on the picture by clicking at a certain
> point of the picture and thereby define the middle of the circle and it then
> draws a circle with defined radius.
>
> Is there a workaround with the normal imagej functions or does anybody know
> a plugin that would make the job?
>
> Thanks and best wishes,
>
> daniyard
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/draw-circles-with-defined-diameter-according-to-scale-bar-tp5003317.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[carlo bianco]

hi try this  macro
maybe can help u
(is an oval)




makeOval(774, 528, 1428, 1344);


run("Line Width...", "line=10");
run("Draw");
run("Clear Outside");

run("Analyze Particles...", "size=0-Infinity circularity=0.00-1.00 show=Nothing display clear include summarize record add in_situ");

close();



________________________________
 Da: Daniyard <[hidden email]>
A: [hidden email]
Inviato: Lunedì 10 Giugno 2013 16:20
Oggetto: draw circles with defined diameter according to scale bar
 

Dear all,

I am using imagej to analyse EM pictures. Now I would like to count
particles within a defined circular region. This would require that in the
simpliest case I can overlay circles on the picture by clicking at a certain
point of the picture and thereby define the middle of the circle and it then
draws a circle with defined radius.

Is there a workaround with the normal imagej functions or does anybody know
a plugin that would make the job?

Thanks and best wishes,

daniyard



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[Daniyard]

Thank you very much for the replies...I will test the macros and see if they will help solve the problem.

Best,

Daniyard

[Krs5]

Dear Daniyard,

The macro below will draw your circular ROIs on left-mouse click.

// This macro draws a circle on left-mouse click defining the
// centre of the circle. User can set the radius of the circle.
// Right-mouse click stops the macro.

macro CircleOn_MouseClick{
        setOption("DisablePopupMenu", true);
        getPixelSize(unit, pixelWidth, pixelHeight);
        setTool("rectangle");
        leftButton=16;
        rightButton=4;
        radius = 100;
        Dialog.create("Settings");
                Dialog.addNumber("Set radius of circle", radius);
        Dialog.show();
        radius = Dialog.getNumber();
        height = 2*pixelHeight*radius;
        width = 2*pixelWidth*radius;
        x2=-1; y2=-1; z2=-1; flags2=-1;
        getCursorLoc(x, y, z, flags);
        while (flags&rightButton==0){
                getCursorLoc(x, y, z, flags);
                if (flags&leftButton!=0) {
                        if (x!=x2 || y!=y2 || z!=z2 || flags!=flags2) {
                                x = x - width/2;
                                y = y - height/2;
                                makeOval(x, y, width, height);
                                x2=x; y2=y; z2=z; flags2=flags;

                                // Here you can add code to do something
                        }

                }
        }
}

Best wishes

Kees


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


ImageJ workshops: 29 and 30 July 2013 http://www.le.ac.uk/biochem/microscopy/ImageJ2013.html 

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Daniyard
Sent: 10 June 2013 15:20
To: [hidden email]
Subject: draw circles with defined diameter according to scale bar

Dear all,

I am using imagej to analyse EM pictures. Now I would like to count particles within a defined circular region. This would require that in the simpliest case I can overlay circles on the picture by clicking at a certain point of the picture and thereby define the middle of the circle and it then draws a circle with defined radius.

Is there a workaround with the normal imagej functions or does anybody know a plugin that would make the job?

Thanks and best wishes,

daniyard



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