DRAWING A CONTOUR A SPECIFIC DISTANCE FROM THE SURFACE

[koronfelina]

Hey all,

Is there a way that I can draw a contour surrounding a surface but with a specific distance between the surface and the contour? In other words I want to detect specific bodies located within 10 um from the surface of a cell. I thought of a way to do that through which I draw a contour that I can crop and do the analysis, with confidence, within the obviously detected 10 um of the cell's surface.

Your help is greatly appreciated :) Thanks in advance.

Lina

[Joel Sheffield]

I have no answer to this, but if someone has a solution, I can imagine that
it might be a useful first step in an analysis of bands on an
electrophoretic gel, as an alternative to the scanning procedure that is
part of ImageJ.  I am thinking of a system that would threshold bands in an
image, and then select a contour that would be a fixed number of pixels
outside the band, and calculate the integrated density under the contour.
That would act as a local background control.

Joel



Joel B. Sheffield, Ph.D
Department of Biology
Temple University
Philadelphia, PA 19122
Voice: 215 204 8839
e-mail: [hidden email]
URL:  *http://tinyurl.com/khbouft <http://tinyurl.com/khbouft>*


On Mon, Aug 25, 2014 at 10:33 AM, koronfelina <[hidden email]> wrote:

> Hey all,
>
> Is there a way that I can draw a contour in surrounding a surface but with
> a
> specific distance between the surface and the contour? In other words I
> want
> to detect specific bodies located within 10 um from the surface of a cell.
> I
> thought of a way to do that through which I draw a contour that I can crop
> and do the analysis, with confidence, within the obviously detected 10 um
> of
> the cell's surface.
>
> Your help is greatly appreciated :) Thanks in advance.
>
> Lina
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/DRAWING-A-CONTOUR-A-SPECIFIC-DISTANCE-FROM-THE-SURFACE-tp5009330.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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[Aryeh Weiss]

On 8/25/14, 7:33 AM, koronfelina wrote:

> Hey all,
>
> Is there a way that I can draw a contour in surrounding a surface but with a
> specific distance between the surface and the contour? In other words I want
> to detect specific bodies located within 10 um from the surface of a cell. I
> thought of a way to do that through which I draw a contour that I can crop
> and do the analysis, with confidence, within the obviously detected 10 um of
> the cell's surface.
>
> Your help is greatly appreciated :) Thanks in advance.
>
> Lina
>

If you have the contour,  you create a binary filled object and dilate
it, in order to enlarge it by the desired distance. Then you can create
an roi that follows the boundary of the contour (for example, with
Edit>Create Selection ).

--aryeh

--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]

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[Gabriel Landini]

> If you have the contour,  you create a binary filled object and dilate
> it, in order to enlarge it by the desired distance. Then you can create
> an roi that follows the boundary of the contour (for example, with
> Edit>Create Selection ).

Another way: draw the ROI, then Selection>Make Band by the number of pixels
corresponding to 10um.
You can use the particle analyzer with that "doughnut" shaped ROI to find what
is inside that region.

Cheers
Gabriel

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[Heeschen, Bill (WA)]

[I didn't see this option in the "digest mode" summary - hopefully not a repeat!]

If you can select the surface (wand tool, ROI manager, etc.), then you can use the Edit=>Selection=>Enlarge... command to expand (or shrink) the traced outline of the surface:

/*
Quick demo macro to illustrate Edit=>Selection=>Enlarge...
By Bill Heeschen
[hidden email]
*/

newImage("Enlarge ROI Demo", "8-bit white", 256, 256, 1);
setForegroundColor(0, 0, 0);//setting up ImageJ so that it works right
setBackgroundColor(255, 255, 255);
makeRectangle(80, 70, 90, 80);
run("Fill", "slice");
run("Select None");
doWand(128,128);//auto-click wand tool in center of rectangle to trace it's outline
run("Enlarge...", "enlarge=15");//the value for "enlarge" is in pixels


You should now have a selection that is 15 pixels wider than the original object
Note that corners are rounded to obey the 15-pixel rule around the traced outline of the rectangle

Hope this helps,
Bill
William A. Heeschen, Ph.D.
Microscopy, Digital Imaging
The Dow Chemical Company
Midland, MI  48667
[hidden email]

> Date:    Mon, 25 Aug 2014 07:33:47 -0700
> From:    koronfelina <[hidden email]>
> Subject: DRAWING A CONTOUR A SPECIFIC DISTANCE FROM THE SURFACE
>
> Hey all,
>
> Is there a way that I can draw a contour in surrounding a surface but with a
> specific distance between the surface and the contour? In other words I want
> to detect specific bodies located within 10 um from the surface of a cell. I
> thought of a way to do that through which I draw a contour that I can crop
> and do the analysis, with confidence, within the obviously detected 10 um of
> the cell's surface.
>
> Your help is greatly appreciated :) Thanks in advance.
>
> Lina

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