Creation of a 3D ROIs

[Galathorn]

Hi all,

I would like to create a rectangular 3D ROI grid to measure the spatial homogeneity of particles in a 3D volume. I tried the following macro but it only works in 2D. When I make a 3D object and if I modify the macro adding a third component it doesn't work... I'm not very good for coding macros, I found the model of the code for 2D ROI grid in this forum. Any idea? Thanks.

x = 130;
y = 80;
width =160;
height = 160;
spacing = 0;
numRow = 4;
numCol = 4;

for(i = 0; i < numRow; i++)
{
for(j = 0; j < numCol; j++)
{
xOffset = j * (width + spacing);
print(xOffset);
yOffset = i * (height + spacing);
print(yOffset);
makeRectangle(x + xOffset, y + yOffset, width, height);
roiManager("Add");
if (roiManager("count") > 500)
{
print("Maximum reached: 500 entries have been created.");
exit;
}
}
}

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

On Mar 12, 2014, at 6:41 AM, Galathorn wrote:

> Hi all,
>
> I would like to create a rectangular 3D ROI grid to measure the spatial
> homogeneity of particles in a 3D volume. I tried the following macro but it
> only works in 2D. When I make a 3D object and if I modify the macro adding a
> third component it doesn't work... I'm not very good for coding macros, I
> found the model of the code for 2D ROI grid in this forum. Any idea? Thanks.

Here is an example macro that opens the "T1 Head" sample stack, creates a 3D ROI (as an overlay) and measures each ROI in the 3D ROI. It uses an overlay because that is faster and more reliable than using the ROI Manager.

-wayne

  run("T1 Head (2.4M, 16-bits)");
  width = getWidth;
  height = getHeight;
  depth = nSlices;
  x0 = width/4;
  y0 = height/4;
  z0 = depth/4;
  w = width/2;
  h = height/2;
  d = depth/2;
  for (z=0; z<depth; z++) {
     if (z>=z0 && z<=z0+d) {
        makeRectangle(x0,y0,w,h);
        Overlay.addSelection;
        Overlay.setPosition(z+1);
     }
  }

  run("Clear Results");
  setOption("Stack Position");
  for (i=0; i<Overlay.size; i++) {
     Overlay.activateSelection(i);
     run("Measure");
  }
  run("Select None");

> x = 130;
> y = 80;
> width =160;
> height = 160;
> spacing = 0;
> numRow = 4;
> numCol = 4;
>
> for(i = 0; i < numRow; i++)
> {
> for(j = 0; j < numCol; j++)
> {
> xOffset = j * (width + spacing);
> print(xOffset);
> yOffset = i * (height + spacing);
> print(yOffset);
> makeRectangle(x + xOffset, y + yOffset, width, height);
> roiManager("Add");
> if (roiManager("count") > 500)
> {
> print("Maximum reached: 500 entries have been created.");
> exit;
> }
> }
> }
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Creation-of-a-3D-ROIs-tp5006882.html
> Sent from the ImageJ mailing list archive at Nabble.com.

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Galathorn]

Thanks a lot for your rapid answer. When I run your macro an error message appears: "No overlay in line 14. Overlay.<add Selection>"
As I never use Overlays before, I don't know what it means and what I have to change in the macro.

Moreover, how can I insert my macro in your macro to get a grid with multiple rectangles and not only one in the middle of the image?
I tried this but it seems that it doesn't work...

run("T1 Head (2.4M, 16-bits)");
  width = getWidth;
  height = getHeight;
  depth = nSlices;
  x = 50;
  y = 50;
  z0 = depth/4;
  d = depth/2;
numRow= 4;
numCol=4;

for(i = 0; i< numRow; i++)
{
for(j=0;j<numCol;j++)
{
xOffset = j * (width);
yOffset = i * (height);

  for (z=0; z<depth; z++) {
     if (z>=z0 && z<=z0+d) {
        makeRectangle(x+ xOffset,y+yOffset,width,height);
        Overlay.addSelection;
        Overlay.setPosition(z+1);
     }
  }
}
}

  run("Clear Results");
  setOption("Stack Position");
  for (i=0; i<Overlay.size; i++) {
     Overlay.activateSelection(i);
     run("Measure");
  }
  run("Select None");


Thanks.



Thibaut