Drawing 3D rois

[m_a_x]

Hi everyone,
I would like draw a roi in more than one slice and analyze the grey values. I know that its possible to draw many rois in one slice but is it also possible to draw a roi in many slices and analyze it as one roi?
I hope anybody can help me.

Best regards,
Max

[Thomas Boudier]

Hi,

I may refer you to SegmentationEditor in order to create a 3D mask of
your rois and then use 3DObjectCounter or 3DManager to analyse the 3D mask.

http://132.187.25.13/home/?category=Download&page=SegmentationEditor

http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:3d_roi_manager:start

Thomas




Le 29/10/2012 14:41, m_a_x a écrit :

> Hi everyone,
> I would like draw a roi in more than one slice and analyze the grey values.
> I know that its possible to draw many rois in one slice but is it also
> possible to draw a roi in many slices and analyze it as one roi?
> I hope anybody can help me.
>
> Best regards,
> Max
>
>
>
> --
> View this message in context: http://imagej.1557.n6.nabble.com/Drawing-3D-rois-tp5000564.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

... [show rest of quote]

--
   /**********************************************************/
      Thomas Boudier, MCU Université Pierre et Marie Curie,
      Modélisation Cellulaire et Imagerie Biologique (EE1),
      IFR 83, Bat B 7ème étage, porte 723, Campus Jussieu.
      Tel : [phone]   Fax : [phone]
/*******************************************************/

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[m_a_x]

Thank you for you quick reply! I tried the segmentation editor but it doesnt work fine for me. When I use it, a new window opens with black slices where the 3D roi occurs after drawing it. Unfortunately the 3D manager cant analyze the grey values of those slices as they are all black. I think there is a simple solution for that problem but I dont get it. Can you please help me with that?
Thank you very much!

Max

[Thomas Boudier]

Hi,

here a simple macro that reads the rois (assuming one per slice) and
draws the mask in a new image.

w=getWidth();
h=getHeight();
s=nSlices();
newImage("Mask", "8-bit Black", w, h, s);
setForegroundColor(255, 255, 255);
nb=roiManager("count");
for(i=0;i<nb;i++) {
        roiManager("Select",i);
run("Fill", "slice");
}

Thomas


Le 29/10/2012 17:29, m_a_x a écrit :

> Thank you for you quick reply! I tried the segmentation editor but it doesnt
> work fine for me. When I use it, a new window opens with black slices where
> the 3D roi occurs after drawing it. Unfortunately the 3D manager cant
> analyze the grey values of those slices as they are all black. I think there
> is a simple solution for that problem but I dont get it. Can you please help
> me with that?
> Thank you very much!
>
> Max
>
>
>
> --
> View this message in context: http://imagej.1557.n6.nabble.com/Drawing-3D-rois-tp5000564p5000568.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

... [show rest of quote]

--
   /**********************************************************/
      Thomas Boudier, MCU Université Pierre et Marie Curie,
      Modélisation Cellulaire et Imagerie Biologique (EE1),
      IFR 83, Bat B 7ème étage, porte 723, Campus Jussieu.
      Tel : [phone]   Fax : [phone]
/*******************************************************/

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