Re: Display 3D pseudocolor images with threhshold and transparency adjustment

Posted by Chiz on Apr 19, 2011; 2:09am
URL: http://imagej.273.s1.nabble.com/Display-3D-pseudocolor-images-with-threhshold-and-transparency-adjustment-tp3684926p3684929.html

Hi Dave,

I just had a similar problem; here is what I found out.

Assuming you have 16 bit gray scale stack.

>>(1) Apply a LUT;

Image -> Lookup Tables -> choose a LUT of your choice.


>>(2) Convert the resulting color display to either real RGB or real pseudocolor images; and

Image -> Type -> RGB Color.


>>(3) Final goal: Display trhe result in color with variable transparency and threshold using the ImageJ 3D Viewer or perhaps another similar plug-in if one is available.

Plugins -> 3D -> 3D Viewer. Choose your image stack. Make sure you select "None" for Color.

Then you click on your 3D object; a red bounding box should appear. Go to 3D Viewer's Menu -> Edit -> Attributes -> Adjust threshold or Change transparency.

Good luck,

Ippei Kotera