Attempting to use the interactive 3d surface plot on a 32-bit image *.TIF. The grayscale is unit normalized, in this image. I seem to run out of min/max scale on the z? The smallest value, I may achieve, is about 40 units? Thanks for an advice or suggestions.
Here is the documentation of the 3d surface plot:
Try out this recipe:
The “Perspective” and “Scale” sliders allow the 3D-projection and the size of the surface
plot to be changed. The plot height may be scaled with the ZRatio slider. The "Min and "Max
sliders will limit the height range of the plot data.
Thanks for the link and your description. But I already adjusted all possible slider controls over their limits (in the GUI?) and do not resolve the issue. I am, additionally, missing what is meant by the zratio slider. I see checkbox z = xyRatio (see it’s impact, but this is not it). I see the sliders scale, z-scale,min,and max. That is all I see in the GUI. I just confirmed, that in the test case at hand, the limits I achieve are 41…42.4 over the z-axis for a min = 0%, max = 1% (if all that is additional information)
Try the command
A screenshot or example image would help, too.
Or contact the author of the plugin for help.
I don’t know where to execute the recommended macro command. I am attempting to use the plug-in (as built) and would appreciate further instructions.
Copy the command in the editor “Plugins->New->Macro” and then press run or in the ImageJ editor menu “Macro->Run macro” before you open it in the 3D surface plot.
Apropos what do you get when you aplly a surface plot? “Analyze->Surface Plot”.
If you apply a LUT this will give you a fine 3D surface plot, too.
Your instruction worked great! The only modification (which was in the help documentation you alluded to earlier), necessary to run on my installation, is to enclose the resetMinandMax() in a Macro subroutine.
Thanks. As a side question, since I now achieved the real-time visualization desired with the proper amount of smoothing, may I save the smoothed surface back to a *.tiff?