Display 3D matrix with its thickness information

Question

I have a problem about plotting 3D matrix. Assume that I have one image with its size 384x384. In loop function, I will create about 10 images with same size and store them into a 3D matrix and plot the 3D matrix in loop. The thickness size is 0.69 between each size (distance between two slices). So I want to display its thickness by z coordinate. But it does not work well. The problem is that slice distance visualization is not correct. And it appears blue color. I want to adjust the visualization and remove the color. Could you help me to fix it by matlab code. Thank you so much

    for slice = 1 : 10

       Img = getImage(); %  get one 2D image.
       if slice == 1
         image3D = Img;
       else
         image3D = cat(3, image3D, Img);
      end
      %Plot image
       figure(1)
       [x,y,z] = meshgrid(1:384,1:384,1:slice);
       scatter3(x(:),y(:),z(:).*0.69,90,image3D(:),'filled')

    end

Answer 1

The blue color can be fixed by changing the colormap. Right now you are setting the color of each plot point to the value in image3D with the default colormap of jet which shows lower values as blue. try adding colormap gray; after you plot or whichever colormap you desire.

I'm not sure what you mean by "The problem is that slice distance visualization is not correct". If each slice is of a thickness 0.69 than the image values are an integral of all the values within each voxel of thickness 0.69. So what you are displaying is a point at the centroid of each voxel that represents the integral of the values within that voxel. Your z scale seems correct as each voxel centroid will be spaced 0.69 apart, although it won't start at zero.

I think a more accurate z-scale would be to use (0:slice-1)+0.5*0.69 as your z vector. This would put the edge of the lowest slice at zero and center each point directly on the centroid of the voxel.

I still don't think this will give you the visualization you are looking for. 3D data is most easily viewed by looking at slices of it. you can check out matlab's slice which let's you make nice displays like this one:

slice view http://people.rit.edu/pnveme/pigf/ThreeDGraphics/thrd_threev_slice_1.gif