There are a few ways: using functions like volumeViewer, volshow, or slicechan. Alternatively, you could create a 3D volume from your images and color-code based on depth with a colormap. For surfaces, using patch or scatter3 is an option. I think volumeViewer could work well with this, especially if you combine your image stacks into one volumetric object.
You can treat your focal stack as a 3D point cloud and color-code by the slice index (depth). For example, if your stack is a cell array of images or a 3-D array V(:,:,k), do something like:
% Assume V is H×W×D and zDepths is a 1×D vector of depths
[H,W,D] = size(V);
zDepths = 1:D; % or actual depth in mm/cm/etc
[X,Y,Z] = meshgrid(1:W, 1:H, zDepths);
% Flatten into vectors
X = X(:); Y = Y(:); Z = Z(:);
% Use Z for color (one color per depth)
scatter3(X, Y, Z, 4, Z, '.');
colormap(jet(D));
colorbar('Ticks',1:D,'TickLabels',zDepths);
axis image; view(3);
xlabel('X'); ylabel('Y'); zlabel('Depth');
This plots every pixel at its (x,y,depth) location and colors it according to the depth index. Adjust zDepths to your actual focal distances.
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