3D view of atoms and Lattice (or perspective View)

3D view of atoms and Lattice (or perspective View)

I'd like to show substrate and layers that growth on it in the 3D view. For my master thesis. For example, I have a 3D Matrix that shows where is each atom. And want to show a 3D view (or perspective View) of it (For example as attached pictures).

can anyone help me?

My English does not good, Excuse me for any unintelligible sentences.

pictures:

zoom Images to see the atoms and shadows.

I need the same perspective view. to can print it. and also can zoom it in PDF print. https://image.ibb.co/kBH8SF/atoms_3_D_view_on_substrate_1.jpg

https://image.ibb.co/kBH8SF/atoms_3_D_view_on_substrate_2.jpg

[KSSV]

What data you have to plot the pictures?

[mostafa]

the data is a 3-Dimension matrix. Each pixel has a number that shows which kind of atom exist (for example, "1" for Ga atoms, "2" for another atom, and "0" for vacancies.).

you can create a random matrix by "Mat = randi(2,6,6,10);" that is similar to my data.

I need to show each pixel as a ball with gray color respect to its value and also has a shadow respect to a view point (as similar to the images attached above).