Make a new layer underneath the inked eyes. Get the base color ready for both eyes. I use the ink pen or pencil to fill it in. The base color shouldn't be too light or too dark.
Next, make a new layer above the base color and check next to clipping group in the layer settings. Choose a darker shading color, not completely black, and draw the shape of the pupil and make a thin border around the eye.
Make a new layer underneath the colored pupil, clip it. Use the pencil or ink pen to draw in the shadow in the upper part of the eye. I suggest using more than one color.
Now take the water tool, it's just water color with the setting I'm using, and blend the colors of the shadow. It should look something like this.
Make a new layer above the shadow layer, clip it, and set the layer mode to luminosity. This will make the colors appear like they're bright and glowing. Use the pencil or ink pen to draw what I have just done with a very light green tone, or whatever color eyes you have.
Take the water tool and blend.
Make a new layer above all the layers you made, clip it, and set to luminosity (again). Mark the places you want highlight with a white pen or pencil.
Take the water tool and blend the edges of the highlights just a little bit.
Now make a new layer below all the layers you made and fill it with some dark color using the paint bucket tool, I'm using blue. Why? You'll see in a second.
Make a new layer above the blue one we just made. Take a white color and ink in the eyeball. See why we used the blue now? It's so you can actually see where your putting the color.
Your almost done! This step's optional, but it's recommended. Make a new layer above the eyeball layer (that sounded weird)and clip it. Take a gray color and fill the top of the white. Use the blur and water tool to make it smoother. This adds some depth to the eyes.
Eyes are an important part in anime. This is just my way of coloring eyes, you can find your own way. I'm using Paint Tool SAI, but most programs can do something similar. This will hopefully appeal to people who are familiar with the program.
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