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Divide the batter equally among three bowls. For the first batch of batter, add a few drops of red food coloring or edible gel paste to the bowl and stir with a clean spoon until the color is fully incorporated. Add more color as necessary to achieve the desired intensity. Repeat with the blue and yellow food coloring.  You can actually use any colors you like for tie-dye cupcakes, and can also use more than just three colors. Be sure to use a fresh bowl and a fresh spoon for each batch of colored batter, otherwise the colors will become muddy. You can also mix and match food coloring to achieve different colors. For instance, you can mix blue and red to achieve purple. To have white in your mix, leave one of the bowls of batter uncolored. Prepare a cupcake tin by lining it with white cupcake liners. Into the bottom of each liner, drop 1 to 2 tablespoons (15 to 30 ml) of red batter. Then place one or two spoons of yellow batter on top of that, followed by an equal quantity of blue batter on top. Stop when the liners are filled half way.  You can layer the colors in any way you like, and don’t have to use the red, yellow, blue pattern. different spoons for each color. If you're using more colors, use ½ to 1 tablespoon (7.5 to 15 ml) of batter for each color. Instead of spooning the colors into the liners, you can also transfer each batter color to a separate pastry bag, and pipe in the batters one color at a time. To create the tie-dye effect, take a clean toothpick and gently swirl around the batter in each liner. Don’t mix too much, or you will end up blending the colors and they’ll become muddy.  You can create circular tie-dye patterns by swirling the toothpick in circles. Create wavy patterns by zig zagging the toothpick in the batter. Make tie-dye spikes by dipping the toothpick into the batter in a few places and pulling it straight out. This will lift the bottom batter colors to the top.

Summary:
Dye the batter. Spoon the colors separately into cupcake liners. Swirl the colors.