Preheat oven to 350°F (175°C). Line a muffin tin with cupcake liners.
Whisk together flour, sugar, baking powder, and salt in a medium bowl.
In a large bowl, cream together butter and sugar until light and fluffy.
Beat in eggs one at a time, then stir in vanilla bean seeds.
Gradually add dry ingredients to wet ingredients, alternating with milk, beginning and ending with dry ingredients. Mix until just combined.
Fill cupcake liners about 2/3 full.
Bake for 18-20 minutes, or until a toothpick inserted into the center comes out clean.
Let cupcakes cool in the muffin tin for a few minutes before transferring them to a wire rack to cool completely.
Make the frosting: In a large bowl, beat together cream cheese and butter until smooth and creamy.
Gradually add powdered sugar, beating until smooth.
Stir in vanilla seeds.
Frost cooled cupcakes.