So far I know of at least blue red and black from the layers and purple made by laying solid blue (layer 1) on red paint (layer 2). But you might be able to learn more by going to Hatena. Even if you don't have an account. But try pressing the L button on any screen you want and hidden things appear.
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There is no way to add colors to flipnote studio, but you can make colors by mixing. e.g. red + blue = purple. here is how... 1.(layer 1-blue) fill the screen 2.(layer 2-red) use paint on tool 5 and fill the screen. try experimenting and making your own
First, go to the studio and click on view flipnote, then on your flipnote, then click on the frog, then the 2, then on layer 1 or 2 click on the black color box and then the color you want. Also, you can mix colors. For example, for the first layer use blue, put some blue paint on the screen. For second layer, use red. DRAW red OVER the blue paint. You will make purple.
If it is no longer in your System Memory, go to your Creator's Room and download your Flipnote. If you already have this Flipnote in your memory, you may skip that step. Once you have the Flipnote saved, go to Hatena. Choose a channel to post to. When you re-post your Flipnote, DO NOT choose "Lock." Now your Flipnote is unlocked.
Flipnote Hatena is a software on the Nintendo dsi. In order to get on it, you need to gt internet on it. In Flipnote Hatena you can watch other peoples flipnotes and even post your flipnotes you made in flipnote studio. That is what flipnote hatena is.
You can combine different layers of colors. For example, layer 1 = blue, Layer 2 = red. Use red pen underneath blue paint. Just use different combos of pens, paint, and colors.