You need to understand that your spritesheet must be divided into many same sized(in pixels) sections, for example 32x32's or 64x64's for example, so now all the sprites you will use will not have any pixel errors.
And each of your characters animations must follow each other smoothly by the laws of basic cartoon making, for example if your character is supposed to wave his arms in 5 frames, then you should draw the arms waving smoothly frame after frame accordingly - supposedly make the last frame smoothly follow the first frame, but at the same time keep his feet on the ground at exactly the same place.
And reading that you are drawing your animations on some program, and then scaling all the different frames by hand sounds so wrong. What I would really suggest is that if you know your way around photoshop, then what you would need to do is create 6 layers, each the same size, 1:1(32x32;64x64...) or 2:1(64x32;128x64...) and then draw a simple stickman in the mid process of running in the first frame. Then on the next frame, add some transparency so that you can see the previous frame and draw the next animation smoothly after the next.
Maybe dig something up on youtube on making basic spritesheet or 2d animations, and it doesn't have to do anything with Unity too, I would go for the Macromedia Flash animation tutorials, since it focuses mostly on 2d animations and has for years. I hope this wasn't too long and it helped.
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