I'm unsure what you mean by clear. I think you mean sharp, but you could mean a lighter/darker image than you expected it to be.
Your picture quality issue will be largely due to the lens you're using and focusing accuracy. Setting your aperture to very small can make the image soft (everything in focus, but not pin point sharp). Setting your aperture very large (small number, say f/1.8) will reduce the depth of field (whats in focus) and only have what is in focus pin point sharp. If you've focused in the wrong place you can expect a blurry image.
Cropping by itself shouldn't effect the image quality. Are you cropping and then stretching the image? Stretching an image will always degrade the image to some extent.
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Your picture quality issue will be largely due to the lens you're using and focusing accuracy.
Setting your aperture to very small can make the image soft (everything in focus, but not pin point sharp). Setting your aperture very large (small number, say f/1.8) will reduce the depth of field (whats in focus) and only have what is in focus pin point sharp. If you've focused in the wrong place you can expect a blurry image.
Cropping by itself shouldn't effect the image quality. Are you cropping and then stretching the image? Stretching an image will always degrade the image to some extent.