In most cases, you don't want to thaw your berries before using them in baking recipes. Frozen berries in muffins? Great. Frozen berries in pie? Even better. If you thaw them, the moisture content will likely be off, and you'll end up with a soggy pie and blueberry muffins that are blueish green.
The real issue with defrosting a berry like blueberries, for example, is that they tend to "bleed," which causes those blueish green welts throughout the batter and muffins. I always roll my frozen berries in a little bowl of flour and coat them well before adding them to batters to prevent this even further. So bake away with fresh fruit straight from the farmers' market or your freezer. No one will know the difference.
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