If its a 60d v 60da, I am leaning towards 60Da, for the following reasons:
1. It's a dedicated camera (therefore preserves manufacturers warranty).
2. The inside of the 60Da is designed to minimise thermal/amp glow. This means you may not need to cool the camera for optimal performance, whereas a modded DSLR would need cooling to minimise amp glow and optimise image for long exposurs and long sessions.
3. You can always get aftermarket clip in filters which will not affect the warranty and still achieve what you are after (OIII etc).
That's just my thoughts only, others might disagree.
Bo
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