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Mark - am only just experimenting with time lapses myself.
I tried to do a raw run recently, but my memory card died permanently... Not sure if it was the camera or the card (have been having problems with the camera).
I had planned to use a piece of software LRTimelapse that interfaces with Lightroom - looks very interesting and lots of tips on the website and forum.
I did a JPEG run last night that I will hopefully fiddle with this afternoon. Will try the camera with a few JPEG runs with a smaller sacrificial memory card before trying a RAW one again with a larger card.
I think RAW may have advantages, but if I shoot RAW with my new camera, the resulting data will kill me in post processing (40Mb files x 1000+ shots a night = way too much data)
Cheers
DT
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