Set it to ON, which should be the default but isn't.
Mirror Lock-up
Mirror
This setting is used to lock up the mirror to clean the CCD. I never use this, since I find it easier to set the camera to Bulb and hold open the shutter. I'd never stick anything into the camera to touch the CCD; the only people who suggest this are the people who want to sell you the tools to clean your CCD.
Firmware Version
This lets me confirm if my D40 is
Mine, as of 02 January 2007, reads A 1.00 and B 1.00.
Dust Off Ref Photo
This is used to take a picture of the dust on your sensor. If you pay Nikon another $150 for Nikon Capture software you can use this to erase the dust more easily from your images shot in raw. You people know who you are. I don't do this!
I've made 80,000 combined shots on my Nikon D70, D200, D40 and D80 and have had no problems with dust. Thankfully the modern Nikon sensors have filters far enough in front of the imaging surface to throw dust sufficiently out of focus.
All I ever use is an air bulb to blow off the big chunks. The small ones remain invisible. If I ever had a problem, I'd let no one but Nikon clean my sensor, since they'll replace the camera if they screw up.
The additional work involved in shooting raw, for the amount of images I create every day, is far more than any need, once in a blue moon, to spot an image in Photoshop. See also Raw vs. JPG.
Auto Image Rotation
This sets a flag in vertical images which keys most software to display the image vertically.
It does not actually rotate the images; it merely sets a flag. Someday the camera's firmware will work properly and rotate the image itself, but no camera does this yet.
I rotate the images themselves later in iView.
Auto Image Rotation helps me identify which of hundreds of images I shoot each day need rotation.
Auto Image Rotation is easy to fool if you're shooting directly up or down.Turn it off if you're photographing your shoes on your feet.
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