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Underwater Video: Auto Focus vs. Manual Focus

I'm at 100 feet with the reef at my back, shooting into the blue. All the action is in the deeper parts of the ocean where Grey Reef Reef sharks and barracuda jockey for position in the current. It's a wide-angle fiesta and I had everything dialed: exposure, lighting, filtration'focus? Unfortunately I was in auto focus, and as the silver/grey fish procession swam by in the deep blue water I may have been stoked, but my camera's auto focus was lost. While I thought I was shooting clear, well-focused footage, my camera was making a series of focus adjustments, which I was unable to see through my viewfinder and monitor. The adjustments were definitely noticeable when I viewed the footage at home. The camera was 'seeking' or constantly searching for proper focus, resulting in footage that was fuzzy one second and sharp the next. My shot was ruined!
This sample shows a camera trying to auto focus in a low light, low contrast situation. You can clearly see the auto focus searching at the beginning of the clip. This seeking can happen anytime you're in auto focus mode, possibly ruining a shot.
The reason my camera's auto focus 'failed' so miserably is because video cameras use contrast to judge whether a shot is in or out of focus. Contrast is essentially the difference in visual properties that separates an object from its background. If the scene you're shooting lacks contrast, the camera will be unable to pinpoint and hold focus on your subject. A silver/blue fish swimming on a blue background will blend into the background and therefore never auto focus properly.
So how do you stop your camera from seeking in a low contrast situation? Lock your focus! This is what I do now when I first jump into the water:
1. I make sure my camera is zoomed out to its widest setting.
2. I find a high contrast object within 3 feet of me and set auto focus. A well-lit chunk of coral, my fin, or a dive buddy will do nicely.

Video cameras use a black and white image for auto focusing. You can see here how colors blend into tones when converted to black and white. This makes auto focus untrustworthy in low contrast situations.
How you lock focus is dependant on your housing. Light and Motion has a momentary auto focus button. If you buy a Light and Motion housing this button will become your best underwater friend. After the momentary auto focus button is pressed and held, your camera auto focuses. Allow the camera time to properly auto focus and release the button to lock it. Your camera will lock focus in its current position. This ability to focus on the fly using only your thumb is an incredible asset. Other housings such as Gates and Sea & Sea have an auto focus button that toggles you between manual and auto focus. Press it once and you're in auto focus; press it again and you're in manual focus but locked in position. You can also manually focus your image and to keep it locked. But I must warn you, this can be tricky as you may not be able to see sufficient detail in your displays in bright reef situations.
Once you've locked your focus, everything within 2 feet to 'infinity' will be in focus. Your depth of field, the distance or field in front of and behind your subject where everything is in focus, will be expansive and you will rarely need to refocus. You an also use a wide-angle lens to greatly improve your depth of field. As a rule the smaller the lens's focal length, or the wider angle the lens, the greater the depth of field.

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