Many photographers like lenses with wide apertures precisely because of their shallow depths of field. However, if you need to take a picture of a relatively deep subject in low light, the shallow depth of field can become a detriment. If you're willing to be flexible in how you photograph your subject, you can squeeze a deeper focal plane out of an otherwise shallow wide aperture.
Flatten the Subject
If you can, try to make the subject that you shoot more shallow. For example, if you're shooting an array of objects, try to align them with each other. Alternately, you may be able to take the picture from a different angle that helps to minimize differences in the distance between your subject's elements and the lens.
Step Back and Crop
If you keep your lens' focal length the same and step back, the effective depth of field will increase. A three-inch deep subject has a lot of variation in depth if you're six inches from it, but relatively little if you're two feet away. Given the high megapixel counts of many digital cameras, you should have enough resolution to crop out the area that surrounds your subject when you step back, leaving you with a sharper image of your subject. Please note that if you step back and zoom in, it will not have the same effect.
Embracing Selective Focus
Another option is to learn to use your lens' optical characteristics as a way of telling your story. When you use a wide aperture lens, its shallow depth of field means that your subject can be extremely sharp while everything else that is a different distance from your camera is blurred. This helps to draw the viewer's eyes to your subject and can even increase its perceived sharpness. However, you will have to settle for having the rest of your image blurry.
Alternatives to Wide Apertures
Just because your lens has a wide aperture doesn't mean that you need to use it wide open. If you're not opening your aperture for creative reasons, you're usually doing it to let as much light in as possible for a proper exposure. However, if you can use a slower shutter speed, increase your camera's ISO light sensitivity or use a flash, you'll also increase the amount of light that gets used in the exposure. Doing this and closing your aperture makes the depth of field less shallow, making more of your image sharp.
Solving Focus Problems
Because of the shallow depth of field, shooting at a wide aperture poses an additional problem. It can be hard to get the right part of the image sharp. The best solution for this is to put the camera on a tripod so that its distance to the subject doesn't change. Try to put your subject right in the middle of the frame so that your camera's middle autofocus sensor can focus on it. If the sensor is just the slightest bit off of your intended subject, it could focus at the wrong distance and give you a shot that's blurry in the wrong place. You can also manually focus the image yourself if you can't get your camera's autofocus to do what you want.
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