The trouble with digital photography is the ever present restrictions of Defraction. Defraction, in basic terms, is when your aperture is greater than what your lens and sensor can handle. You reach a point of diminishing returns and will actually make your photo less sharp by increasing your aperture past a certain point. For me, I shoot with a Canon 7D. With the 18 megapixel sensor and combining in the crop factor (for Canon it is 1.6x) I reach my defraction limiting aperture (DLA) at f/6.9. Bryan at The-Digital-Picture has a great chart for refraction and I suggest checking that out if you are at all interested. Full frame sensors are much better at handling defraction, but you gain some DOF by having a crop sensor so it all kind of evens out in the end.
Back to my point. Shooting at macro distances, your DOF becomes smaller and smaller the closer you get to your subject. The only way to get your DOF larger is either increase your aperture and risk the effects of defraction or take multiple pictures and combine those photos in software (Focus Stacking). My method of choice is Focus Stacking.
I previously wrote and brief tutorial some time ago on focus stacking. This article included multiple pictures of a fly. I know that isn't a subject the majority of people want to see so I have decided to use one of my bubble photos to illustrate focus stacking.
To illustrate the process and what can be achieved here is the final image. This is an image stacked with 12 different photos of the same bubble.
I will display the process with the bubble wand photo, but it all follows the same principle. The photos below were the 12 photos I used to stack and make the photo above. Each part of the bubble had a different section in focus and when combined, all photos create the final image.
This is the final image composed of the 9 photos that follow. Here is how it is done.
Next, we import the photos into a photo editor of your choosing. I prefer to use Lightroom for my Raw file editing. It is a simple way to keep your photos categorized and organized. Plus copy and pasting your settings is super easy. After the files are imported into your editing software, I flag all of the photos I think will want to combine into the final image. I select one of those photos and edit it in the develop module. Once I have the single photo as I like, I select the files I am using and sync settings for all of the photos I am including in the final image.
Once the files load into photoshop the process gets pretty simple. Select the top photo of the layers stack in photoshop, hold the shift key and click on the very bottom photo. This should select all of the layers. Then move your mouse to the edit tab and select auto align layers. After a couple of seconds your files should all snap into alignment. Next, go to the same edit tab and select auto blend layers.
A pop up box will show and you will want to select stack images. This will take a couple minutes to complete depending on the processing power of your computer. Once it is done, you will see the magic of focus stacking before your eyes. The images will combine and the photo will automatically snap into a perfectly focus photo. I usually combine them all into a single layer by command(control on PC)-alt-shift-E. Clean up what you would like about the newly stacked photo and save away.
I hope you have found this informative and simple to use. Now go photograph something and give it a try. Trying is the only way to learn!