Helicon Focus by HeliconSoft is typically regarded as the top focus stacking option. This way, if you ever see that color you know you have a "hole" in your merged stack. To help keep an eye out for this, first create a new layer underneath all your stacked layers and fill it with neon pink or some obnoxious color that will be highly visible if it shows through at any point.
If you paint black on the mask for the layer as sharpest at some point you will have a transparent spot in the composite image unless you also paint white on some other layer. This isn't as easy as it might seem though as you have to be careful to have at least one layer visible at each point. This means the merge process is completely lossless and you can paint on the masks just like normal to tweak things. When Photoshop does finish, you will have a mask on each layer to control what is visible from each. This is not one of the faster things Photoshop can do, so be prepared to wait if you have a number of high resolution images to merge. Now you have to wait for the merge to complete. The "seamless tones and colors" checkbox at the bottom of the dialog should be turned on to avoid abrupt edges in the result. For focus stacking, you obviously want the second choice. The dialog gives you the choice to create a panorama or a stacked image blend. When this finishes, you can proceed to the Edit > Auto-Blend Layers menu command. Just select the "Auto" option here and don't worry about the other choices. The next step is to select all of your document layers and go to Edit > Auto-Align Layers to compensate for any slight camera movement between frames as well as adjust for minor magnification ratio differences due to lens extension that comes from changing focus. What you get is a single Photoshop document with one layer for each of your source images. The command is oddly called "Open in Photoshop Layers" rather than something more obvious but this actually makes sense when you realize it's really only the first step of the process. If you create a stack in Bridge of all images to be merged, you can open the set easily in Photoshop.
It wasn't until CS5 though that it was really ready for prime time in my opinion. Starting with the CS4 release, Adobe added focus stacking directly into Photoshop. This week I'll look at several software programs to help you do it. Last week I discussed merging multiple shots of the same subject taken at different focus distances to create images with extended depth of field using a technique known as focus stacking.
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