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Clarifying that this is a feature in Photoshop, and that it still works in more recent versions
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In Photoshop CS5 or later, load your images into layers.

  • Select Edit > Auto Align Layers (at macro distances even on a tripod small changes in focus will alter the perspective of each shot)

  • Select Edit > Auto Blend Layers. This will select the sharpest parts of each layer and create a mask. The masks can be quite complex, but it does a very good job.

There is an open source program CombineZP

In CS5, load your images into layers.

  • Select Edit > Auto Align Layers (at macro distances even on a tripod small changes in focus will alter the perspective of each shot)

  • Select Edit > Auto Blend Layers. This will select the sharpest parts of each layer and create a mask. The masks can be quite complex, but it does a very good job.

There is an open source program CombineZP

In Photoshop CS5 or later, load your images into layers.

  • Select Edit > Auto Align Layers (at macro distances even on a tripod small changes in focus will alter the perspective of each shot)

  • Select Edit > Auto Blend Layers. This will select the sharpest parts of each layer and create a mask. The masks can be quite complex, but it does a very good job.

There is an open source program CombineZP

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MikeW
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In CS5, load your images into layers.

  • Select Edit > Auto Align Layers (at macro distances even on a tripod small changes in focus will alter the perspective of each shot)

  • Select Edit > Auto Blend Layers. This will select the sharpest parts of each layer and create a mask. The masks can be quite complex, but it does a very good job.

There is an open source program CombineZP