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I am taking a series of photos using a dSLR camera attached to a microscope that will be used in a stack to produce a single image with high depth of field. Can anyone recommend a level of resolution that I should use for each shot? The camera has a capacity of 18 megapixels, but I am concerned that if each picture is shot at such high resolution, I may introduce noise and the size of the final image will be huge. The software I am using does not address this. I expect to combine somewhere between 6 and 15 images.

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My only comment is that I would expect that the lower resolution you use, the fewer shots you need to make it look seamless. – Itai Jan 24 at 3:09

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Always use as much data as you can. It's actually easier to reduce noise when there's more information to begin with. (Reducing resolution is a brute-force noise removal tool, throwing away both noise and signal.)

If you're concerned about the size final image, reduce the resolution at that point.

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The final image may be huge, but if it's a satisfactory end result you can flatten the file and it will be no bigger than a normal image file. – BobT Jan 24 at 0:55
I was interpreting the question as suggesting that a single 18mpix image seemed huge, but, yeah, that too. – mattdm Jan 24 at 17:18
I figured he was commenting on the stack of layers, one for each image, which would have been pretty big, depending... – BobT Jan 25 at 2:10
Yes, also possible. – mattdm Jan 25 at 2:11
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I don't have too much to add, but I have some limited experience with focus stacking on microscopes that I can share.

I've done focus stacking on an SEM, the following image is a stack of only two images. I wish I had a third to fill in the blur in the middle.

Image of a flower I took with a scanning electron microscope. The near foreground and the 'sky' background are one image. The subject is a second exposure. I wanted to maximize blur of the background and maximize the clarity of the foreground. SEM Image of Flower

Unless you are optically photographing a fixed subject, the subject will drift, so it is important to take the images quickly, and sequentially to minimize the impact. Frame a bit wider than normal so the final crop can be perfect.

mattdm has the answer you are looking for: Use full resolution as long as possible. Focus stacking will not reduce noise, it will improve image clarity by chooing regions that have better focus. Reducing noise would require a set of exposures at each focal distance to average out the noise- get more data for each pixel.

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