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Merging a focus stack with Photoshop

From: Foundations of Photography: Macro and Close-Up

Video: Merging a focus stack with Photoshop

So, I've taken my massive data, my huge stack of images, out of my camera, and copied them onto my computer. I am ready to start the merging process. I am going to do that using Photoshop CS6. Now, if you are using an earlier version of Photoshop, you might still have the same feature. You can find out by going to the Edit menu, and seeing if there is an Auto-Align Layers, and Auto Blend Layers. Doesn't matter if they are grayed out; you just need to have them there. If you have got them there, then you're going to be able to follow along here. I'm going to switch over to Bridge now, where I am browsing the folder, where I copied all of my images. [00:00:3.15] As you will recall, I shot RAW+JPEG.

Merging a focus stack with Photoshop

So, I've taken my massive data, my huge stack of images, out of my camera, and copied them onto my computer. I am ready to start the merging process. I am going to do that using Photoshop CS6. Now, if you are using an earlier version of Photoshop, you might still have the same feature. You can find out by going to the Edit menu, and seeing if there is an Auto-Align Layers, and Auto Blend Layers. Doesn't matter if they are grayed out; you just need to have them there. If you have got them there, then you're going to be able to follow along here. I'm going to switch over to Bridge now, where I am browsing the folder, where I copied all of my images. [00:00:3.15] As you will recall, I shot RAW+JPEG.

My idea was merging raw files takes such a long time that, because I don't know yet if my shot really works, I would also shoot lo- res JPEG files, so that I could get a quick speedy merge to find out if my lighting is okay, if I like the shot, if it set up well. So, that's what we are going to do. We're going to merge these JPEG files. First thing I would like to do is get all of the jpegs into one folder. You can do that any way you want. You can go to the File Manager of your Operating System, and move them. I think there's an easy way to do that in Bridge, which is I am going to go to the Filter tab here, and tell it to Filter for JPEG's. That shows me only the JPEG images.

Now, I'm going to select all, and go to File> Move to, and I am going to create a new folder, inside the folder where my RAWS and JPEGs are. I am going to create a new folder called jpegs, and move my files into there, so that's going to get them all into one place. So, now I'll just navigate over to that folder. And here we go. I have an entire folder that's nothing but JPEG's. Now, I want to you to watch something. I had told you before that we needed to pad our composition with some extra space, because as we push in, we will be cropping.

You can really see that here if you scroll through the images. See that? You can see how the zoom goes in. I am going to lose a lot of detail here on the left side. I am going to lose a lot of that wing. I am going to lose some stuff down below. Basically, my final image will probably have this composition. We are just getting a little close to his face there. But we will see. We might have a little more than that. Lets take a look at a single one of the images. I am just going to preview it here in Bridge, and you can see that, sure enough, my depth of field is razor thin. The antenna here is in focus, but not all the way to the end, and there's not much else that is. And remember, this was at f/11.

So, I should have pretty deep depth of field at a normal scale, but here Macro goes razor thin, so this is a fine candidate for focus stacking. So, here's what I do. I am going to select all, and then I am going to up to the Tools menu, and choose Photoshop> Load files into Photoshop Layers. Now, if you worked through the manual focus stacking lesson that we did earlier, you've already seen this process. What this does is it creates a new Photoshop document. It takes each one of those files that I have selected, and that puts it in its own layer. Now, I'll be able to manipulate, and combine those layers into a finished image that has deep depth of field.

In the manual lesson, we did that by hand. Fortunately, here we don't have to. So, it loaded those pretty quickly, because they are such lower resolution JPEG's. First thing I need to do is get them all aligned. As you saw from that push in with each image, different details in the image are in a different part of the layer, so I need to get all those lined up. Click on the topmost layer in the Layers palette. And then, I am going to scroll down to the bottom, and Shift+Click on the bottom layer that selects them all. [00:03:2.01] Now, I can go up to Edit>Auto-Align Layers, and I am going to take the Auto Projection, which will attempt to find the best way to align these. And, in my experience, it always does a very good job.

So, it's now shifting the layers around, trying to get whatever details it can find lined up together. It is then, in our next step, going to do what we did by hand earlier. It's going to create a layer mask on each layer, and it's going to fill in that layer mask to reveal only the parts of each layer that are in focus. When the whole stack is viewed, with each layer stacked on top of each other, with these layer masks in place, I should have an image where everything is in focus, so at least most of the bee is in focus. The downside to this technique is that if I want to make a change to one of those masks, it's very difficult to figure which mask has the change, and which mask needs to be left alone. This is an advantage of Helicon Focus, which we will see in the next movie. All right! It's done. And, that looks pretty good. You can see that I have got this extra space around my image here. That's because Photoshop had to expand the canvas size a little bit. But we're going to crop all that out anyway, so it's okay.

My layers are still selected. Now, I'm ready to just move on to Edit>Auto-Blend Layers. You might have used the Auto-Blend Layers feature before if you've shot panoramas, and stitched them in Photoshop. This is the exact same tool. But instead of using the panorama blend method, I'm going to stack images. And, you'll notice that that came on auto already selected. Photoshop does a good job of figuring out which one needs to be selected. I'm just going to hit OK, and it's going to set off to work. Now, as I said before, I'm doing these lo-res JPEG's, because I don't really know for sure that my final image works here.I don't know how these highlights on the wing are going to look.

I don't how to final crop is going to look. If I like the result, then I will go back, and merge the RAWS. This is a pretty simple stack we're doing here, As complex as it is, and, as much data as we generated for it -- this is around 2GB of data just to get this one image. 2GB of data, and all this processing for a single image, -- as simple as it is or as complex as that is, it's actually pretty simple compared to some stacks. If this bee was much larger, well, it would be real scary. It would also be a more difficult stack, because doing those really deep depth of field moves can be tricky to merge, because it's so much data. You might have 175, 200 images.

I find, very often, that even with these lo-res JPEG's, I can't do all 175 or 200 layers at one time. So, I will divide things into groups. I'll do 25 layers, or 25 images, at a time. I will load 25 images, merge them, save the results, get the next 25 images, merge those, save those results. And, at the end, I might have 25 interim documents that I then load into Photoshop, and merge to get my final, completely merged image. One thing to know about that technique is it is possible. There is a limit to how much depth you can shoot in a focus stack.

Sometimes, if you do too far push your geometry in, your scene will just change too much, and Photoshop won't be able to align and blend them. At other times, there might be a foreground element that blurs out to such a large degree that it starts to obscure the details that are further back, and you can't get a good merge. So, doing really, really deep merges can be difficult, and you very often need to experiment. Here we are. This is our final merge, and it looks pretty good. Look, it's sharp all the way through. Boy, you can really get a sense of the papery texture of the wing.

Check around the edges here. There are these areas that are blurred and weird. Those are areas where we didn't have data in every single layer, because as we pushed in, we effectively got to pan to the right a little bit. So, that's going to have to be cropped. Now, something else to notice as I zoom in here. First of all, I notice that these are very dirty. Second, I notice that focus is really good. It really did get sharp all the way back. That said, there are some curious little focus artifacts here.

This is soft right here. This is soft. There is a patch of softness right there. And there. You'll find these throughout the image. There's another one there. I've never been clear on if this is simply an artifact of the merging process, or if it means that I didn't have my slices overlapping enough. So, I might want to try and experiment where I go to a smaller interval, and shoot more shots. I'm starting to believe, as I do more of this, that it's actually just a merging artifact, and it's always going to be there. Now, I can fix this by flattening the image, and going in with the Rubber Stamp tool, and trying to hand retouch some of those blurry areas.

Fact is, I don't think this is really going to be a problem at any reasonable print size. You're just not going to notice it. Now again, this is not our full data set. This is just the lo-res JPEG image. Even that . . . look at all the detail we have got on his eye here. I can actually see the little compound bits. But we've got more data if we want it. We have those raw files. I am not going to do that merge now, because it will take a while. Instead, I am just going to pull out the finished raw image that I merged earlier, and let you see just how much more detail there is to be had. And, here it is.

This is the full pixel count raw merge. And, if I go into 100% . . . Wow! I can get a lot closer. So, we can see a lot more detail in there. I could print this image very large. This is Canon 5D Mark2 that I am shooting with, so it's about 21 megapixels. I would also say, though, that as I get into 100% -- I was shooting this image at 1600 ISO, -- I am not crazy about the noise that's in here, not because I think it's going to be that visible, but because it limits the amount of sharpening that I am going to do, and this image definitely needs some sharpening.

Let me quickly call up the Smart Sharpen dialog box, and you can see that if I go too far, I am going to start exaggerating that noise. So, I think I would like to try another one at ISO 800. I've still got the rig set up the same way. I don't have to on to anything other than dial ISO down to 800 make sure my exposure is correct, and start the stacking process, because the Stackshot control box still has all the correct settings in it. Nevertheless, even if I, even if that doesn't turn out to be much better, I think this is a really nice image. The noise doesn't bother me.

So, next steps would be, maybe I would want to play with the lighting a little more. I think it's okay. It might be nice to have a little more light right on the front of the bee. I could possibly do that with a reflector over here. But that's basically the focus merging process. I start with the JPEG's to see if my image is right. If I need to redo something, I redo it. If not, I merge the RAW. If I do redo the image, and it turns out to be okay, then I'll probably just go and start with the RAW file. One thing to know is I had some trouble getting the RAW file merged. This is a MacBook Air.

It's a speedy little computer. It has got 8 Gigabytes of RAM. But when I threw 27 RAW files at it, it choked. And, it choked because it didn't have enough scratch disk space. So, I hooked up another hard drive. And, I have taken care to kind of architect my scratch disk settings. I have my scratch disks to be set on one external hard drive and my internal hard drive. And, I have got my source data on yet another external hard drive. That's so that it's not reading the data from the same place that is reading and writing scratch disk. That simply speeds things up, because it is not have to do all these different seeks on the same drive.

27 images is enough that I can merge all of them at once on this computer if I have enough scratch disk space. If I was doing a hundred images, then I probably would've needed to have broken it into different steps. Because we were shooting with controlled lighting, Photoshop is not our only option for doing this merge. We can also do it with Helicon Focus. As I mentioned earlier, one of the great advantages of Photoshop is that it can work with images with a great brightness differential. That's one reason I like it, and it's where I do most of my merging. But for times when you have controlled lighting, you'll probably find that Helicon is much faster and easier, and we'll look at that next.

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This video is part of

Image for Foundations of Photography: Macro and Close-Up
Foundations of Photography: Macro and Close-Up

47 video lessons · 15140 viewers

Ben Long
Author

 
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  1. 3m 54s
    1. Welcome
      2m 17s
    2. What you need to know for this course
      1m 37s
  2. 20m 33s
    1. What is close up?
      2m 21s
    2. Understanding minimum focus distance
      3m 55s
    3. Comparing wide lens and telephoto
      1m 55s
    4. Understanding depth of field and focus
      2m 11s
    5. Working with extension tubes
      4m 30s
    6. Working with close-up lenses
      5m 41s
  3. 28m 7s
    1. What is a macro photo?
      4m 15s
    2. Understanding how to shoot macro with a reversed lens
      5m 37s
    3. Using a point-and-shoot camera for macro
      1m 55s
    4. Working with backdrops for macro
      3m 45s
    5. Practicing macro by shooting in the kitchen
      12m 35s
  4. 58m 38s
    1. Choosing a macro lens
      2m 4s
    2. Exploring macro lens features: Focal length
      3m 16s
    3. Understanding macro lens shutter speed
      7m 6s
    4. Shooting basics with a macro lens
      8m 24s
    5. Getting closer with macro lenses and extension tubes
      11m 13s
    6. Working with depth of field and macro
      5m 1s
    7. Understanding depth and composition in macro
      6m 43s
    8. Working with subject holders and support
      6m 36s
    9. Shooting with the Canon 65 mm
      8m 15s
  5. 13m 12s
    1. Working with macro stabilizing options
      5m 45s
    2. Working with sliders for macro
      2m 44s
    3. Working with a bellows
      1m 55s
    4. Working with viewfinders in macro
      2m 48s
  6. 52m 59s
    1. Working with direct light
      6m 13s
    2. Macro and the angle of light
      2m 24s
    3. Augmenting direct light with reflectors
      6m 42s
    4. Continuous lighting to add fill to a macro shot
      5m 55s
    5. Lighting your macro scene with continuous light
      4m 50s
    6. Lighting the macro scene with strobes
      4m 59s
    7. Setting up a macro-specific flash unit
      3m 21s
    8. Shooting with the Canon Macro Twin Lite
      7m 56s
    9. Shooting macro in a light tent
      3m 31s
    10. Shooting macro on a light table
      7m 8s
  7. 19m 44s
    1. Field shooting for macro, starting at home
      7m 5s
    2. Managing backgrounds in the field
      7m 39s
    3. Shooting macro water droplets
      5m 0s
  8. 56m 19s
    1. Creating a simple manual focus stack
      4m 40s
    2. Creating a focus stacked image with manual merge
      6m 17s
    3. Creating a focus stacked image using Helicon Remote
      11m 6s
    4. Working with a StackShot rail for focus stacking
      11m 46s
    5. Merging a focus stack with Photoshop
      11m 12s
    6. Merging photo stacks with Helicon
      6m 53s
    7. Understanding the aesthetics of depth of field
      4m 25s
  9. 1m 5s
    1. Next steps
      1m 5s

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