The Basics of Focus Stacking. by Michael K. Miller

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1 The Basics of Focus Stacking by Michael K. Miller

2 Introduction Focus (or image) stacking is a method to increase the depth of field (DOF) by combining a series of images taken at either different focus settingsor at a fixed focus and at different camera-tosubject distances, and then combining the resulting images with software. It is particularly useful in macro photography due to the extremely small DOF that is available at the close focusing distances, but can also be useful for other types of images, such as in landscape and nature photography, etc. Image stacking can also be used to reduce noise in astrophotography. 100 mm DOF The DOF in the framecan be significantly increased so that all parts of a subject in the final image are in focus at the same time. In this head-on photo of a lily, the stigma is approximately 100 mm (4 inches) from the base of the trumpet and everything is in focus. 2

3 Image capture for focus stacking A series of images at different focus or distances is captured. 1 Example below is a ruler set at 45 to focal plane of camera After capture, a focus stacking program is used to automaticallyalign and choose the in-focus regions of each image to combine into the final image. The shape of the in-focus regions depends on the depth profile of the subject. The output may be a single jpg, tiff, or dngfile of the stacked image. 8 3

4 Image acquisition methods 1. Turn the lens focus ring manually, shoot and repeat Very difficult to do accurately, especially over long stacks 2. Automatically step the focus motor inside your lens between shots with software, such as Helicon Remote, ControlMyNikon, CamRanger, digicamcontrol, etc. A compatible autofocus lens with a computer chip is required 3. After each shot with the lens manually set at a fixed focus, move the camera + lens (or subject) along the optical axis with a manual focusing rail, or automatically with StackShot macro focusing rail package (cognisys-inc.com) Subject must not move during shooting Simplest to tether the camera to a computer for remote operation Time-consuming compared to regular shooting Good for extended distances and/or high magnifications Clean sensor before starting sensor spots will appear as dark lines stuck pixels will appear as coloured lines Short stack: up to 20 frames: Tradition stack: up to hundreds of frames 4

5 Helicon Remote (Shooting preferences) Helicon Remote has several options for the shooting parameters. Default settings are appropriate for most situations Pause duration for flash to recharge always use fresh batteries Live view uses a lot of battery power, so disable when possible, especially after finishing a stack. Active live view should be No for Stackshotand Yes for camera focus Default step sizes depend on camera 5

Helicon Remote (Image saving preferences) Helicon Remote enables moving or copying RAW and/or JPG image files directly to the computer and/or leaving on the camera.

6 Helicon Remote (Image saving preferences) Helicon Remote enables moving or copying RAW and/or JPG image files directly to the computer and/or leaving on the camera. Can also define the folder and filenames for the images Lists options Yes prevents confusion File transfer options: Move to computer files only on computer Copy to computer files both on camera s card and on computer Leave on camera files only on camera s memory card 6

7 Helicon Remote (Camera preferences) Helicon Remote should automatically detect the camera body on startup. Different camera parameters can be set in the File>Preferences menu Also need to set camera body set up parameters in camera s menu, such as AF-S auto focus mode Release mode to single frame S AF-S priority release See Helicon Remote documentation Default settings are reasonable for most cases 7

8 Helicon Remote (Stackshot preferences) Helicon Remote should automatically detect and use Stackshot to move the focusing rail when connected, otherwise it uses lens auto-focus. Pause after movement to allow all vibrations to settle and also to recharge the flash 8

110V Power USB port 1 USB port 2 Shutter

9 Stackshot macro focusing rail setup cognisys-inc.com/products/stackshot3x/stackshot3x.php Helicon Remote Camera s USB port 110V Power USB port 1 USB port 2 Shutter release X AC adapter USB power AC power adapter for camera eliminates the need to change batteries Minimum step size is mm over the 100 or 200 mm travel of the rail. Connect USB cable directly from computer to camera no USB hubs. 9

Helicon Remote (Exposure settings) Select camera (first use only) and check battery charge state Exposure mode (Manual or M mode recommended) Shutter speed (for flash or proper exposure) Aperture

10 Helicon Remote (Exposure settings) Select camera (first use only) and check battery charge state Exposure mode (Manual or M mode recommended) Shutter speed (for flash or proper exposure) Aperture (for optimum quality usually f/5.6 or f/8) ISO (base value 100 or 200) Exposure compensation Image quality (all available options on camera) <= then check histogram for proper exposure note warning symbol when not correct See Helicon Remote manual for the exposure bracketing and advanced settings options Use Auto or appropriate setting for White Balance and Temperature 10

Helicon Remote (Operation) Blue highlighting indicates the in-focus portion of each image.

focal length and lens correction factor and measured in focusing steps (lens motor steps) not

com/heliconremotehelp/english/heliconremote.html for more details.

(or right click and ) and set, step size (interval) or check Auto) box, and direction.

11 Helicon Remote (Operation) Blue highlighting indicates the in-focus portion of each image. DOF values provided by the DOF calculator are based on the current aperture of primary lens, focal length and lens correction factor and measured in focusing steps (lens motor steps) not distance (as in other DOF calculators). See heliconsoft.com/heliconremotehelp/english/heliconremote.html for more details. Set initial (A) and final (B) distance points by moving the stage with the arrows, then press and (or right click and ) and set, step size (interval) or check Auto) box, and direction. Take a picture and inspect histogram to check correct exposure. Check focus range with arrows next to the and buttons. Then click Start shooting icon in menu bar to record the image sequence. 11

12 Helicon Remote (Shortcut keys menu) Several of the common functions in Helicon Remote are assigned to shortcut keys 12

How many frames and optimum step size Some stacking software will suggest and set the step size for the focus of camera lens or the focusing rail between the frames Step size = 2 cn(m+1)/(mx m) c=

13 How many frames and optimum step size Some stacking software will suggest and set the step size for the focus of camera lens or the focusing rail between the frames Step size = 2 cn(m+1)/(mx m) c= circle of confusion n= f-number m= magnification Use at least a 20% overlap. Steps can be very thin when very close to subject Thinner than a credit card (0.76 1X = 0.45 mm with a 20% = mm with a 20% overlap Out-of-focus bands (known as focus banding) of can be observed in the focus stack when the step size is too large 13

Selection of start and stop distances and step size/aperture The selection of the start and stop distances of the image capture should include all of the subject and the necessary background.

14 Selection of start and stop distances and step size/aperture The selection of the start and stop distances of the image capture should include all of the subject and the necessary background. The step size should be small enough to have at least a 20% overlap between frames for the chosen aperture. In this example, the starting point was too far into the image and part of the front wings of this damselfly were cropped out. 14

Before reconstruction Before reconstruction, the images should be checked for correct positioning, lighting and exposure, and any artifacts.

15 Before reconstruction Before reconstruction, the images should be checked for correct positioning, lighting and exposure, and any artifacts. One frame here is overexposed probably due to an anomalous higher level of flash. To speed up the reconstructions, frames at the start and end of the set may also be deleted (or unchecked) if no regions are in focus. 15

Focus stacking software Stacking software is then required to align and combine the infocus portions from each image in the image stack. 1. Helicon Focus - www.heliconsoft.

16 Focus stacking software Stacking software is then required to align and combine the infocus portions from each image in the image stack. 1. Helicon Focus Zerene Stacker - zerenesystems.com/cms/stacker 2. Limited to jpg or tiff file formats but can convert 3. raw to tiff in Adobe Lightroom, etc. 3. Photoshop - adobe.com/products/photoshop/ Limited number of frames and slow compared to others Can be used to finalize the image after reconstruction 4. See en.wikipedia.org/wiki/focus_stacking for other focus stacking software Alignment Parameters: If your camera (or subject) moves between shots, you may need to increase the values for the allowable alignment parameters (vertical and horizontal positioning, angle of rotation, and magnification of images in the stack). In Helicon Focus: Main menu > Edit > Preferences... "Auto adjustments" tab. 16

17 Parameters for the Depth Map method Pyramid (Pmax) method has NO adjustable parameters Depth map (Dmap) method finds the source image where the sharpest pixel is located and creates a "depth map" from this information. Radius and Smoothing parameters The Radius Parameter: Radius is the most important parameter. Start from the default value (8 HF/10 ZS) and then set it to its minimum (1) and observe the changes. Then increase the value to get rid of any noise or artifacts, particularly halos along the edges. If your image has fine details and thin lines, a low radius level (3-5) will probably yield the best results, although you will probably get more noise and a halo effect. If there is a halo, try increasing the radius to minimize halo, then stop to preserve as much detail as possible. The Smoothing Parameter: Low smoothing produces a sharper image, but the transition areas may have some artifacts. High smoothing will result in a slightly blurry image without any visible transition areas. Start with the default smoothing (4 HF/5 ZS). For more detail, decrease the smoothing value; if get too much noise and too many artifacts, increase the value. HF = Helicon Focus; ZS = Zerene Stacker (Options> Preferences> Dmap settings 17

Popular focus stacking algorithms Pyramid (Pmax) method is very good at finding and preserving detail even in low contrast or slightly blurred areas.

18 Popular focus stacking algorithms Pyramid (Pmax) method is very good at finding and preserving detail even in low contrast or slightly blurred areas. It gives good results in complex cases (intersecting objects, edges, deep stacks) but increases noise, contrast and glare. It can alter colors. Depth map (Dmap) method does a better job keeping the original smoothness and colors, but it's not as good at finding and preserving detail. Images must be in distance order. Substackslabbing for troublesome regions or to overcome large file size/computer memory issues. 18

19 Workflow for stacks of RAW files Shoot the stack of RAW images Remove any sensor spots and stuck pixels in Lightroom or Photoshop Check suitability of stack for focus stacking (see previous slides) For Zerene stacker Import into Lightroom or Bridge and then export tiffs to Zerene Stacker For Helicon Focus Load RAW files Stack Photos with both Pmaxand Dmapmethods Retouch Use Dmapas the base image and overwrite with areas from Pmaxor the individual stacked layers Commit the retouching and Save image Open in Photoshop for final retouching e.g., clone tool Save final image 19

Select Preferences Edit>Preferences(on General tab) Load Raw, tiff, or

.. or Drag files in main window, or Export directly from Helicon Remote

20 How to stack images in Helicon Focus 1.Open Helicon Focus and set focus method in Edit> Focus 2. Select Preferences Edit>Preferences(on General tab) Load Raw, tiff, or jpgs, etc.* files into layers - 3 methods File> Open Images... or Drag files in main window, or Export directly from Helicon Remote Drag files to this window Files will appear here *For a full list of supported files: File> Open Images.. then pull down the Imagesmenu 20

Rendering in Helicon Focus Number of images selected is shown at the top of this pane To remove any frame(s) from the rendering process uncheck the checkmark to the left of its thumbnail 1.

21 Rendering in Helicon Focus Number of images selected is shown at the top of this pane To remove any frame(s) from the rendering process uncheck the checkmark to the left of its thumbnail 1. Select rendering method A. Weighted average method B. Dmax method C. Pyramid method 2. Optional Downscale resolution to 50%, 33% or 25% for smaller file size Change Radius and Smoothing parameters (see previous slide) 3. Select one of the Render buttons Progress bar shows state of rendering process 4. Optional retouch image (on tab above image) to remove artifacts. 5. Save output file (tiff, tiff with compression, jpg or DNG) 1.Right click highlighted output file then Save or 2.File> Save or 3.Saving button (above image has the most options) Use mouse wheel to change magnification of resulting image 21

Load jpgsor tiff files into layers File> Add files... or Drag files in main window 3.

22 How to stack images in ZereneStacker 1. Open Zerene Stacker and set parameters in Option> Preferences 2.Load jpgsor tiff files into layers File> Add files... or Drag files in main window 3. Open Stack menu and select method Align & Stack All (Pmax) Align & Stack All (Dmap) Align & Stack All (both) Drag files to this pane 4. Save Output file File> Save Output Image(s) 22

23 How to stack images in Photoshop CC 1. Open Photoshop CC 2.Load files into layers - File> Scripts> Load files into Script... 3.Browse for the files and add them (<CTRL> click to select multiple files) 23

24 Select all layers 1. File> Scripts> Load Files into Stack Browse for the files and add them (<CTRL> click to select multiple files) Selected files will have a lighter grey box around them 24

you change focus distance Click OK -a progress bar should appear Edit> Auto blend

25 Align and Stack (blend) layers Next ensure all layers are selected Edit>Auto align layers and ensure that the auto setting is selected Required as image size changes as you change focus distance Click OK -a progress bar should appear Edit> Auto blend layers Stack Images should be automatically selected then click OK A progress bar should appear 25

26 Stack layers The stacked image should appear at top of the list of images. The white regions are the parts of the focus sequence that were used in each frame. Note the order that the images from the Olympus OM-D E1 were taken is 2,1,3,4,5,6,7,8, where 1 is the bottom and 8 is the top 26

27 Photoshop CC Focus Stacked Image Note the out-of-focus regions top and bottom in the automatically generated image Top is due to the autogenerated masks being slightly off. Bottom is due to the original set of images not covering the entire range of focus required 27

28 Refine masks for each in-focus region Select brush tool and an appropriate size Click on the thumbnail of the mask to edit. Click Mask Edge button on pop-up menu To subtract from the mask and reveal the layer, paint the mask with white. To add to the mask and hide the layer or group, paint the mask with black. The layers below become visible. Uncheck the eye symbol of the merged image at the top (as shown) Refer to Photoshop Help for more information on layers and masks 28

29 Some lens and reconstruction artefacts Halos around edges of objects and in the out-of-focus background regions Colouredstraight lines running perpendicularly to the edge(s) of the frame Strings of dots sometimes replicated Dmapreconstructions can introduced noise similar to sensor spots and stuck pixels 29

30 Summary Focus stacking is an effective method to substantially increase the Depth-of-Field for static subjects Both the data acquisition and processing steps are time consuming. The number of frames required increases with the reduction of the depth-of-field when the focus distance is very small. Constant lighting and hence exposures during acquisition of the entire stack is essential. The Stackshot focusing rail greatly simplifies data acquisition when combined with a manual lateral focusing rail to position the subject in the frame Read the instructions to set up your specific camera and the acquisition parameters. 30

How to combine images in Photoshop

How to combine images in Photoshop In Photoshop, you can use multiple layers to combine images, but there are two other ways to create a single image from mulitple images. Create a panoramic image with