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Focus stacking

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Series of images demonstrating a six-image focus bracket of a Tachinid fly. First two images illustrate typical DOF of a single image at f/10 while the third image is the composite of six images.
Focus stacking (for extended depth of field) in bright field light microscopy. This example is of a diatom microfossil in diatomaceous earth. Three source images at different focus distances (top left) are combined with masks (top right) to obtain the contributions of their respective images to the final focus stacked image (bottom). Black is no contribution; white is full.

Focus stacking – also called focal plane merging, z-stacking,[1] or focus blending – is a digital image processing technique which combines multiple images taken at different focus distances to give a resulting image with a greater depth of field (DOF) than any of the individual source images.[2][3] Focus stacking can be used in any situation where individual images have a very shallow depth of field; macro photography and optical microscopy are two typical examples. Focus stacking can also be useful in landscape photography.

Focus stacking offers flexibility: since it is a computational technique, images with several different depths of field can be generated in post-processing and compared for best artistic merit or scientific clarity. Focus stacking also allows generation of images physically impossible with normal imaging equipment; images with nonplanar focus regions can be generated. Alternative techniques for generating images with increased or flexible depth of field include wavefront coding, light-field cameras and tilt.

Technique

The starting point for focus stacking is a series of images captured at different focus distances; in each image different areas of the sample will be in focus. While none of these images has the sample entirely in focus they collectively contain all the data required to generate an image which has all parts of the sample in focus. In-focus regions of each image may be detected automatically, for example via edge detection or Fourier analysis, or selected manually. The in-focus patches are then blended together to generate the final image.

This processing is also called z-stacking, focal plane merging (or zedification in French).[4][5]

In photography

Getting sufficient depth of field can be particularly challenging in macro photography, because depth of field is smaller (shallower) for objects nearer the camera, so if a small object fills the frame, it is often so close that its entire depth cannot be in focus at once. Depth of field is normally increased by stopping down aperture (using a larger f-number), but beyond a certain point, stopping down causes blurring due to diffraction, which counteracts the benefit of being in focus. It also reduces the luminosity of the image. Focus stacking allows the depth of field of images taken at the sharpest aperture to be effectively increased. The images at right illustrate the increase in DOF that can be achieved by combining multiple exposures.

Stacked image of the Curiosity Rover's first sampling hole in Mount Sharp. The hole is 1.6 cm (0.63 in) wide and 6.7 cm (2.6 in) deep.

The Mars Science Laboratory mission has a device called Mars Hand Lens Imager (MAHLI), which can take photos that can later be focus stacked.[6]

In microscopy

In microscopy, high numerical apertures are desirable to capture as much light as possible from a small sample. A high numerical aperture (equivalent to a low f-number) gives a very shallow depth of field. Higher magnification objective lenses generally have shallower depth of field; a 100× objective lens with a numerical aperture of around 1.4 has a depth of field of approximately 1 μm. When observing a sample directly, the limitations of the shallow depth of field are easy to circumvent by focusing up and down through the sample; to effectively present microscopy data of a complex 3D structure in 2D, focus stacking is a very useful technique.

Atomic resolution scanning transmission electron microscopy encounters similar difficulties, where specimen features are much larger than the depth of field. By taking a through-focal series, the depth of focus can be reconstructed to create a single image entirely in focus.[7]

Software/application

Focus stacking software
Name Primary author Application type Platform License
Adobe Photoshop[8] CS4, CS5, CS6 Adobe Desktop Windows, Mac OS X Proprietary
Affinity Photo 'Focus Merge' Serif Desktop Windows, Mac OS X Proprietary
Aphelion with Multifocus extension ADCIS Desktop Windows Proprietary, 30-day trial
Amira / Avizo 'Image Stack Projection'[9] Thermo Fisher Desktop Windows, Mac OS X, Linux Proprietary
CamRanger CamRanger Desktop / Mobile iOS, Android, Mac OS X, Windows Proprietary
Chasys Draw IES John Paul Chacha Desktop Windows Proprietary
CombineZ Alan Hadley Desktop Windows GPL
CUVI Vision & Imaging Library TunaCode Desktop / Embedded Windows, Linux Proprietary
Enfuse (combined with align_image_stack or similar) Andrew Mihal and hugin development team Desktop Multiplatform GPL
FocusFusion DelphiTools Desktop Windows Proprietary
Focus Stacker Alexander Boltnev, Olga Kacher Desktop Mac OS X Proprietary
Focus Stacking Online[10] Focus Stacking Online Web application All Proprietary
Shutter Stream Product Photography Software Iconasys Desktop Windows, Mac OS X Proprietary
Helicon Focus Danylo Kozub Desktop Windows, Mac OS X Proprietary, 30-day trial
ImageJ with Extended Depth of Field Plugin Alex Prudencio, Jesse Berent, Daniel Sage Desktop Unix, Linux, Windows, Mac OS 9 and Mac OS X Public domain
MacroFusion[11] Dariusz Duma Desktop Linux GPL
Mathematica via ImageFocusCombine[12] Wolfram Research Desktop / Web Windows, Mac OS X, Linux Proprietary, 15-day trial
Picolay Heribert Cypionka Desktop Windows Freeware
QuickPHOTO with Deep Focus extension Promicra Desktop Windows Proprietary, 30-day trial
Zerene Stacker Rik Littlefield Desktop Windows, Mac OS X, Linux Proprietary, 30-day trial

Pictures

  • Pepper mill, stack of 28 frames
    Pepper mill, stack of 28 frames
  • Stacked image of 3 × 2.5 mm electric wires
    Stacked image of 3 × 2.5 mm electric wires
  • Shaver head, stack of 36 frames, retouched
    Shaver head, stack of 36 frames, retouched
  • Macrolepiota procera, stack of 15 frames
    Macrolepiota procera, stack of 15 frames
  • Stacked image of the inner ridge of an orchid blossom
    Stacked image of the inner ridge of an orchid blossom
  • Stacked image of two Arecaceae viewed through a hole in a tree trunk
    Stacked image of two Arecaceae viewed through a hole in a tree trunk
  • Pellet, stack of 32 frames
    Pellet, stack of 32 frames
  • Alluaudia comosa, stack of 10 frames
    Alluaudia comosa, stack of 10 frames
  • Mold on Litchi chinensis, stack of 20 frames
    Mold on Litchi chinensis, stack of 20 frames
  • Skull, stack of 6 frames
    Skull, stack of 6 frames
  • Sympetrum flaveolum male, stack of 36 frames
    Sympetrum flaveolum male, stack of 36 frames
  • Pinot Gris grape, stack of 12 frames.
    Pinot Gris grape, stack of 12 frames.

Videos

  • Video example of how focus stacking is applied to images

Diagrams

  • Software creates from the sharpest areas in a stack of sections.
    Software creates from the sharpest areas in a stack of sections.

See also

References

  1. ^ "Malin Space Science Systems - Mars Science Laboratory (MSL) Mars Hand Lens Imager (MAHLI) Instrument Description". Msss.com. Retrieved 2012-12-10.
  2. ^ Johnson, Dave (2008). How to Do Everything: Digital Camera (5th ed.). McGraw-Hill Osborne Media. p. 336. ISBN 978-0-07-149580-6. There are a number of programs that allow you to get the equivalent of infinite depth of field in your photos, with sharp focus from the foreground all the way back to the rear. How is this possible? By taking multiple photos of the same scene and stacking them afterwards into a composite that features only the sharpest bits of each image. One of the best is Helicon Focus.
  3. ^ Ray 2002, 231–232
  4. ^ "Afficher le sujet - Proposition d'un terme français pour "focus stacking" • Le Naturaliste". Lenaturaliste.net (in French). Retrieved 2012-10-05.
  5. ^ "Malin Space Science Systems - Mars Science Laboratory (MSL) Mars Hand Lens Imager (MAHLI) Instrument Description". Msss.com. Retrieved 2012-10-05.
  6. ^ "MSL Science Corner: Mars Hand Lens Imager (MAHLI)". MSL-SciCorner.JPL.NASA.gov. Archived from the original on 2009-03-20. Retrieved 2012-10-05.
  7. ^ Hovden, Robert; Xin, Huolin L.; Muller, David A. (2010). "Extended Depth of Field for High-Resolution Scanning Transmission Electron Microscopy". Microscopy and Microanalysis. 17 (1): 75–80. arXiv:1010.4500. Bibcode:2011MiMic..17...75H. doi:10.1017/S1431927610094171. PMID 21122192. S2CID 17082879.
  8. ^ "Focus Stacking Made Easy with Photoshop". Envato Tuts+. 2013-03-14. Retrieved 2023-04-17.
  9. ^ "Avizo User Guide, Module "Image Stack Projection"" (PDF). 2018-03-30.
  10. ^ "Focus stacking online - free online focus stacking application". FocusStackingOnline.com. Retrieved 2020-08-02.
  11. ^ "GUI to Combine Photos to Get Deeper DOF or HDR". SourceForge.net. 27 November 2016. Retrieved 2017-10-19.
  12. ^ "ImageFocusCombine". Retrieved 2021-09-11.
  • Ray, Sidney. 2002. Applied Photographic Optics. 3rd ed. Oxford: Focal Press. ISBN 0-240-51540-4.
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