Focus stacking

Last updated
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 Tachinid fly.jpg
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. FocusStack BrightFieldLightMicroscopy DiatomaceousEarth.jpg
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 known as focal plane merging and 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.

Contents

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 and light-field cameras.

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 Rovers first sampling hole in Mount Sharp. The hole is 1.6 cm (0.63 in) wide and 6.7 cm (2.6 in) deep. PIA18609 - First Sampling Hole in Mount Sharp .jpg
Stacked image of the Curiosity Rovers 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
NamePrimary authorApplication typePlatformLicense
Adobe Photoshop [8] CS4, CS5, CS6AdobeDesktopWindows, Mac OS XProprietary
Affinity Photo 'Focus Merge'SerifDesktopWindows, Mac OS XProprietary
Aphelion with Multifocus extensionADCISDesktopWindowsProprietary, 30-day trial
Amira / Avizo 'Image Stack Projection' [9] Thermofisher DesktopWindows, Mac OS X, LinuxProprietary
CamRangerCamRangerDesktop / MobileiOS, Android, Mac OS X, WindowsProprietary
Chasys Draw IES John Paul ChachaDesktopWindowsProprietary
CombineZ Alan HadleyDesktopWindows GPL
CUVI Vision & Imaging Library TunaCodeDesktop / EmbeddedWindows, LinuxProprietary
Enfuse (combined with align_image_stack or similar)Andrew Mihal and hugin development teamDesktopMultiplatform GPL
Focus StackerAlexander Boltnev, Olga KacherDesktopMac OS XProprietary
Focus Stacking Online [10] Focus Stacking OnlineWeb applicationAllProprietary
Shutter Stream Product Photography SoftwareIconasysDesktopWindows, Mac OS XProprietary
Helicon Focus Danylo KozubDesktopWindows, Mac OS XProprietary, 30-day trial
ImageJ with Extended Depth of Field PluginAlex Prudencio, Jesse Berent, Daniel SageDesktopUnix, Linux, Windows, Mac OS 9 and Mac OS XPublic domain
MacroFusion [11] Dariusz DumaDesktopLinux GPL
Mathematica via ImageFocusCombine [12] Wolfram Research Desktop / WebWindows, Mac OS X, LinuxProprietary, 15-day trial
PicolayHeribert CypionkaDesktopWindowsFreeware
QuickPHOTO with Deep Focus extensionPromicraDesktopWindowsProprietary, 30-day trial
Zerene StackerRik LittlefieldDesktopWindows, Mac OS X, LinuxProprietary, 30-day trial

Pictures

Videos

Diagrams

See also

Related Research Articles

<span class="mw-page-title-main">Depth of field</span> Distance between the nearest and the furthest objects that are in focus in an image

The depth of field (DOF) is the distance between the nearest and the furthest objects that are in acceptably sharp focus in an image captured with a camera.

<span class="mw-page-title-main">Aperture</span> Hole or opening through which light travels

In optics, an aperture is a hole or an opening through which light travels. More specifically, the aperture and focal length of an optical system determine the cone angle of a bundle of rays that come to a focus in the image plane.

<span class="mw-page-title-main">Bokeh</span> Aesthetic quality of blur in the out-of-focus parts of an image

In photography, bokeh is the aesthetic quality of the blur produced in out-of-focus parts of an image. Bokeh has also been defined as "the way the lens renders out-of-focus points of light". Differences in lens aberrations and aperture shape cause very different bokeh effects. Some lens designs blur the image in a way that is pleasing to the eye, while others produce distracting or unpleasant blurring. Photographers may deliberately use a shallow focus technique to create images with prominent out-of-focus regions, accentuating their lens's bokeh.

<span class="mw-page-title-main">Cinematography</span> Art of motion picture photography

Cinematography is the art of motion picture photography.

In photography, bracketing is the general technique of taking several shots of the same subject using different camera settings. Bracketing is useful and often recommended in situations that make it difficult to obtain a satisfactory image with a single shot, especially when a small variation in exposure parameters has a comparatively large effect on the resulting image. Given the time it takes to accomplish multiple shots, it is typically, but not always, used for static subjects. Autobracketing is a feature of many modern cameras. When set, it will automatically take several bracketed shots, rather than the photographer altering the settings by hand between each shot.

<span class="mw-page-title-main">Apochromat</span>

An apochromat, or apochromatic lens (apo), is a photographic or other lens that has better correction of chromatic and spherical aberration than the much more common achromat lenses.

<span class="mw-page-title-main">Prime lens</span> Camera lens with fixed focal length

In film and photography, a prime lens is a fixed focal length photographic lens, typically with a maximum aperture from f2.8 to f1.2. The term can also mean the primary lens in a combination lens system. Confusion between these two meanings can occur without clarifying context. Alternate terms, such as primary focal length, fixed focal length, or FFL are sometimes used to avoid ambiguity.

<span class="mw-page-title-main">Macro photography</span> Photography genre and techniques of extreme close-up pictures

Macro photography is extreme close-up photography, usually of very small subjects and living organisms like insects, in which the size of the subject in the photograph is greater than life size . By the original definition, a macro photograph is one in which the size of the subject on the negative or image sensor is life size or greater. In some senses, however, it refers to a finished photograph of a subject that is greater than life size.

<span class="mw-page-title-main">Confocal microscopy</span> Optical imaging technique

Confocal microscopy, most frequently confocal laser scanning microscopy (CLSM) or laser confocal scanning microscopy (LCSM), is an optical imaging technique for increasing optical resolution and contrast of a micrograph by means of using a spatial pinhole to block out-of-focus light in image formation. Capturing multiple two-dimensional images at different depths in a sample enables the reconstruction of three-dimensional structures within an object. This technique is used extensively in the scientific and industrial communities and typical applications are in life sciences, semiconductor inspection and materials science.

The science of photography is the use of chemistry and physics in all aspects of photography. This applies to the camera, its lenses, physical operation of the camera, electronic camera internals, and the process of developing film in order to take and develop pictures properly.

<span class="mw-page-title-main">Light field camera</span> Type of camera that can also capture the direction of travel of light rays

A light field camera, also known as a plenoptic camera, is a camera that captures information about the light field emanating from a scene; that is, the intensity of light in a scene, and also the precise direction that the light rays are traveling in space. This contrasts with conventional cameras, which record only light intensity.

The following are common definitions related to the machine vision field.

<span class="mw-page-title-main">Sports photography</span> Photography genre

Sports photography refers to the genre of photography that covers all types of sports.

Tilted plane focus

Tilted plane photography is a method of employing focus as a descriptive, narrative or symbolic artistic device. It is distinct from the more simple uses of selective focus which highlight or emphasise a single point in an image, create an atmospheric bokeh, or miniaturise an obliquely-viewed landscape. In this method the photographer is consciously using the camera to focus on several points in the image at once while de-focussing others, thus making conceptual connections between these points.

Köhler illumination is a method of specimen illumination used for transmitted and reflected light optical microscopy. Köhler illumination acts to generate an even illumination of the sample and ensures that an image of the illumination source is not visible in the resulting image. Köhler illumination is the predominant technique for sample illumination in modern scientific light microscopy. It requires additional optical elements which are more expensive and may not be present in more basic light microscopes.

<span class="mw-page-title-main">Optical sectioning</span> Imaging of focal planes within a thick sample

Optical sectioning is the process by which a suitably designed microscope can produce clear images of focal planes deep within a thick sample. This is used to reduce the need for thin sectioning using instruments such as the microtome. Many different techniques for optical sectioning are used and several microscopy techniques are specifically designed to improve the quality of optical sectioning.

In photography, a long-focus lens is a camera lens which has a focal length that is longer than the diagonal measure of the film or sensor that receives its image. It is used to make distant objects appear magnified with magnification increasing as longer focal length lenses are used. A long-focus lens is one of three basic photographic lens types classified by relative focal length, the other two being a normal lens and a wide-angle lens. As with other types of camera lenses, the focal length is usually expressed in a millimeter value written on the lens, for example: a 500 mm lens. The most common type of long-focus lens is the telephoto lens, which incorporate a special lens group known as a telephoto group to make the physical length of the lens shorter than the focal length.

The Pentax Q series is a series of mirrorless interchangeable-lens cameras made by Pentax and introduced in 2011 with the initial model Pentax Q. As of September 2012, it was the world's smallest, lightest interchangeable lens digital camera. The first models used a 1/2.3" back-illuminated sensor CMOS image sensor. The Q7, introduced in June 2013, uses a larger 1/1.7" type sensor. The Q system is now discontinued.

<span class="mw-page-title-main">Mars Hand Lens Imager</span>

Mars Hand Lens Imager (MAHLI) is one of seventeen cameras on the Curiosity rover on the Mars Science Laboratory mission.

<span class="mw-page-title-main">Brenizer Method</span>

The Brenizer Method, sometimes referred to as Bokeh Panorama or Bokehrama, is a photographic technique characterized by the creation of a digital image exhibiting a shallow depth of field in tandem with a wide angle of view. Created by use of panoramic stitching techniques applied to portraiture, it was popularized by photographer Ryan Brenizer.

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". photo.tutsplus.com. Retrieved 2013-07-01.
  9. "Avizo User Guide, Module "Image Stack Projection"". 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. Retrieved 2017-10-19.
  12. "ImageFocusCombine" . Retrieved 2021-09-11.