Focus stacking
Encyclopedia
Focus stacking 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 (Johnson 2008, 336; Ray 2002, 231–232). 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 offers flexibility; as focus stacking is a computational technique images with several different depths of field can be generated in postprocessing 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 plenoptic camera
s.
or fourier analysis, or selected manually. The in-focus patches are then blended together to generate the final image.
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. 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.
s are desirable to capture as much light as possible from a small sample. A high numerical aperture is equivalent to a low f number and 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 microscopes encounter 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.
Digital image processing
Digital image processing is the use of computer algorithms to perform image processing on digital images. As a subcategory or field of digital signal processing, digital image processing has many advantages over analog image processing...
technique which combines multiple images taken at different focus distances to give a resulting image with a greater depth of field
Depth of field
In optics, particularly as it relates to film and photography, depth of field is the distance between the nearest and farthest objects in a scene that appear acceptably sharp in an image...
(DOF) than any of the individual source images (Johnson 2008, 336; Ray 2002, 231–232). Focus stacking can be used in any situation where individual images have a very shallow depth of field, macro photography
Macro photography
Macrophotography is close-up photography, usually of very small subjects. Classically a macrophotograph is one in which the size of the subject on the negative is greater than life size. However in modern use it refers to a finished photograph of a subject at greater than life size...
and optical microscopy
Optical microscope
The optical microscope, often referred to as the "light microscope", is a type of microscope which uses visible light and a system of lenses to magnify images of small samples. Optical microscopes are the oldest design of microscope and were possibly designed in their present compound form in the...
are two typical examples.
Focus stacking offers flexibility; as focus stacking is a computational technique images with several different depths of field can be generated in postprocessing 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
Wavefront coding
In optics and signal processing, wavefront coding is a method for creating optical transfer functions of lenses with specially designed phase masks, encoding, to produce point spread functions of visible light, images, with manipulatable information such as depth of field and distance.Wavefront...
and plenoptic camera
Plenoptic camera
A light-field camera, also called a plenoptic camera, is a camera that uses a microlens array to capture 4D light field information about a scene...
s.
Technique
The starting point for focus stacking is a series of images captured at different focal depths, in each image different areas of the sample will be in focus. While none of these images have 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 detectionEdge detection
Edge detection is a fundamental tool in image processing and computer vision, particularly in the areas of feature detection and feature extraction, which aim at identifying points in a digital image at which the image brightness changes sharply or, more formally, has discontinuities...
or fourier analysis, or selected manually. The in-focus patches are then blended together to generate the final image.
In photography
Getting sufficient depth of fieldDepth of field
In optics, particularly as it relates to film and photography, depth of field is the distance between the nearest and farthest objects in a scene that appear acceptably sharp in an image...
can be particularly challenging in macro photography
Macro photography
Macrophotography is close-up photography, usually of very small subjects. Classically a macrophotograph is one in which the size of the subject on the negative is greater than life size. However in modern use it refers to a finished photograph of a subject at greater than life size...
, 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. 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.
In microscopy
In microscopy high numerical apertureNumerical aperture
In optics, the numerical aperture of an optical system is a dimensionless number that characterizes the range of angles over which the system can accept or emit light. By incorporating index of refraction in its definition, NA has the property that it is constant for a beam as it goes from one...
s are desirable to capture as much light as possible from a small sample. A high numerical aperture is equivalent to a low f number and 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 microscopes encounter 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.
Software
| Name | Primary author | Platform | License |
|---|---|---|---|
| ALE | David Hilvert | Linux, Windows | GPL GNU General Public License The GNU General Public License is the most widely used free software license, originally written by Richard Stallman for the GNU Project.... |
| CombineZM CombineZM CombineZM is an open source image processing software package for creating extended depth of field images. It runs on Windows XP and 2000. CombineZM is based on CombineZ5, a program which runs on older versions of Windows and is no longer maintained... / CombineZP |
Alan Hadley | Windows | GPL GNU General Public License The GNU General Public License is the most widely used free software license, originally written by Richard Stallman for the GNU Project.... |
| Helicon Focus Helicon Focus Helicon Focus is a proprietary commercial digital image processing tool, first released in 2003, developed and published by Helicon Soft Limited... |
Danylo Kozub | Windows, Mac OS X | Proprietary, 30-day trial |
| Extended Depth of Field plugin for ImageJ ImageJ ImageJ is a public domain, Java-based image processing program developed at the National Institutes of Health. ImageJ was designed with an open architecture that provides extensibility via Java plugins and recordable macros. Custom acquisition, analysis and processing plugins can be developed using... |
Alex Prudencio | Multi-platform (Java) | Free for use for research purposes |
| PhotoAcute Studio | Almalence Inc | Windows, Mac OS X, Linux | Proprietary, time-unlimited trial |
| Stack Focuser plugin for ImageJ ImageJ ImageJ is a public domain, Java-based image processing program developed at the National Institutes of Health. ImageJ was designed with an open architecture that provides extensibility via Java plugins and recordable macros. Custom acquisition, analysis and processing plugins can be developed using... |
Michael Umorin | Multi-platform (Java) | GPL GNU General Public License The GNU General Public License is the most widely used free software license, originally written by Richard Stallman for the GNU Project.... |
| Adobe Photoshop Adobe Photoshop Adobe Photoshop is a graphics editing program developed and published by Adobe Systems Incorporated.Adobe's 2003 "Creative Suite" rebranding led to Adobe Photoshop 8's renaming to Adobe Photoshop CS. Thus, Adobe Photoshop CS5 is the 12th major release of Adobe Photoshop... CS4 |
Adobe | Windows, Mac OS X | Proprietary |
| Enfuse (combined with align_image_stack or similar) | Andrew Mihal and hugin Hugin (software) Hugin is a cross-platform open source panorama photo stitching and HDR merging program developed by Pablo d'Angelo and others. It is a GUI front-end for Helmut Dersch's Panorama Tools and Andrew Mihal's Enblend and Enfuse... development team |
Multiplatform | GPL GNU General Public License The GNU General Public License is the most widely used free software license, originally written by Richard Stallman for the GNU Project.... |
| Macnification | Peter Schols | Mac OS X | Proprietary, 30-day trial |
| Zerene Stacker | Rik Littlefield | Windows, Mac OS X, Linux | Proprietary, 30-day trial |
| Image Pro Plus | Media Cybernetics | Windows | Proprietary |
| Zeiss Axiovision | Carl Zeiss AG | Windows | |
| Tufuse | Max Lyons | Windows |
See also
- High dynamic range imagingHigh dynamic range imagingIn image processing, computer graphics, and photography, high dynamic range imaging is a set of techniques that allows a greater dynamic range between the lightest and darkest areas of an image than current standard digital imaging techniques or photographic methods...
(HDR) - Image stitchingImage stitchingImage stitching or photo stitching is the process of combining multiple photographic images with overlapping fields of view to produce a segmented panorama or high-resolution image. Commonly performed through the use of computer software, most approaches to image stitching require nearly exact...
- Deconvolution microscopy
- Focus bracketing
External links
- Online article by Rik Littlefield.
- Link directory Focus stacking (Extended Depth of Field).
- Focus stacking Pictures and technic.