Light Field Microscopy
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Light Field Microscopy
Light field microscopy (LFM) is a scanning-free 3-dimensional (3D) microscopic imaging method based on the theory of light field. This technique allows sub-second (~10 Hz) large volumetric imaging ( 0.1 to 1 mmsup>3) with ~1 μm spatial resolution in the condition of weak scattering and semi-transparence, which has never been achieved by other methods. Just as in traditional light field rendering, there are two steps for LFM imaging: light field capture and processing. In most setups, a microlens array is used to capture the light field. As for processing, it can be based on two kinds of representations of light propagation: the ray optics picture and the wave optics picture. The Stanford University Computer Graphics Laboratory published their first prototype LFM in 2006 and has been working on the cutting edge since then. Light field generation A light field is a collection of all the rays flowing through some free space, where each ray can be parameterized with four ...
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Light Field
The light field is a vector function that describes the amount of light flowing in every direction through every point in space. The space of all possible '' light rays'' is given by the five-dimensional plenoptic function, and the magnitude of each ray is given by its radiance. Michael Faraday was the first to propose that light should be interpreted as a field, much like the magnetic fields on which he had been working. The phrase ''light field'' was coined by Andrey Gershun in a classic 1936 paper on the radiometric properties of light in three-dimensional space. Modern approaches to light field display explore co-designs of optical elements and compressive computation to achieve higher resolutions, increased contrast, wider fields of view, and other benefits. The term “radiance field” may also be used to refer to similar concepts. The term is used in modern research such as neural radiance fields. The plenoptic function For geometric optics—i.e., to incoherent ligh ...
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Light-field Camera
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 at various wavelengths. One type uses an array of micro-lenses placed in front of an otherwise conventional image sensor to sense intensity, color, and directional information. Multi-camera arrays are another type. Holograms are a type of film-based light field image. History Early research The first light field camera was proposed by Gabriel Lippmann in 1908. He called his concept "integral photography". Lippmann's experimental results included crude integral photographs made by using a plastic sheet embossed with a regular array of microlenses, or by partially embedding small glass beads, closely packed in a random pattern, into the sur ...
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Aperture Synthesis
Aperture synthesis or synthesis imaging is a type of interferometry that mixes signals from a collection of telescopes to produce images having the same angular resolution as an instrument the size of the entire collection. At each separation and orientation, the lobe-pattern of the interferometer produces an output which is one component of the Fourier transform of the spatial distribution of the brightness of the observed object. The image (or "map") of the source is produced from these measurements. Astronomical interferometers are commonly used for high-resolution optical, infrared, submillimetre and radio astronomy observations. For example, the Event Horizon Telescope project derived the first image of a black hole using aperture synthesis. Technical issues Aperture synthesis is possible only if both the amplitude and the phase of the incoming signal are measured by each telescope. For radio frequencies, this is possible by electronics, while for optical frequencies, th ...
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Tomography
Tomography is imaging by sections or sectioning that uses any kind of penetrating wave. The method is used in radiology, archaeology, biology, atmospheric science, geophysics, oceanography, plasma physics, materials science, astrophysics, quantum information, and other areas of science. The word ''tomography'' is derived from Ancient Greek τόμος ''tomos'', "slice, section" and γράφω ''graphō'', "to write" or, in this context as well, "to describe." A device used in tomography is called a tomograph, while the image produced is a tomogram. In many cases, the production of these images is based on the mathematical procedure tomographic reconstruction, such as X-ray computed tomography technically being produced from multiple projectional radiographs. Many different reconstruction algorithms exist. Most algorithms fall into one of two categories: filtered back projection (FBP) and iterative reconstruction (IR). These procedures give inexact results: they represent a compr ...
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Microlens
A microlens is a small lens, generally with a diameter less than a millimetre (mm) and often as small as 10 micrometres (µm). The small sizes of the lenses means that a simple design can give good optical quality but sometimes unwanted effects arise due to optical diffraction at the small features. A typical microlens may be a single element with one plane surface and one spherical convex surface to refract the light. Because micro-lenses are so small, the substrate that supports them is usually thicker than the lens and this has to be taken into account in the design. More sophisticated lenses may use aspherical surfaces and others may use several layers of optical material to achieve their design performance. A different type of microlens has two flat and parallel surfaces and the focusing action is obtained by a variation of refractive index across the lens. These are known as gradient-index (GRIN) lenses. Some micro-lenses achieve their focusing action by both a variation ...
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Light Field
The light field is a vector function that describes the amount of light flowing in every direction through every point in space. The space of all possible '' light rays'' is given by the five-dimensional plenoptic function, and the magnitude of each ray is given by its radiance. Michael Faraday was the first to propose that light should be interpreted as a field, much like the magnetic fields on which he had been working. The phrase ''light field'' was coined by Andrey Gershun in a classic 1936 paper on the radiometric properties of light in three-dimensional space. Modern approaches to light field display explore co-designs of optical elements and compressive computation to achieve higher resolutions, increased contrast, wider fields of view, and other benefits. The term “radiance field” may also be used to refer to similar concepts. The term is used in modern research such as neural radiance fields. The plenoptic function For geometric optics—i.e., to incoherent ligh ...
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Zebrafish
The zebrafish (''Danio rerio'') is a freshwater fish belonging to the minnow family ( Cyprinidae) of the order Cypriniformes. Native to South Asia, it is a popular aquarium fish, frequently sold under the trade name zebra danio (and thus often called a "tropical fish" although both tropical and subtropical). It is also found in private ponds. The zebrafish is an important and widely used vertebrate model organism in scientific research, for example in drug development, in particular pre-clinical development. It is also notable for its regenerative abilities, and has been modified by researchers to produce many transgenic strains. Taxonomy The zebrafish is a derived member of the genus '' Brachydanio'', of the family Cyprinidae. It has a sister-group relationship with ''Danio aesculapii''. Zebrafish are also closely related to the genus ''Devario'', as demonstrated by a phylogenetic tree of close species. Distribution Range The zebrafish is native to fresh water h ...
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Calcium Imaging
Calcium imaging is a microscopy technique to optically measure the calcium (Ca2+) status of an isolated cell, tissue or medium. Calcium imaging takes advantage of calcium indicators, fluorescent molecules that respond to the binding of Ca2+ ions by fluorescence properties. Two main classes of calcium indicators exist: chemical indicators and genetically encoded calcium indicators (GECI). This technique has allowed studies of calcium signalling in a wide variety of cell types. In neurons, electrical activity is always accompanied by an influx of Ca2+ ions. Thus, calcium imaging can be used to monitor the electrical activity in hundreds of neurons in cell culture or in living animals, which has made it possible to dissect the function of neuronal circuits. Chemical indicators Chemical indicators are small molecules that can chelate calcium ions. All these molecules are based on an EGTA homologue called BAPTA, with high selectivity for calcium (Ca2+) ions versus magnesium (Mg2+) io ...
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Shot Noise
Shot noise or Poisson noise is a type of noise which can be modeled by a Poisson process. In electronics shot noise originates from the discrete nature of electric charge. Shot noise also occurs in photon counting in optical devices, where shot noise is associated with the particle nature of light. Origin In a statistical experiment such as tossing a fair coin and counting the occurrences of heads and tails, the numbers of heads and tails after many throws will differ by only a tiny percentage, while after only a few throws outcomes with a significant excess of heads over tails or vice versa are common; if an experiment with a few throws is repeated over and over, the outcomes will fluctuate a lot. From the law of large numbers, one can show that the relative fluctuations reduce as the reciprocal square root of the number of throws, a result valid for all statistical fluctuations, including shot noise. Shot noise exists because phenomena such as light and electric current co ...
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Fresnel Diffraction
In optics, the Fresnel diffraction equation for near-field diffraction is an approximation of the Kirchhoff–Fresnel diffraction that can be applied to the propagation of waves in the near field. It is used to calculate the diffraction pattern created by waves passing through an aperture or around an object, when viewed from relatively close to the object. In contrast the diffraction pattern in the far field region is given by the Fraunhofer diffraction equation. The near field can be specified by the Fresnel number, , of the optical arrangement. When F \gg 1 the diffracted wave is considered to be in the near field. However, the validity of the Fresnel diffraction integral is deduced by the approximations derived below. Specifically, the phase terms of third order and higher must be negligible, a condition that may be written as \frac \ll 1, where \theta is the maximal angle described by \theta \approx a/L, and the same as in the definition of the Fresnel number. The m ...
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Bessel Function
Bessel functions, first defined by the mathematician Daniel Bernoulli and then generalized by Friedrich Bessel, are canonical solutions of Bessel's differential equation x^2 \frac + x \frac + \left(x^2 - \alpha^2 \right)y = 0 for an arbitrary complex number \alpha, the ''order'' of the Bessel function. Although \alpha and -\alpha produce the same differential equation, it is conventional to define different Bessel functions for these two values in such a way that the Bessel functions are mostly smooth functions of \alpha. The most important cases are when \alpha is an integer or half-integer. Bessel functions for integer \alpha are also known as cylinder functions or the cylindrical harmonics because they appear in the solution to Laplace's equation in cylindrical coordinates. Spherical Bessel functions with half-integer \alpha are obtained when the Helmholtz equation is solved in spherical coordinates. Applications of Bessel functions The Bessel function is a generalizat ...
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Numerical Aperture
In optics, the numerical aperture (NA) 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 material to another, provided there is no refractive power at the interface. The exact definition of the term varies slightly between different areas of optics. Numerical aperture is commonly used in microscopy to describe the acceptance cone of an objective (and hence its light-gathering ability and resolution), and in fiber optics, in which it describes the range of angles within which light that is incident on the fiber will be transmitted along it. General optics In most areas of optics, and especially in microscopy, the numerical aperture of an optical system such as an objective lens is defined by :\mathrm = n \sin \theta, where is the index of refraction of the medium i ...
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