Microscope image processing is a broad term that covers the use of digital image processing techniques to process, analyze and present images obtained from a microscope. Such processing is now commonplace in a number of diverse fields such as medicine, biological research, cancer research, drug testing, metallurgy, etc. A number of manufacturers of microscopes now specifically design in features that allow the microscopes to interface to an image processing system.
Three-dimensional space is a geometric setting in which three values are required to determine the position of an element. This is the informal meaning of the term dimension.
Microscopy is the technical field of using microscopes to view objects and areas of objects that cannot be seen with the naked eye. There are three well-known branches of microscopy: optical, electron, and scanning probe microscopy, along with the emerging field of X-ray microscopy.
The restoration is based on different deconvolutionalgorithms, that permit the recovery of objects from images that are degraded by blurring and noise. In microscopy the blurring is largely due to diffraction limited imaging by the instrument; the noise is usually photon noise.
In mathematics, deconvolution is an algorithm-based process used to reverse the effects of convolution on recorded data. The concept of deconvolution is widely used in the techniques of signal processing and image processing. Because these techniques are in turn widely used in many scientific and engineering disciplines, deconvolution finds many applications.
In mathematics and computer science, an algorithm is an unambiguous specification of how to solve a class of problems. Algorithms can perform calculation, data processing, automated reasoning, and other tasks.
Diffraction refers to various phenomena that occur when a wave encounters an obstacle or a slit. It is defined as the bending of waves around the corners of an obstacle or aperture into the region of geometrical shadow of the obstacle. In classical physics, the diffraction phenomenon is described as the interference of waves according to the Huygens–Fresnel principle that treats each point in the wave-front as a collection of individual spherical wavelets. These characteristic behaviors are exhibited when a wave encounters an obstacle or a slit that is comparable in size to its wavelength. Similar effects occur when a light wave travels through a medium with a varying refractive index, or when a sound wave travels through a medium with varying acoustic impedance. Diffraction has an impact on the acoustic space. Diffraction occurs with all waves, including sound waves, water waves, and electromagnetic waves such as visible light, X-rays and radio waves.
Scientific visualization is an interdisciplinary branch of science concerned with the visualization of scientific phenomena. It is also considered a subset of computer graphics, a branch of computer science. The purpose of scientific visualization is to graphically illustrate scientific data to enable scientists to understand, illustrate, and glean insight from their data.
The Simulated Fluorescence Process (SFP) is a computing algorithm used for scientific visualization of 3D data from, for example, fluorescence microscopes. By modeling a physical light/matter interaction process an image is computed showing the data as it would have appeared in reality when viewed under these conditions.
An isosurface is a three-dimensional analog of an isoline. It is a surface that represents points of a constant value within a volume of space; in other words, it is a level set of a continuous function whose domain is 3D-space.
Huygens software is named after the Dutch physicist Christiaan Huygens who is perhaps best known for his argument that light behaves like waves. Since wave diffraction plays a key role in the Huygens Software, it was named after him.
Christiaan Huygens was a Dutch physicist, mathematician, astronomer and inventor, who is widely regarded as one of the greatest scientists of all time and a major figure in the scientific revolution. In physics, Huygens made groundbreaking contributions in optics and mechanics, while as an astronomer he is chiefly known for his studies of the rings of Saturn and the discovery of its moon Titan. As an inventor, he improved the design of the telescope with the invention of the Huygenian eyepiece. His most famous invention, however, was the invention of the pendulum clock in 1656, which was a breakthrough in timekeeping and became the most accurate timekeeper for almost 300 years. Because he was the first to use mathematical formulae to describe the laws of physics, Huygens has been called the first theoretical physicist and the founder of mathematical physics.
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Angular resolution or spatial resolution describes the ability of any image-forming device such as an optical or radio telescope, a microscope, a camera, or an eye, to distinguish small details of an object, thereby making it a major determinant of image resolution. In physics and geosciences, the term spatial resolution refers to the precision of a measurement with respect to space.
Tomography is imaging by sections or sectioning, through the use of 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". A device used in tomography is called a tomograph, while the image produced is a tomogram.
Unsharp masking (USM) is an image sharpening technique, often available in digital image processing software.
In scientific visualization and computer graphics, volume rendering is a set of techniques used to display a 2D projection of a 3D discretely sampled data set, typically a 3D scalar field.
The point spread function (PSF) describes the response of an imaging system to a point source or point object. A more general term for the PSF is a system's impulse response, the PSF being the impulse response of a focused optical system. The PSF in many contexts can be thought of as the extended blob in an image that represents an unresolved object. In functional terms it is the spatial domain version of the optical transfer function of the imaging system. It is a useful concept in Fourier optics, astronomical imaging, medical imaging, electron microscopy and other imaging techniques such as 3D microscopy and fluorescence microscopy. The degree of spreading (blurring) of the point object is a measure for the quality of an imaging system. In non-coherent imaging systems such as fluorescent microscopes, telescopes or optical microscopes, the image formation process is linear in power and described by linear system theory. This means that when two objects A and B are imaged simultaneously, the result is equal to the sum of the independently imaged objects. In other words: the imaging of A is unaffected by the imaging of B and vice versa, owing to the non-interacting property of photons. The image of a complex object can then be seen as a convolution of the true object and the PSF. However, when the detected light is coherent, image formation is linear in the complex field. Recording the intensity image then can lead to cancellations or other non-linear effects.
Super-resolution imaging (SR) is a class of techniques that enhance the resolution of an imaging system. In some SR techniques—termed optical SR—the diffraction limit of systems is transcended, while in others—geometrical SR—the resolution of digital imaging sensors is enhanced.
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. 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.
SVI may refer to:
Coherent diffractive imaging (CDI) is a “lensless” technique for 2D or 3D reconstruction of the image of nanoscale structures such as nanotubes, nanocrystals, porous nanocrystalline layers, defects, potentially proteins, and more. In CDI, a highly coherent beam of x-rays, electrons or other wavelike particle or photon is incident on an object.
Ptychography is a computational method of microscopic imaging. It generates images by processing many coherent interference patterns that have been scattered from an object of interest. Its defining characteristic is translational invariance, which means the interference patterns are generated by one constant function moving laterally by a known amount with respect to another constant function. The interference patterns occur some distance away from these two components, so that the scattered waves spread out and ‘fold into’ one another, as shown in the figure.
Vertico spatially modulated illumination (Vertico-SMI) is the fastest light microscope for the 3D analysis of complete cells in the nanometer range. It is based on two technologies developed in 1996, SMI and SPDM. The effective optical resolution of this optical nanoscope has reached the vicinity of 5 nm in 2D and 40 nm in 3D and surpasses the 200 nm resolution limit predicted by Abbe‘s law. Abbe postulated in 1873 the theoretical limit of resolution of optical microscopy.
Image Restoration is the operation of taking a corrupt/noisy image and estimating the clean, original image. Corruption may come in many forms such as motion blur, noise and camera mis-focus. Image restoration is performed by reversing the process that blurred the image and such is performed by imaging a point source and use the point source image, which is called the Point Spread Function (PSF) to restore the image information lost to the blurring process.
Super-resolution microscopy, in light microscopy, is a term that gathers several techniques, which allow images to be taken with a higher resolution than the one imposed by the diffraction limit. Due to the diffraction of light, the resolution in conventional light microscopy is limited, as stated by Ernst Abbe in 1873. In this context, a diffraction-limited microscope with numerical aperture N.A. and light with wavelength λ reaches a lateral resolution of d = λ/(2 N.A.) - a similar formalism can be followed for the axial resolution. The resolution for a standard optical microscope in the visible light spectrum is about 200 nm laterally and 600 nm axially. Experimentally, the attained resolution can be measured from the full width at half maximum (FWHM) of the point spread function (PSF) using images of point-like objects. Although the resolving power of a microscope is not well defined, it is generally considered that a super-resolution microscopy technique offers a resolution better than the one stipulated by Abbe.
Single particle analysis is a group of related computerized image processing techniques used to analyze images from transmission electron microscopy (TEM). These methods were developed to improve and extend the information obtainable from TEM images of particulate samples, typically proteins or other large biological entities such as viruses. Individual images of stained or unstained particles are very noisy, and so hard to interpret. Combining several digitized images of similar particles together gives an image with stronger and more easily interpretable features. An extension of this technique uses single particle methods to build up a three-dimensional reconstruction of the particle. Using cryo-electron microscopy it has become possible to generate reconstructions with sub-nanometer resolution and near-atomic resolution first in the case of highly symmetric viruses, and now in smaller, asymmetric proteins as well.
Digital holographic microscopy (DHM) is digital holography applied to microscopy. Digital holographic microscopy distinguishes itself from other microscopy methods by not recording the projected image of the object. Instead, the light wave front information originating from the object is digitally recorded as a hologram, from which a computer calculates the object image by using a numerical reconstruction algorithm. The image forming lens in traditional microscopy is thus replaced by a computer algorithm.
Other closely related microscopy methods to digital holographic microscopy are interferometric microscopy, optical coherence tomography and diffraction phase microscopy. Common to all methods is the use of a reference wave front to obtain amplitude (intensity) and phase information. The information is recorded on a digital image sensor or by a photodetector from which an image of the object is created (reconstructed) by a computer. In traditional microscopy, which do not use a reference wave front, only intensity information is recorded and essential information about the object is lost.
Holographic interference microscopy
(HIM) is holographic interferometry applied for microscopy for visualization of phase micro-objects. Phase micro-objects are invisible because they do not change intensity of light, they insert only invisible phase shifts. The holographic interference microscopy distinguishes itself from other microscopy methods by using a hologram and the interference for converting invisible phase shifts into intensity changes.
The Aphelion Imaging Software Suite is a software suite that includes three base products - Aphelion Lab, Aphelion Dev, and Aphelion SDK for addressing image processing and image analysis applications. The suite also includes a set of extension programs to implement specific vertical applications that benefit from imaging techniques.
