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Amira (ah-MEER-ah) is a software platform for visualization, processing, and analysis of 3D and 4D data. It is being actively developed by Thermo Fisher Scientific in collaboration with the Zuse Institute Berlin (ZIB), and commercially distributed by Thermo Fisher Scientific — together with its sister software Avizo.
PSF Lab is a software program that allows the calculation of the illumination point spread function (PSF) of a confocal microscope under various imaging conditions. The calculation of the electric field vectors is based on a rigorous, vectorial model that takes polarization effects in the near-focus region and high numerical aperture microscope objectives into account.
Fluorescence and confocal microscopes operating principle. Confocal microscopy, most frequently confocal laser scanning microscopy (CLSM) or laser scanning confocal microscopy (LSCM), 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. [1]
Confocal endoscopy, or confocal laser endomicroscopy (CLE), is a modern imaging technique that allows the examination of real-time microscopic and histological features inside the body. In the word "endomicroscopy", endo- means "within" and -skopein means "to view or observe".
Confocal microscopy was then introduced in 1960 which decreased the background and exposure time of the sample by directing light to a pinpoint and illuminating cones of light into the sample. In the 1980s, the introduction of TIRFM further decreased background and exposure time by only illuminating the thin section of the sample being examined.
Taking the example of a current high definition (HD) video system, with 1920 by 1080 pixels, the Nyquist theorem states that it should be possible, in a perfect system, to resolve fully (with true black to white transitions) a total of 1920 black and white alternating lines combined, otherwise referred to as a spatial frequency of 1920/2=960 ...
Avizo (pronounce: ‘a-VEE-zo’) is a general-purpose commercial software application for scientific and industrial data visualization and analysis.. Avizo is developed by Thermo Fisher Scientific and was originally designed and developed by the Visualization and Data Analysis Group [1] at Zuse Institute Berlin (ZIB) under the name Amira.
Confocal stacks will require 3D processing and widefield pseudo-stacks will often benefit from digital deconvolution to remove the out-of-focus light. The advent of automated microscopes that can acquire many images automatically is one of the reasons why analysis cannot be done by eye (otherwise, annotation would rapidly become the research ...