A key difference between confocal microscopy and widefield microscopy is that the aim of confocal is to explore the structure and structural relationships along the optical (Z) axis as well as in the X-Y plane. In other words, the investigation of spatial relationships is being evaluated in at least three dimensions. Often, this involves the collection of a series of planar images along the Z axis and the reconstruction of the data into an image that depicts all three dimensions. However, even when the interest is solely in a single X-Y plane, the goal is to separate as thin a plane of information as possible from the planes directly above and below. Obviously, in order to acquire and analyze three-dimensional (3D) structural information, the 3D structural relationships must be preserved during the preparation of the sample. In contrast, in standard widefield microscopy information along the Z-axis is merged into a single 2D image. Because of the added need to preserve the 3D structure for confocal images, methods suitable for preparing samples for widefield microscopy must often be altered to accommodate the additional demand of preserving relationships in the third dimension.
Objective lens Paraformaldehyde/formaldehyde Photobleaching Refractive index Refractive index mismatch Signal-to-noise ratio Working distance
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