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Confocal microscopy forms an image by scanning a localized illumination spot and preferentially detecting light from the same small region. In a thick specimen emitting fluorescence, a conventional fluorescence microscope also collects a haze from material away from the selected optical focus. Confocal optical sectioning suppresses that haze, revealing structure at a chosen depth without cutting the specimen. The useful idea is a paired selection: where excitation occurs, and which emitted photons reach the photodetector. ^[ref]

The scope here is single-point, linear fluorescence imaging. Confocal microscopy can also use reflected light; its broader implementations need not all have the same scanning mechanism. The patent Microscopy apparatus, US3013467A, by Marvin Minsky describes a point source imaged onto a specimen, a second pinhole receiving its image, specimen scanning, and a synchronized display. It was filed on 7 November 1957 and published on 19 December 1961; the filing date should not be described as the grant date. This is evidence for that apparatus and those dates, rather than a claim that all later fluorescence instruments were already present in it. ^[ref]

At one depth, scan the illumination spot across $x$ and $y$ and assign the detector reading during each dwell interval to a pixel. Move the specimen or objective optical lens axially to acquire the next depth. A stack of these optical sections samples three-dimensional structure. With beam scanning, the returning fluorescence commonly retraces the scanning optics: this descanning holds the image of the currently illuminated point at the detection pinhole. With stage scanning, the fixed spot and pinhole remain aligned while the specimen moves. ^[ref]

An optical section is a depth-weighted image of an intact specimen, with a finite axial response and tails. A physical cut actually separates a slice of material; its thickness and cutting damage are properties of the preparation. Changing optical focus selects another optical section without removing a slice, although illumination can still damage a specimen. Neither a thin physical slice nor a sharply displayed optical section makes the imaging point spread function infinitely narrow. ^[ref]

Point response and section thickness answer different questions. For a spatially uniform, very thin fluorescent sheet, its response versus axial displacement is proportional to the lateral integral of the three-dimensional confocal response,Consequently a trace through a single bead, $H_a(0,0,z)$, does not by itself give the sheet's optical-section thickness. State which object and which full width at half maximum are being measured. A smaller axial sampling step gives more samples of the same response, rather than automatically improving diffraction-limited resolution. ^[ref]