A laser scanning cytometer (LSC) is a device used to make stoichiometric measurements of a population of cells on a microscope slide. A researcher will stain a slide with one or more fluorescent dyes. The cells will take up the dyes and the dyes will attach to various chemicals (for instance DNA or a particular protein) in proportion to that constituent's presence in the cell. The LSC then scans the slide with a laser which causes the dye at the laser spot to flouresce. The LSC records the magnitude of the resultant light which is proportional to the amount of chemical in the cell.

The LSC has a passing resemblance to a confocal microscope(Marvin Minsky's most useful invention). It scans a laser spot across a slide and its optics are arranged so that the light both travels down and up the same path; this is the same mechanism used by laser scanning confocal microscopes. However, the LSC has more in common with a flow cytometer in that its optics are designed so that the laser spot has a large depth of field and the laser thus illuminates a cylinder cross-section through the whole of the cell. The LSC scans this cylinder across the slide, creating a pixel image of the cells on the slide. It then uses image proceessing techniques to identify groups of pixels as a cell and performs arithmetic and morphological measurements on those pixels to generate useful metrics.

The LSC has some advantages over traditional flow cytometry. In flow cytometry, the cells pass in a fluid through a capillary tube and afterwards are difficult to capture or re-identify. In laser scanning cytometry, the cells are fixed to a slide and their position is recorded; a researcher can return to the location of a cell and inspect it visually and can examine galleries of cells, all of which fall within a defined range of measured parameters. Also, since laser scanning cytometry uses cells mounted on a slide, it uses smaller volumes of reagent than flow. Some preparations are easier to make on a slide, enabling the LSC to measure some specimens that are inaccessible for flow.

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