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About Confocal Microscopy: From the Pinhole to Quantitative 3D Imaging

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You will learn why a pinhole conjugate to the focal plane rejects out-of-focus light, and how that single trick turns a fluorescence microscope into an optical sectioning instrument. You will be able to choose between point-scanning and spinning-disk architectures, set pinhole size in Airy units, pick filters or spectral detection, and tune detector gain and offset for the photon budget you actually have. You will acquire Nyquist-sampled z-stacks, reconstruct them in 3D, and control photobleaching and phototoxicity in live cells. Finally you will separate overlapping dyes by linear unmixing, quantify colocalization defensibly, and place confocal correctly next to widefield deconvolution and super-resolution methods.