Total internal reflection microscopy is a technique ideal for imaging the cell membrane, as it allows for selective excitation of fluorophores at or near the coverglass. When a beam enters a high NA objective off-axis, it produces an evanescent field, the penetration depth of which is dependent on the refractive index difference between the glass substrate and sample. A pitfall of this method is that sample refractive index varies across a cell surface and organelles, causing unwanted light refraction and scattering. By introducing a Bertrand lens into the detection optics, the critical angle on the back focal plane can be imaged, which allows to calculate the sample refractive angle, and emission from near-membrane and deeper fluorophores can be separated, too. Here, we use a scanning TIR-SAF system to measure the local cellular refractive index across the cell's “footprint” region. The excitation path contains a radial polarizer, and two axicon lenses to form evanescent Bessel beam illumination, allowing for an excitation “needle”. Tightly focused radially and azimuthally polarized Bessel beams are desirable as they allow for a smaller excitation spot size. However, neither effects of azimuthally nor radially polarized excitation on evanescent field formation have been characterized. We built and characterized a confocal TIR-SAF system, and the effects of polarization were assessed.
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