Improved correction of axial geometrical distortion in index-mismatched fluorescent confocal microscopic images using high-aperture objective lenses.

Extracting quantitative data from microscopic volume images is straightforward when the refractive indices of the immersion medium and the mounting medium are equal. The readings of the position of the specimen stage can be directly used to measure depth and width. Imperfectly matched immersion and mounting media result in axial geometrical distortion. Linear correction of the axial distortion using the paraxial estimate of the axial scaling factor yields results that may differ as much as 4% from the actual values. From calculations based on a theoretical expression of the 3-D point-spread function in the focal region of a high-aperture microscope focussing into a mismatched mounting medium, we derived axial scaling factors that result in quantitative results accurate to better than 1%. From a non-linear correction procedure, an improved formula for the paraxial estimate of the axial scaling factor is derived.

A procedure to determine the correct thickness of an object with confocal microscopy in case of refractive index mismatch.

A difference in refractive index (n) between immersion medium and specimen results in increasing loss of intensity and resolution with increasing focal depth and in an incorrect axial scaling in images of a confocal microscope. Axial thickness measurements of an object on such images are therefore not exact. The present paper describes a simple procedure to determine the correct axial thickness of an object with confocal fluorescence microscopy. We study this procedure for a specimen that has a higher refractive index than the immersion medium and with a thickness up to 100 microm. The measuring method was experimentally tested by comparing the thickness of polymer layers measured on axial images of a confocal microscope in case of a water-polymer mismatch to reference values obtained from an independent technique, i.e. scanning electron microscopy. The case when the specimen has a lower refractive index than the immersion medium is also shown by way of illustration. Measured thickness data of a water layer and an oil layer with the same actual thickness were obtained using an oil-immersion objective lens with confocal microscopy. Good agreement between theory and experiment was found in both cases, consolidating our method.

A simple method for checking the illumination profile in a laser scanning microscope and the dependence of resolution on this profile.

One of the conditions for a laser scanning microscope to reach its optimal performance is for it to operate at its full numerical aperture (NA). In most commonly used systems, the illumination intensity at the back focal plane of the objective lens is apodized. This paper presents a simple method using a photodiode for checking the actual illumination intensity profile. We show as an example the measured profiles of a laser beam when working with two high-NA immersion objectives in two different confocal systems, and also show that in theoretical studies of the point-spread function, the assumption of a flat compared with a truncated Gaussian beam profile gives rise to severe discrepancies. The measured profiles also serve as an indication of the necessity of a realignment of the optical system.