Reconstruction from Fluorescence Confocal Microscopy Images

The fluorescence confocal microscopy is one of the most important tools in biomedical and pharmaceutic research. The main advantage of this technique over the traditional optical microscopy is the fact that it allows the selection of a thin cross-section of the sample by rejecting the visual information coming from the out of focus planes. Additionally, it uses fluorescence synthetic molecules that radiate in a wave length different from the one of the incident laser. It is easy to track these molecules inside the cell. In this paper we present two related algorithms for fluorescence confocal microscopy, both of them derived from an alignment-by-reconstruction algorithm originally developed for 3D ultrasound. The first algorithm, estimates a 3D region from a set of images corresponding to a stack of parallel cross sections taken from the cell. The second algorithm, estimates one 2D cross-section from a set of images taken during a long period of time. This last algorithm also estimates a 2D function describing the intensity exponential decay fluorescence coefficients for each position on the 2D region of interest. This decrease of the image intensity, called photobleaching, must be compensated but it is useful from a biological point of view because it is related with the chemical and transport phenomena that occur inside the cell.