Software Control of a Confocal Microscope

Abstract: Confocal fluorescence microscopy is an optical imaging technique that has high resolution and can be used to detect individual fluorescing molecules. It is commonly used in biology, medicine and materials research. A confocal microscope system contains scanning mirrors, objective lens, laser and detector. The laser beam is directed by 2 scanning mirrors and it will be focused by an objective lens onto the sample and the emitted fluorescent light is collected by a photodetector. In order to obtain an image of the sample, the laser beam is scanned along the x-y axis and the intensity is function of the coordinate I(x,y). When a photon hits the photodetector, a short TTL pulse is generated. In order to obtain light intensity we need to know the number of photons (TTL pulses) over a fixed time interval (for example 10 ms). This has been realized with a National Instruments Data Acquisition (DAQ) card model NI 6602, which contains 8 high frequency counters. This master thesis is about developing a LabView software to control the scanning and the DAQ card. It is divided into four different programs, the first for controlling the mirrors, the second is for plotting the intensity on a graph and save the data in a binary file, the third is for counting the number of pulses on one specific spot and the last is for analysing data.