In fluorescence microscopy, the sample is completely bathed in light, whereas in confocal microscopy, emitted light is focused on a pinhole, eliminating out of focus fluorescent light/reducing glare. A computer constructs the image pixel by pixel. What's cool about confocal microscopy is that you can focus on a single point and have the sample sliced at evenly spaced intervals from top to bottom to create a 3D image. Of course, all this comes with a hefty price tag, about $250K, which is why many ordinary labs will chip in and share one instrument.