Neuron Detection and Decoding in Fluorescence Microscopy

One method for recording neuronal activity is fluorescence microscopy, in which neurons in the brain express a fluorescent marker whose emission is modulated by the “firing” of the neuron. Our work is based on the integrated fluorescence microscope of the Schnitzer group [GBC11] which enables the acquisition of activity from large numbers of neurons in freely-behaving mice and rats. As shown in Fig. 1(a), the fluorescence microscope is surgically attached to the skull of a laboratory mouse. Fig. 1(b) shows a typical microscope image with individually outlined neurons. In a prototypical experiment, the animal is permitted to wander about its environment, while the microscope images the hippocampus – a region of the brain associated with spatial representation.