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Abstract Objective.Elucidating neurological processes in the mammalian brain requires improved methods for imaging and detecting neuronal subtypes. Transgenic mouse models utilizing Cre/lox recombination have been developed to selectively label neuronal subtypes with fluorophores, however, light-scattering attenuation of both excitation light and emission light limits their effective range of detection.Approach. To overcome these limitations, this study investigates the use of a near-infrared fluorophore, iRFP713, for subtype labeling of neurons found within brain regions that are typically inaccessible by optical methods. Towards this goal, a custom photoacoustic (PA) system is developed for detection of iRFP in neurons in brain slices, expressed via Cre/lox, and withinin vitrocell culture.Main results. In this study, a custom system is developed to detect iRFP in neuronal cells both in brain slices andin vitro. Furthermore, this work validates iRFP expression in the brains of transgenic mice and neuronal cell culture.Significance. Combining iRFP with advanced imaging and detection strategies, such as PA microscopy, is critical for expanding the type and variety of neurons that scientists can observe within the mammalian brain. 

Glass micropipette electrodes are commonly used to provide high resolution recordings of neurons. Although it is the gold standard for single cell recordings, it is highly dependent on the skill of the electrophysiologist. Here, we demonstrate a method of guiding micropipette electrodes to neurons by collecting fluorescence at the aperture, using an intra-electrode tapered optical fiber. The use of a tapered fiber for excitation and collection of fluorescence at the micropipette tip couples the feedback mechanism directly to the distance between the target and electrode. In this study, intra-electrode tapered optical fibers provide a targeted robotic approach to labeled neurons that is independent of microscopy.