This paper presents the NeuroSelect software for managing the electronic depth control of cerebral CMOS-based microprobes for extracellular in vivo recordings. These microprobes contain up to 500 electronically switchable electrodes which can be appropriately selected with regard to specific neuron locations in the course of a recording experiment. NeuroSelect makes it possible to scan the electrodes electronically and to (re)select those electrodes of best signal quality resulting in a closed-loop design of a neural acquisition system. The signal quality is calculated by the relative power of the spikes compared with the background noise. The spikes are detected by an adaptive threshold using a robust estimator of the standard deviation. Electrodes can be selected in a manual or semi-automatic mode based on the signal quality. This electronic depth control constitutes a significant improvement for multielectrode probes, given that so far the only alternative has been the fine positioning by mechanical probe translation. In addition to managing communication with the hardware controller of the probe array, the software also controls acquisition, processing, display and storage of the neural signals for further analysis.