Deep brain stimulation (DBS) is an interventional treatment for Parkinson's disease which involves the precise positioning of stimulated electrodes within deep brain structures, such as the SubThalamic Nucleus (STN). Although originally identified via imaging, additional inter-operative guidance is necessary to localize the target anatomy. Analysis of Micro-Electrode Recordings (MERs) allows for a trained neurophysiologist to infer the underlying anatomy at a particular electrode position using human audition, although it is subjective and requires a high degree of expertise. Various approaches to assist MER analysis during DBS are proposed in the literature, including deep learning methods, which rely on a static input description, that is, a pre-defined number of features or input size. In this paper, we propose two dynamic deep learning approaches adaptable to the complexity of MERs signal, by using an arbitrary long listening time (in 1s chunks), while providing feedback to the neurophysiologist as to the model's certainty. We evaluated five different deep learning based classifiers which can use arbitrary length MERs for STN segmentation. We found that a Bayesian extension using the highlevel features from SepaConvNet performed the best, increasing the balanced accuracy to 83.5%. This work represents a step forward in integrating automated analysis of MERs into the DBS surgical workflow by automatically finding and exploiting possible efficiencies in MER acquisition.