Reflectance confocal microscopy (RCM) is an effective non-invasive tool for cancer diagnosis. However, acquiring and reading RCM images requires extensive training and experience, and novice clinicians exhibit high discordance in diagnostic accuracy. Quantitative tools to standardize image acquisition could reduce both required training and diagnostic variability. To perform diagnostic analysis, clinicians collect a set of RCM mosaics (RCM images concatenated in a raster fashion to extend the field view) at 4-5 specific layers in skin, all localized in the junction between the epidermal and dermal layers (dermal-epidermal junction, DEJ), necessitating locating that junction before mosaic acquisition. In this study, we automate DEJ localization using deep recurrent convolutional neural networks to delineate skin strata in stacks of RCM images collected at consecutive depths. Success will guide to automated and quantitative mosaic acquisition thus reducing inter operator variability and bring standardization in imaging. Testing our model against an expert labeled dataset of 504 RCM stacks, we achieved [Formula: see text] classification accuracy and nine-fold reduction in the number of anatomically impossible errors compared to the previous state-of-the-art.