Abstract This work is motivated by the mostly unsolved task of parsing biological images with multiple overlapping articulated model organisms (such as worms or larvae). We present a general approach that separates the two main challenges associated with such data, individual object shape estimation and object groups disentangling. At the core of the approach is a deep feed-forward singling-out network (SON) that is trained to map each local patch to a vectorial descriptor that is sensitive to the characteristics (e.g. shape) of a central object, while being invariant to the variability of all other surrounding elements. Given a SON, a local image patch can be matched to a gallery of isolated elements using their SON-descriptors, thus producing a hypothesis about the shape of the central element in that patch. The image-level optimization based on integer programming can then pick a subset of the hypotheses to explain (parse) the whole image and disentangle groups of organisms