Collaborative deep learning inference between low-resource endpoint devices and edge servers has received significant research interest in the last few years. Such computation partitioning can help reducing endpoint device energy consumption and improve latency, but equally importantly also contributes to privacy-preserving of sensitive data. This paper describes Edge-PRUNE, a flexible but light-weight computation framework for distributing machine learning inference between edge servers and one or more client devices. Compared to previous approaches, Edge-PRUNE is based on a formal dataflow computing model, and is agnostic towards machine learning training frameworks, offering at the same time wide support for leveraging deep learning accelerators such as embedded GPUs. The experimental section of the paper demonstrates the use and performance of Edge-PRUNE by image classification and object tracking applications on two heterogeneous endpoint devices and an edge server, over wireless and physical connections. Endpoint device inference time for SSD-Mobilenet based object tracking, for example, is accelerated 5.8x by collaborative inference.