In this paper we describe an unmanned aerial system equipped with a thermal-infrared camera and software pipeline that we have developed to monitor animal populations for conservation purposes. Taking a multi-disciplinary approach to tackle this problem, we use freely available astronomical source detection software and the associated expertise of astronomers, to efficiently and reliably detect humans and animals in aerial thermal-infrared footage. Combining this astronomical detection software with existing machine learning algorithms into a single, automated, end-to-end pipeline, we test the software using aerial video footage taken in a controlled, field-like environment. We demonstrate that the pipeline works reliably and describe how it can be used to estimate the completeness of different observational datasets to objects of a given type as a function of height, observing conditions etc. - a crucial step in converting video footage to scientifically useful information such as the spatial distribution and density of different animal species. Finally, having demonstrated the potential utility of the system, we describe the steps we are taking to adapt the system for work in the field, in particular systematic monitoring of endangered species at National Parks around the world.