Small satellite constellations are an attractive alternative to provide ubiquitous connectivity to Internet of Things (IoT) and 5G machine-type communication (MTC) applications in areas where terrestrial network coverage is limited. In order to provide global coverage using small satellite networks flying in low earth orbit (LEO), a large constellation of at least hundreds of satellites is needed. As LEO satellites can only connect directly to the ground earth station (GES) sporadically, they need to forward data over inter-satellite links (ISLs) to reach the GES. In this paper, we propose a novel self-organising architectural design for small satellite constellations with ISLs, supporting automated commissioning and control of the satellite network. We specifically present an algorithm for autonomous ISL establishment and channel selection,that avoids interference among ISLs of the same satellite.