The BioEmergences platform (UPS in 2014) develops, applies to specific case studies, and offers as services, original methodologies and tools for the multi-scale phenomenological and theoretical reconstruction of the development of model organisms, animal or vegetal. The work is organized along the lines of an applied epistemology that we defined in the context of the Institute for Complex Systems which is part of the national and international roadmap established by the Complex Systems community http://roadmaps.csregistry.org/. We developed a workflow going from photonic microscopy for in vivo and in toto imaging of developing organisms to the automated reconstruction of 3D+time data, analysis of digital specimens and modeling of morphogenetic processes. In this context provide collaborative services that most of the time, correspond to new challenging applications (WP1b, WP1d, WP2, WP3). FBI funding is used to develop a so-called artificial assistant based on a SPIM or MLMS imaging concept with real time image processing and feedback on the imaging scheme. All our activity involves image processing (WP4), that’s why we are involved in IPDM node too. We expect to provide the community with original webservices to access the BioEmergences reconstruction workflow and grid computing.