Genome discoveries at the core of biology are made by visual description and exploration of the cell, from microscopic sketches and biochemical mapping to computational analysis and spatial modeling. We outline the experimental and visualization techniques that have been developed recently which capture the three-dimensional interactions regulating how genes are expressed. We detail the challenges faced in integration of the data to portray the components and organization and their dynamic landscape. The goal is more than a single data-driven representation as interactive visualization for de novo research is paramount to decipher insights on genome organization in space.

We received funding from the European Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013)/ERC Synergy under grant agreement no 609989 (4Dgenome) as well as under the European Union's Horizon 2020 research and innovation program (grant agreement 676556). We also acknowledge the co-financing by the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) with funds from the European Regional Development Fund (ERDF) corresponding to the 2014-2020 Smart Growth Operating Program, the support of the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) to the EMBL partnership (BFU2017-85926-P) and through the Instituto de Salud Carlos III, the Centro de Excelencia Severo Ochoa (SEV-2012-0208), the CERCA Programme / Generalitat de Catalunya, and the Generalitat de Catalunya through Departament de Salut and Departament d'Empresa i Coneixement. This work reflects only the authors' views and the funding bodies are not liable for any use that may be made of the information contained therein.