We thank T. Hyman and I. Poser for donating multiple mouse BAC protein–GFP cell lines and T. Hirota for giving us the eGFP–CENPA cell line. The automatic imaging would not have been possible without R. Höfler and D. W. Gerlich, who developed the Micronaut software. We thank all members of the Ellenberg and Peters laboratories for support, especially M. Isokane, M. J. Roberti, J. Mergenthaler, S. Otsuka, W. Tang and D. Cisneros for generating cell lines, reagents and constructs. We thank A. Callegari for supporting the U2OS data generation. We also thank W. Huber, B. Fischer, B. Klaus and L. P. Coelho for discussions, the EMBL mechanical and electronic workshop, the EMBL advanced light microscopy facility, the EMBL flow cytometry core facility and the IMP BioOptics Facility for their support. This study has benefited from the collaboration with Carl ZEISS Jena, especially with T. Ohrt. The work was supported by grants from EU-FP7-MitoSys (Grant Agreement 241548) to J.E. and J.M.P., EU-FP7-SystemsMicroscopy NoE (Grant Agreement 258068), EU-H2020-iNEXT (Grant Agreement 653706) and the 4D Nucleome/4DN National Institutes of Health common fund (5 U01 EB021223-04 / 8 U01 DA047728-04) all to J.E., as well as by the European Molecular Biology Laboratory (Y.C., M.J.H., J.-K.H., A.Z.P., N.W., B.K., M.W., B.N., M.K., S.A. and J.E.). Y.C. and N.W. were also supported by the EMBL International PhD Programme (EIPP). Research in the laboratory of J.M.P. was further supported by Boehringer Ingelheim, the Austrian Science Fund (FWF special research program SFB F34 ‘Chromosome Dynamics’ and Wittgenstein award Z196-B20), the Austrian Research Promotion Agency (Headquarter grants FFG-834223 and FFG-852936) and the European Research Council (ERC) under the European Union Horizon 2020 research and innovation programme (Grant Agreement 693949).

Reviewer information

Nature thanks R. Murphy, J. Swedlow and the other anonymous reviewer(s) for their contribution to the peer review of this work.