ChromoTrace: Computational reconstruction of 3D chromosome configurations for super-resolution microscopy. - Carl Barton; Sandro Morganella; Øyvind Ødegård-Fougner; Stephanie Alexander; Jonas Ries; Tomas W. Fitzgerald; Jan Ellenberg; Ewan Birney (PLoS Comput. Biol., 2018)

Topological data analysis quantifies biological nano-structure from single molecule localization microscopy. - Jeremy A. Pike; Abdullah O. Khan; Chiara Pallini; Steven G. Thomas; Markus Mund; Jonas Ries; Natalie S. Poulter; Iain B. Styles (Bioinform., 2020)

EMU: reconfigurable graphical user interfaces for Micro-Manager. - Joran Deschamps; Jonas Ries (BMC Bioinform., 2020)

Simulating structurally variable nuclear pore complexes for microscopy. - Maria Theiss; Jean-Karim Hériché; Craig Russell; David Helekal; Alisdair Soppitt; Jonas Ries; Jan Ellenberg; Alvis Brazma; Virginie Uhlmann (Bioinform., 2023)