Ries Lab

We are studying nanoscale multi-protein machineries in their functional cellular context, and elucidates their dynamic structural organisation using tailor-made superresolution microscopy technologies.

Research in the Ries Lab

Previous and current research

Like nanoscopic machines, protein complexes and assemblies carry out a variety of essential cellular processes. Understanding their function and mechanics requires knowing their in situ structural organisation, which is barely accessible to classical structural biology techniques (EM, NMR, crystallography). Recently developed superresolution microscopy techniques however are ideal tools that allow us to study these assemblies in their natural cellular environment and to understand their modus operandi.

In our group, we push the limits of the technology by developing optical, biological and computational methods for superresolution microscopy:

We are developing novel techniques to achieve highest 3D resolution of single fluorophores using Supercritical Angle Localization Microscopy and correlative superresolution and electron microscopy, and are implementing quantitative superresolution imaging based on counting reference standards. Lattice-light sheet microscopy allows us to dynamically visualise structures in thick samples and organisms.

High-content superresolution microscopy and a computational analysis framework enables the acquisition of large datasets of structures with powerful statistics.

In the past, we introduced nanobodies as versatile superresolution labels and pioneered superresolution microscopy in yeast, where strain libraries with tags and mutations allow system-wide superresolution studies.

We then apply our newly developed technologies to exciting cell biological systems:

In one project, we study the complex and dynamic protein machinery that performs clathrin-mediated endocytosis in yeast. Using automated high-content superresolution imaging and quantitative data analysis, we determined how more than a dozen endocytic proteins are organised at the nanoscale. The architectural principles we discovered allowed us to understand how the endocytic machinery achieves remarkably high regularity and efficiency. Our vision is to reconstruct the time-resolved distributions of all endocytic proteins and integrate this data with mathematical modelling, to understand key aspects of the endocytic mechanism, including how the machinery assembles, how membrane curvature is induced and how vesicle scission is mediated.

In other projects, we are studying the structure of the kinetochore, we are investigating intracellular aggregation of Parkinsons’ alpha-synuclein and we aim at reconstructing the 3D organisation of DNA in a cell nucleus.

Future projects and goals

Our vision is to further extend superresolution microscopy as a tool for structural cell biology in situ. We aim to push its limits on all fronts to establish a technique which combines nanometre 3D resolution with maximum labelling efficiencies, absolute measurements of protein copy numbers, precise multi-colour measurements, high-throughput for large scale statistics and novel data analysis approaches, to address the vast array of exciting biological questions at the nanoscale, which are becoming accessible only now.


Ries Lab 2018

Group Members

Jonas Ries
Group Leader
Takahiro Deguchi
Takahiro Deguchi
Joran Deschamps
Joran Deschamps
Scientific Officer
Angelica Maria Estrada Pacheco
Angelica Maria Estrada Pacheco
Research Technician
Philipp Hoess
Philipp Hoess
PhD Student
Sheng Liu
Sheng Liu
Ulf Matti
Ulf Matti
Research Technician
Aline Tschanz
Aline Tschanz
PhD Student
Jervis Vermal Thevathasan
Jervis Vermal Thevathasan
Yu-Le Wu
Yu-Le Wu
PhD Student
Lucas-Raphael Mueller
Lucas-Raphael Mueller
Master Student
Vincent Casamayou
Vincent Casamayou
Lisa Nechyporenko
Lisa Nechyporenko
Tomas Noordzij
Tomas Noordzij
Master Student

Associated PostDocs

Rafael Martins Galupa
Markus Mund

Open positions

We are always looking for motivated Masters students and interns with a background in physics, programming or biology. Please contact Jonas directly.

If you want to join as a PhD student, please note that admission is exclusively via the EMBL PhD program.


Name Position Topic Period Current affiliation
Leonard Krupnik Master Student SMLM of α-synuclein 10.2019 - 05.2020  
Robin Diekmann PostDoc Ratiometric SMLM, Camera Calibration, slowSTORM, 4 Pi Microscopy 01.2018 - 04.2020 LaVision BioTec, Bielefeld
Andreas Schoenit Intern The NPC as imaging standard 11.2019 - 03.2020  
Anindita Dasgupta Master Student Supercritical Angle Localization Microscopy 09.2018 - 11.2019 Institute of Applied Optics and Biophysics, Jena
Maurice Kahnwald Master Student The NPC as imaging standard 08.2018 - 11.2019 FMI, Basel
Yiming Li PostDoc 4 Pi Microscopy & Experimental PSF Modeling 01.2016 - 10.2019 Southern University of Science and Technology, Shenzhen
Amir Rahmani Intern Optimizing Dual-Color SMLM 07.2019 - 09.2019  
Cheng-Yu Huang Intern PSF Modeling 06.2019 - 09.2019 Cambridge University
Eric Maurer Intern Super-resolution microscopy using small tags 06.2019 - 08.2019 University of Heidelberg
Konstanty Cieśliński PhD Student & PostDoc Super-resolution imaging of the yeast kinetochore 10.2013 - 12.2018 DKFZ, Heidelberg
Alejandro Colchero Master Student Optimizing Dual-Color SMLM 04.2018 - 09.2018 University of Madrid
Sudheer Kumar Peneti Master Student Quantifying labeling efficiency in SMLM 03.2018 - 07.2018 Newcastle University
Rayka Karimi Intern 4 Pi software development 04.2018 - 06.2018  
Julia Botta Intern Counting by SMLM and Kinetochore 02.2018 - 04.2018 University of Heidelberg
Daniel Heid Intern Quantifying labeling efficiency in SMLM 01.2018 - 03.2018 University of Heidelberg
Li-Ling Yang PostDoc Inverted lattice light-sheet microscope 06.2014 - 12.2017 Charité Berlin
Markus Mund PhD Student & PostDoc Endocytosis 09.2012 - 12.2017 University of Geneva
Sarah Hoerner Master Student Counting with SMLM 06.2017 - 12.2017 Heidelberg University
Daniel Schroeder Master Student Microscopy Development 04.2017 - 10.2017 FU Berlin
Elena Buglakova Intern Modeling of 4Pi-PSF 07.2017 - 09.2017  
Krishna Kasuba Intern Protein counting by SMLM 10.2016 - 08.2017 ETH Zürich
Johanna Mehl Intern Superresolution imaging of endocytosis 10.2016 - 04.2017 ETH Zürich
Jooske Monster Intern Superresolution imaging of endocytosis 10.2016 - 12.2016 Utrecht University
Joanna Zareba Intern Fluorophores 07.2016 - 10.2016 Chicago University
Katharina Lindner Intern Kinetochore 01.2016 - 05.2016 Heidelberg University
Tooba Quidwai Intern Superresolution imaging of platelets 04.2014 – 08.2015 Edinburgh
Jan van der Beek Intern Superresolution imaging of endocytosis 12.2014 – 07.2015 Utrecht University
Rohit Prakash Intern Superresolution imaging of endocytosis 11.2013 – 03.2015 Rochester University
Andreas Rowald Intern Microscopy development 09.2014 – 02.2015 Erlangen University
Nagaraja Chandramohan Intern Programming 01.2014 – 12.2014 HITS
Sven Spachmann Bachelor student Co-localization in superresolution 05.2014 – 07.2014  
Sunil Kumar Dogga Intern Endocytosis 12.2013 – 02.2014  
Sanchari Datta Intern Endocytosis 06.2013 – 07.2013  
Meet Mukesh Paswan Intern Programming 06.2013 – 07.2013  
Johannes Bues Intern Superresolution in yeast 04.2013 – 05.2013  



SMAP (Superresolution Microscopy Analysis Platform) is a comprehensive software framework for single-molecule localization microscopy that can be used for fitting of raw data and subsequent analysis.
It is published as a preprint on bioRxiv.

The most up-to-date source code can be obtained from GitHub.

You can download a compiled version for Windows and Mac, an example dataset and check the documentation.

The additional external software necessary to run SMAP can be downloaded from the respective websites:
Bioformats MATLAB Toolbox (bfmatlab.zip) and Micro-Manager 1.4.22


fit3Dcspline is a GPU based 3D single molecule fitter for arbitrary, experimental point spread functions (PSF).

It was published in Nature Methods and is part of SMAP (see above).

Data obtained from the standalone version can be visualized using Felix Woitzel's Pointcloud-Loader.

Excitation Intensities

dSTORM example data sets (upcoming publication).
SMLM (dSTORM) example data showing the effect of different excitation intensities (unprocessed TIF-stacks and SMAP-fitted localizations files).

Direct Supercritical Angle Localization microscopy (dSALM)

Preprint on bioRxiv
Example data and step-by-step guide for analysing dSALM data



SMAP - A Modular Superresolution Microscopy Analysis Platform for SMLM Data
Ries J.
Direct Supercritical Angle Localization Microscopy for Nanometer 3D Superresolution
Dasgupta A, Deschamps J, Matti U, Hübner U, Becker J, Strauss S, Jungman R, Heintzmann R, Ries J.
Accurate 4Pi single-molecule localization using an experimental PSF model
Li Y, Buglakova E, Zhang Y, Thevathasan JV, Bewersdorf J, Ries J.
Optics Letters doi: 10.1364/OL.397754
Previously on bioRxiv doi: 10.1101/2020.03.18.997163
Identification of novel synaptonemal complex components in C. elegans
Hurlock ME, Čavka I, Kursel LE, Haversat J, Wooten M, Nizami Z, Turniansky R, Hoess P, Ries J, Gall JG, Rog O, Köhler S, Kim Y.
Journal of Cell Biology doi: 10.1083/jcb.201910043
EMU: reconfigurable graphical user interfaces for Micro-Manager
Deschamps J, Ries J.
Corresponding git repository
Nanoscale pattern extraction from relative positions of sparse 3D localisations
Curd A, Leng J, Hughes R, Cleasby A, Rogers B, Trinh C, Baird M, Takagi Y, Tiede C, Sieben C, Manley S, Schlichthaerle T, Jungmann R, Ries J, Shroff H, Peckham M
MINFLUX nanoscopy delivers 3D multicolor nanometer resolution in cells
Gwosch K, Pape JK, Balzarotti F, Hoess P, Ellenberg J, Ries J, Hell SW
Nature Methods doi: 10.1038/s41592-019-0688-0
Previously on bioRxiv doi: 10.1101/734251
Nanoscale subcellular architecture revealed by multicolor three-dimensional salvaged fluorescence imaging
Zhang Y, Schroeder LK, Lessard MD, Kidd P, Chung J, Song Y, Benedetti L, Li Y, Ries J, Grimm JB, Lavis LD, De Camilli P, Rothman JE, Baddeley D & Bewersdorf J
Nature Methods doi: 10.1038/s41592-019-0676-4
Previously on bioRxiv doi: 10.1101/613174
A cost-efficient open source laser engine for microscopy
Schroeder D, Deschamps J, Dasgupta A, Matti U, Ries J.
Biomedical Optics Express doi: 10.1364/BOE.380815
Previously on bioRxiv doi: 10.1101/796482
Corresponding git repository


Organotypic slice culture model demonstrates inter-neuronal spreading of alpha-synuclein aggregates
Elfarrash S, Møller Jensen N, Ferreira N, Betzer C, Thevathasan JV, Diekmann R, Adel M, Mansour Omar N, Boraie MZ, Gad S, Ries J, Kirik D, Nabavi S, Jensen H.
Acta Neuropathologica Communications doi: 10.1186/s40478-019-0865-5
Previously on bioRxiv doi: 10.1101/681064
Three dimensional particle averaging for structural imaging of macromolecular complexes by localization microscopy
Rieger B, Stallinga S, Heydarian H, Schueder F, Jungmann R, Ries J, Przybylski A, Bates M, Keller-Findeisen J, van Werkhoven B.
bioRxiv doi: 10.1101/837575
Topological data analysis quantifies biological nano-structure from single molecule localization microscopy
Pike JA, Khan AO, Pallini C, Thomas SG, Mund M, Ries J, Poulter NS, Styles IB
Bioinformatics doi: 10.1093/bioinformatics/btz788
Previously on bioRxiv doi: 10.1101/400275
Photoactivation of silicon rhodamines via a light-induced protonation
Frei MS, Hoess P, Lampe M, Nijmeijer B, Kueblbeck M, Ellenberg J, Wadepohl H, Ries J, Pitsch S, Reymond L, Johnsson K.
Nature Communications doi: 10.1038/s41467-019-12480-3
Previously on bioRxiv doi: 10.1101/626853
Nuclear pores as versatile reference standards for quantitative superresolution microscopy
Thevathasan JV, Kahnwald M, Cieśliński K, Hoess P, Peneti SK, Reitberger M, Heid D, Kasuba KC, Hoerner SJ, Li Y, Wu Y, Mund M, Matti U, Pereira PM, Henriques R, Nijmeijer B, Kueblbeck M, Sabinina VJ, Ellenberg J, Ries J.
Nature Methods doi: 10.1038/s41592-019-0574-9
Previously on bioRxiv doi: 10.1101/582668
Type-I myosins promote actin polymerization to drive membrane bending in endocytosis
Manenschijn HE, Picco A, Mund M, Rivier-Cordey AS, Ries J, Kaksonen M
Previously on bioRxiv doi: 10.1101/490011
Direct Visualization of Single Nuclear Pore Complex Proteins Using Genetically‐Encoded Probes for DNA‐PAINT
Schlichthaerle T, Strauss MT, Schueder F, Auer A, Nijmeijer B, Kueblbeck M, Sabinina VJ, Thevathasan JV, Ries J, Ellenberg J, Jungmann R.
Angewandte Chemie International Edition doi: 10.1002/anie.201905685
Previously on bioRxiv doi: 10.1101/579961
A tessellation-based colocalization analysis approach for single-molecule localization microscopy
Levet F, Julien G, Galland R, Butler C, Beghin A, Chazeau A, Hoess P, Ries J, Giannone G, Sibarita JB.
Nature Communications doi: 10.1038/s41467-019-10007-4
Depth-dependent PSF calibration and aberration correction for 3D single-molecule localization
Li Y, Wu Y, Hoess P, Mund M, Ries J.
Biomedical Optics Express doi: 10.1364/BOE.10.002708
Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software
Sage D, Pham T, Babcock H, Lukes T, Pengo T, Chao J, Velmurugan R, Herbert A, Agrawal A, Colabrese S, Wheeler A, Archetti A, Rieger B, Ober R, Hagen GM, Sibarita J, Ries J, Henriques R, Unser M, Holden S.
Nature Methods doi: 10.1038/s41592-019-0364-4
Previously on bioRxiv doi: 10.1101/362517


Scanning Fluorescence Correlation Spectroscopy for Quantification of the Dynamics and Interactions in Tube Organelles of Living Cells
Unsay JD, Murad F, Hermann E, Ries J, García-Sáez AJ.
ChemPhysChem doi: 10.1002/cphc.201800705
Systematic Nanoscale Analysis of Endocytosis Links Efficient Vesicle Formation to Patterned Actin Nucleation
Mund M, van der Beek JA, Deschamps J, Dmitrieff S, Hoess P, Monster JL, Picco A, Nédélec F, Kaksonen M, Ries J.
Previously on bioRxiv doi: 10.1101/217836
Dual-Color and 3D Super-Resolution Microscopy of Multi-protein Assemblies.
Hoess P, Mund M, Reitberger M, Ries J.
Methods Mol Biol 1764:237-251. doi: 10.1007/978-1-4939-7759-8_14
Site-specific labeling of Affimers for DNA-PAINT microscopy.
Schlichthaerle T, Eklund A, Schueder F, Strauss M, Tiede C, Curd A, Ries J, Peckham M, Tomlinson D, Jungmann R.
Angew Chem Int Ed Engl doi: 10.1002/anie.201804020
Real-time 3D single-molecule localization using experimental point spread functions.
Li Y, Mund M, Hoess P, Deschamps J, Matti U, Nijmeijer B, Sabinina VJ, Ellenberg J, Schoen I, Ries J.
Nat Methods doi: 10.1038/nmeth.4661
ChromoTrace: Computational reconstruction of 3D chromosome configurations for super-resolution microscopy.
Barton C, Morganella S, Ødegård-Fougner Ø, Alexander S, Ries J, Fitzgerald T, Ellenberg J, Birney E.
PLoS Comput Biol 14(3) doi: 10.1371/journal.pcbi.1006002


Nanoscale invaginations of the nuclear envelope: Shedding new light on wormholes with elusive function.
Schoen I, Aires L, Ries J, Vogel V.
Nucleus 8(5):506-514. doi: 10.1080/19491034.2017.1337621
Aurora-B kinase pathway controls the lateral to end-on conversion of kinetochore-microtubule attachments in human cells.
Shrestha RL, Conti D, Tamura N, Braun D, Ramalingam RA, Cieśliński K, Ries J, Draviam VM.
Nat Commun 8(1) doi: 10.1038/s41467-017-00209-z
Nanoscale invaginations of the nuclear envelope: Shedding new light on wormholes with elusive function.
Schoen I, Aires L, Ries J, Vogel V.
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Ries Lab

EMBL Heidelberg
Meyerhofstr. 1
69117 Heidelberg

Room 402
Phone number: +49 6221 3878199
E-Mail: ries(at)embl.de

Ries Lab website at www.embl.de
European Molecular Biology Laboratory