Structural cell biology in situ using superresolution microscopy

Project Information

CellStructure

Grant agreement ID: 724489

DOI

10.3030/724489

Project closed

EC signature date 28 February 2017

Start date 1 June 2017

End date 31 May 2024

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 686 469,38

EU contribution

€ 1 686 469,38

Coordinated by

UNIVERSITAT WIEN
Austria

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Publications

Peer reviewed articles (33)

Organotypic slice culture model demonstrates interneuronal spreading of alpha-synuclein aggregates

Author(s): Sabry Gad; Nelson Ferreira; Jervis Vermal Thevathasan; Cristine Betzer; Deniz Kirik; Robin Diekmann; Mohamed Z. Boraie; Jonas Ries; Mohamed Adel; Nanna Møller Jensen; Sara Elfarrash; Sara Elfarrash; Poul Henning Jensen; Nisreen Mansour Omar; Sadegh Nabavi
Published in: Acta Neuropathologica Communications, Vol 7, Iss 1, Pp 1-16 (2019), Issue 5, 2019, ISSN 2051-5960
Publisher: BioMed Central
DOI: 10.1101/681064

Implementation of a 4Pi‐SMS super‐resolution microscope

Author(s): J. Wang, E.S. Allgeyer, G. Sirinakis, Y. Zhang, K. Hu, M.D. Lessard, Y. Li, R. Diekmann, M.A. Phillips, I.M. Dobbie§, J. Ries§, M.J. Booth§, J. Bewersdorf
Published in: Nat Protocols, 2021, ISSN 1754-2189
Publisher: Nature Publishing Group
DOI: 10.1038/s41596-020-00428-7

Build and operation of a custom 3D, multicolor, single-molecule localization microscope

Author(s): Rory M. Power, Aline Tschanz, Timo Zimmermann & Jonas Ries
Published in: Nature Protocols, 2024, ISSN 1754-2189
Publisher: Nature Publishing Group
DOI: 10.1038/s41596-024-00989-x

SMAP: a modular super-resolution microscopy analysis platform for SMLM data

Author(s): J. Ries
Published in: Nat Methods, 2020, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-020-0938-1

3D super-resolution fluorescence microscopy maps the variable molecular architecture of the Nuclear Pore Complex

Author(s): V. Jimenez Sabinina, M.J. Hossain, J.-K. Heriche, P. Hoess, B. Nijmeijer, S. Mosalaganti, M. Kueblbeck, A. Callegari, A. Szymborska, M. Beck, J. Ries, J. Ellenberg
Published in: Mol Biol Cell, 2021, ISSN 1759-5029
Publisher: Nature Publishing Group
DOI: 10.1091/mbc.e20-11-0728

Photon-free (s)CMOS camera characterization for artifact reduction in high- and super-resolution microscopy

Author(s): Diekmann, Robin; Deschamps, Joran; Li, Yiming; Deguchi, Takahiro; Tschanz, Aline; Kahnwald, Maurice; Matti, Ulf; Ries, Jonas
Published in: Nature Communications, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-30907-2

Nanoscale structural organization and stoichiometry of the budding yeast kinetochore

Author(s): Cieslinski, Konstanty; Wu, Yu-Le; Nechyporenko, Lisa; Hörner, Sarah Janice; Conti, Duccio; Skruzny, Michal; Ries, Jonas
Published in: Journal of Cell Biology, 2023, ISSN 0021-9525
Publisher: Rockefeller University Press
DOI: 10.1083/jcb.202209094

How good are my data? Reference standards in superresolution microscopy

Author(s): Markus Mund and Jonas Ries
Published in: Molecular Biology of the Cell, 2020, ISSN 1939-4586
Publisher: AMER SOC CELL BIOLOGY
DOI: 10.1091/mbc.e19-04-0189

Direct observation of motor protein stepping in living cells using MINFLUX

Author(s): Deguchi, Takahiro; Iwanski, Malina K.; Schentarra, Eva-Maria; Heidebrecht, Christopher; Schmidt, Lisa; Heck, Jennifer; Weihs, Tobias; Schnorrenberg, Sebastian; Hoess, Philipp; Liu, Sheng; Chevyreva, Veronika; Noh, Kyung-Min; Kapitein, Lukas C.; Ries, Jonas
Published in: Science, Issue 15, 2023, ISSN 1095-9203
Publisher: AAAS
DOI: 10.1126/science.ade2676

Optimizing imaging speed and excitation intensity for single-molecule localization microscopy

Author(s): R. Diekmann, M. Kahnwald, A. Schoenit, J. Deschamps, U. Matti, J. Ries
Published in: Nat Methods, 2020, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1101/2021.04.16.440125

3D particle averaging and detection of macromolecular symmetry in localization microscopy

Author(s): H. Heydarian, M. Joosten, A. Przybylski, F. Schueder, R. Jungmann, B. van Werkhoven, J. Keller-Findeisen, J. Ries, S. Stallinga, M. Bates, B. Rieger
Published in: Nat Commun, 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-22006-5

Deep learning enables fast and dense single-molecule localization with high accuracy

Author(s): A. Speiser, L.-R. Müller, U. Matti, C.J. Obara, W.R. Legant, A. Kreshuk, J. Macke§, J. Ries§, S.C. Turaga§.
Published in: Nat Methods, 2021, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-021-01236-x

Direct Supercritical Angle Localization Microscopy for Nanometer 3D Superresolution

Author(s): A. Dasgupta, J. Deschamps, U. Matti, U. Huebner, J. Becker, S. Strauss, R. Jungmann, R. Heintzmann, J. Ries
Published in: Nat Commun, 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-21333-x

Global fitting for high-accuracy multi-channel single-molecule localization

Author(s): Li, Yiming; Shi, Wei; Liu, Sheng; Cavka, Ivana; Wu, Yu-Le; Matti, Ulf; Wu, Decheng; Koehler, Simone; Ries, Jonas
Published in: Nature Communications, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-30719-4

Clathrin coats partially preassemble and subsequently bend during endocytosis

Author(s): Markus Mund; Aline Tschanz; Yu-Le Wu; Felix Frey; Johanna L. Mehl; Marko Kaksonen; Ori Avinoam; Ulrich S. Schwarz; Jonas Ries
Published in: Journal of Cell Biology, 222 (3), Issue 13, 2023, ISSN 0021-9525
Publisher: Rockefeller University Press
DOI: 10.1083/jcb.202206038

MicroFPGA: an affordable FPGA platform for microscope control

Author(s): Joran Deschamps; Christian Kieser; Philipp Hoess; Takahiro Deguchi; Jonas Ries
Published in: HardwareX, Vol 13, Iss , Pp e00407- (2023), Issue 8, 2023, ISSN 2468-0672
Publisher: Oxford: Elsevier Ltd.
DOI: 10.1016/j.ohx.2023.e00407

Systematic Tuning of Rhodamine Spirocyclization for Super-Resolution Microscopy

Author(s): Nicolas Lardon; Nicolas Lardon; Jonas Ries; Elisa D’Este; Mai Tran; Aline Tschanz; Kai Johnsson; Kai Johnsson; Philipp Hoess; Lu Wang; Lu Wang
Published in: Journal of the American Chemical Society, Issue 2, 2021, ISSN 0002-7863
Publisher: American Chemical Society
DOI: 10.1101/2021.05.20.444797

Real-time 3D single-molecule localization using experimental point spread functions

Author(s): Yiming Li, Markus Mund, Philipp Hoess, Joran Deschamps, Ulf Matti, Bianca Nijmeijer, Vilma Jimenez Sabinina, Jan Ellenberg, Ingmar Schoen, Jonas Ries
Published in: Nature Methods, Issue 15/5, 2018, Page(s) 367-369, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/nmeth.4661

Systematic Nanoscale Analysis of Endocytosis Links Efficient Vesicle Formation to Patterned Actin Nucleation

Author(s): Markus Mund, Johannes Albertus van der Beek, Joran Deschamps, Serge Dmitrieff, Philipp Hoess, Jooske Louise Monster, Andrea Picco, François Nédélec, Marko Kaksonen, Jonas Ries
Published in: Cell, Issue 174/4, 2018, Page(s) 884-896.e17, ISSN 0092-8674
Publisher: Cell Press
DOI: 10.1016/j.cell.2018.06.032

MINFLUX nanoscopy delivers 3D multicolor nanometer resolution in cells

Author(s): Klaus C. Gwosch, Jasmin K. Pape, Francisco Balzarotti, Philipp Hoess, Jan Ellenberg, Jonas Ries, Stefan W. Hell
Published in: Nature Methods, 2020, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-019-0688-0

Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software

Author(s): Daniel Sage, Thanh-An Pham, Hazen Babcock, Tomas Lukes, Thomas Pengo, Jerry Chao, Ramraj Velmurugan, Alex Herbert, Anurag Agrawal, Silvia Colabrese, Ann Wheeler, Anna Archetti, Bernd Rieger, Raimund Ober, Guy M. Hagen, Jean-Baptiste Sibarita, Jonas Ries, Ricardo Henriques, Michael Unser, Seamus Holden
Published in: Nature Methods, Issue 16/5, 2019, Page(s) 387-395, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-019-0364-4

Depth-dependent PSF calibration and aberration correction for 3D single-molecule localization

Author(s): Yiming Li, Yu-Le Wu, Philipp Hoess, Markus Mund, Jonas Ries
Published in: Biomedical Optics Express, Issue 10/6, 2019, Page(s) 2708, ISSN 2156-7085
Publisher: The Optical Society
DOI: 10.1364/boe.10.002708

Photoactivation of silicon rhodamines via a light-induced protonation

Author(s): Michelle S. Frei, Philipp Hoess, Marko Lampe, Bianca Nijmeijer, Moritz Kueblbeck, Jan Ellenberg, Hubert Wadepohl, Jonas Ries, Stefan Pitsch, Luc Reymond, Kai Johnsson
Published in: Nature Communications, Issue 10/1, 2019, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-019-12480-3

Direct Visualization of Single Nuclear Pore Complex Proteins Using Genetically-Encoded Probes for DNA-PAINT

Author(s): Thomas Schlichthaerle, Maximilian T. Strauss, Florian Schueder, Alexander Auer, Bianca Nijmeijer, Moritz Kueblbeck, Vilma Jimenez Sabinina, Jervis V. Thevathasan, Jonas Ries, Jan Ellenberg, Ralf Jungmann
Published in: Angewandte Chemie International Edition, Issue 58/37, 2019, Page(s) 13004-13008, ISSN 1433-7851
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/anie.201905685

Nuclear pores as versatile reference standards for quantitative superresolution microscopy

Author(s): Jervis Vermal Thevathasan, Maurice Kahnwald, Konstanty Cieśliński, Philipp Hoess, Sudheer Kumar Peneti, Manuel Reitberger, Daniel Heid, Krishna Chaitanya Kasuba, Sarah Janice Hoerner, Yiming Li, Yu-Le Wu, Markus Mund, Ulf Matti, Pedro Matos Pereira, Ricardo Henriques, Bianca Nijmeijer, Moritz Kueblbeck, Vilma Jimenez Sabinina, Jan Ellenberg, Jonas Ries
Published in: Nature Methods, Issue 16/10, 2019, Page(s) 1045-1053, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-019-0574-9

Cost-efficient open source laser engine for microscopy

Author(s): Daniel Schröder, Joran Deschamps, Anindita Dasgupta, Ulf Matti, Jonas Ries
Published in: Biomedical Optics Express, Issue 11/2, 2020, Page(s) 609, ISSN 2156-7085
Publisher: The Optical Society
DOI: 10.1364/boe.380815

EMU: reconfigurable graphical user interfaces for Micro-Manager

Author(s): Deschamps, Joran; Ries, Jonas
Published in: BMC Bioinformatics, Issue 13, 2020, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-020-03727-8

The interplay between BAX and BAK tunes apoptotic pore growth to control mitochondrial-DNA-mediated inflammation

Author(s): Cosentino, Katia; Hertlein, Vanessa; Jenner, Andreas; Dellmann, Timo; Gojkovic, Milos; Peña-Blanco, Aida; Dadsena, Shashank; Wajngarten, Noel; Danial, John S.H.; Thevathasan, Jervis Vermal; Mund, Markus; Ries, Jonas; Garcia-Saez, Ana J.
Published in: Molecular Cell, Issue 12, 2022, ISSN 1097-4164
Publisher: Elsevier
DOI: 10.1016/j.molcel.2022.01.008

Identification of novel synaptonemal complex components in C. elegans

Author(s): M.E. Hurlock, I. Čavka, J. Haversat, M. Wooten, Z. Nizami, R. Turniansky, P. Hoess, J. Ries, J.G. Gall, S. Köhler, Y. Kim
Published in: J Cell Biol, 2020, ISSN 0021-9525
Publisher: Rockefeller University Press
DOI: 10.1083/jcb.201910043

Accurate 4Pi single-molecule localization using an experimental PSF model

Author(s): Li, Yiming; Buglakova, Elena; Zhang, Yongdeng; Thevathasan, Jervis Vermal; Bewersdorf, Joerg; Ries, Jonas
Published in: Optics Letters, Issue 10, 2020, ISSN 0146-9592
Publisher: Optical Society of America
DOI: 10.1364/ol.397754

Maximum-likelihood model fitting for quantitative analysis of SMLM data

Author(s): Wu, Yu-Le; Hoess, Philipp; Tschanz, Aline; Matti, Ulf; Mund, Markus; Ries, Jonas
Published in: Nature Methods, 2023, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-022-01676-z

Site-Specifically-Labeled Antibodies for Super-Resolution Microscopy Reveal

Author(s): Susanna M, Früh; Ulf, Matti; Philipp R, Spycher; Marina, Rubini; Sebastian, Lickert; Thomas, Schlichthaerle; Ralf, Jungmann; Viola, Vogel; Jonas, Ries; Ingmar, Schoen
Published in: ACS Nano, Issue 8, 2021, ISSN 1936-0851
Publisher: American Chemical Society
DOI: 10.1021/acsnano.1c03677

Quantitative Data Analysis in Single-Molecule Localization Microscopy

Author(s): Yu-Le Wu; Aline Tschanz; Leonard Krupnik; Jonas Ries
Published in: Trends in Cell Biology, Issue 4, 2020, ISSN 0962-8924
Publisher: Elsevier BV
DOI: 10.1016/j.tcb.2020.07.005

Other (7)

Universal inverse modelling of point spread functions for SMLM localization and microscope characterization

Author(s): Sheng Liu; Jianwei Chen; Jonas Hellgoth; Lucas-Raphael Mueller; Boris Ferdman; Christian Karras; Dafei Xiao; Keith A Lidke; Rainer Heintzmann; Yoav Shechtman; Yiming Li; Jonas Ries
Published in: bioRxiv, 2023
Publisher: bioRxiv
DOI: 10.1101/2023.10.26.564064

Photon-free (s)CMOS camera characterization for artifact reduction in high- and super-resolution microscopy

Author(s): R. Diekmann, J. Deschamps, Y. Li, A. Tschanz, M. Kahnwald, U. Matti, J.
Published in: bioRxiv, 2021
Publisher: bioRxiv

Maximum-Likelihood Model Fitting for Quantitative Analysis of SMLM Data

Author(s): Y.-L. Wu, P. Hoess, A. Tschanz, U. Matti, M. Mund, J. Ries
Published in: 2021
Publisher: bioRxiv
DOI: 10.1101/2021.08.30.456756

Superresolution Microscopy Reveals Partial Preassembly and Subsequent Bending of the Clathrin Coat during Endocytosis

Author(s): M. Mund, A. Tschanz, Y.-L. Wu, F. Frey, J.L. Mehl, M. Kaksonen, O. Avinoam, U.S. Schwarz, J. Ries
Published in: bioRxiv, 2021
Publisher: bioRxiv
DOI: 10.1101/2021.10.12.463947

Fast and robust 3D MINFLUX excitation with a variable phase plate

Author(s): Takahiro Deguchi; Jonas Ries
Published in: bioRxiv, 2023
Publisher: bioRxiv
DOI: 10.1101/2023.10.31.564945

Automated 3D multi-color single-molecule localization microscopy

Author(s): Rory M Power; Aline Tschanz; Timo Zimmermann; Jonas Ries
Published in: bioRxiv, 2023
Publisher: bioRxiv
DOI: 10.1101/2023.10.23.563122

Three dimensional particle averaging for structural imaging of macromolecular complexes by localization microscopy

Author(s): Rieger, B., Stallinga, S., Heydarian, H., Schueder, F., Jungmann, R., Ries, J., Przybylski, A., Bates, M., Keller-Findeisen, J., and van Werkhoven, B.
Published in: bioRxiv, 2019
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/837575