Publications using PYME (and its predecessors)

David Baddeley. Precision measurements with SMI and 4Pi Microscopy. PhD thesis, Ruperto-Carola University of Heidelberg, Germany, 2007. [ DOI ]

David Baddeley, Claudia Batram, Yanina Weiland, Christoph Cremer, and Udo J. Birk. Nanostructure analysis using spatially modulated illumination microscopy. Nature Protocols, 2(10):2640--2646, 2007. [ DOI ]

P. Lemmer, M. Gunkel, D. Baddeley, R. Kaufmann, A. Urich, Y. Weiland, J. Reymann, P. Müller, M. Hausmann, and C. Cremer. SPDM: Light microscopy with single-molecule resolution at the nanoscale. Applied Physics B: Lasers and Optics, 93(1):1--12, 2008. [ DOI ]

Jürgen Reymann, David Baddeley, Manuel Gunkel, Paul Lemmer, Werner Stadter, Thibaud Jegou, Karsten Rippe, Christoph Cremer, and Udo Birk. High-precision structural analysis of subnuclear complexes in fixed and live cells via spatially modulated illumination (SMI) microscopy. Chromosome Research, 16(3):367--382, 2008. [ DOI ]

P. Lemmer, M. Gunkel, Y. Weiland, P. Müller, D. Baddeley, R. Kaufmann, A. Urich, H. Eipel, R. Amberger, M. Hausmann, and C. Cremer. Using conventional fluorescent markers for far-field fluorescence localization nanoscopy allows resolution in the 10-nm range. Journal of Microscopy, 235(2):163--171, 2009. [ DOI ]

David Baddeley, Isuru D. Jayasinghe, Leo Lam, Sabrina Rossberger, Mark B. Cannell, and Christian Soeller. Optical single-channel resolution imaging of the ryanodine receptor distribution in rat cardiac myocytes. Proceedings of the National Academy of Sciences of the United States of America, 106(52):22275--22280, 2009. [ DOI ]

David Baddeley, Isuru D. Jayasinghe, Christoph Cremer, Mark B. Cannell, and Christian Soeller. Light-induced dark states of organic fluochromes enable 30 nm resolution imaging in standard media. Biophysical Journal, 96(2):L22--L24, 2009. [ DOI | http ]

David Baddeley, Mark B. Cannell, and Christian Soeller. Visualization of localization microscopy data. Microscopy and ..., 16(01):64--72, 2010. [ DOI | http ]

D. Baddeley, Y. Weiland, C. Batram, U. Birk, and C. Cremer. Model based precision structural measurements on barely resolved objects. Journal of Microscopy, 237(1):70--78, 2010. [ DOI ]

David Baddeley, Mark B. Cannell, and Christian Soeller. Three-dimensional sub-100 nm super-resolution imaging of biological samples using a phase ramp in the objective pupil. Nano Research, 4(6):589--598, 2011. [ DOI ]

David Baddeley, David Crossman, Sabrina Rossberger, Juliette E. Cheyne, Johanna M. Montgomery, Isuru D. Jayasinghe, Christoph Cremer, Mark B. Cannell, and Christian Soeller. 4D super-resolution microscopy with conventional fluorophores and single wavelength excitation in optically thick cells and tissues. PLoS ONE, 6(5), 2011. [ DOI ]

Isuru D. Jayasinghe, David Baddeley, Cherrie H.T. Kong, Xander H.T. Wehrens, Mark B. Cannell, and Christian Soeller. Nanoscale organization of junctophilin-2 and ryanodine receptors within peripheral couplings of rat ventricular cardiomyocytes. Biophysical Journal, 102(5):L19--L21, 2012. [ DOI | http ]

Joseph Wong, David Baddeley, Eric A. Bushong, Zeyun Yu, Mark H. Ellisman, Masahiko Hoshijima, and Christian Soeller. Nanoscale Distribution of Ryanodine Receptors and Caveolin-3 in Mouse Ventricular Myocytes: Dilation of T-Tubules near Junctions. Biophysical Journal, 104(11):L22--L24, 2013. [ DOI | http ]

Isuru D. Jayasinghe, Harriet P. Lo, Garry P. Morgan, David Baddeley, Robert G. Parton, Christian Soeller, and Bradley S. Launikonis. Examination of the subsarcolemmal tubular system of mammalian skeletal muscle fibers. Biophysical Journal, 104(11):L19--L21, 2013. [ DOI | http ]

Sabrina Rossberger, Gerrit Best, David Baddeley, Rainer Heintzmann, Udo Birk, Stefan Dithmar, and Christoph Cremer. Combination of structured illumination and single molecule localization microscopy in one setup. Journal of Optics (United Kingdom), 15(9), 2013. [ DOI ]

Yufeng Hou, David J. Crossman, Vijay Rajagopal, David Baddeley, Isuru Jayasinghe, and Christian Soeller. Super-resolution fluorescence imaging to study cardiac biophysics: α-actinin distribution and Z-disk topologies in optically thick cardiac tissue slices. Progress in Biophysics and Molecular Biology, 115(2-3):328--339, 2014. [ DOI | http ]

Isuru D. Jayasinghe, Michelle Munro, David Baddeley, Bradley S. Launikonis, and Christian Soeller. Observation of the molecular organization of calcium release sites in fast- and slowtwitch skeletal muscle with nanoscale imaging. Journal of the Royal Society Interface, 11(99), 2014. [ DOI ]

Makoto Sakai and Masaaki Fujii. Super- Resolution Microscopy Methods and Protocols, volume 64. Humana Press, 2015. [ DOI ]

David J. Crossman, Yufeng Hou, Isuru Jayasinghe, David Baddeley, and Christian Soeller. Combining confocal and single molecule localisation microscopy: A correlative approach to multi-scale tissue imaging. Methods, 88:98--108, 2015. [ DOI | http ]

Francesca Bottanelli, Emil B Kromann, Edward S Allgeyer, Roman S Erdmann, Stephanie Wood Baguley, George Sirinakis, Alanna Schepartz, David Baddeley, Derek K Toomre, James E Rothman, and Joerg Bewersdorf. Two-colour live-cell nanoscale imaging of intracellular targets. Nature communications, 7(May 2015):10778, 2016. [ DOI | arXiv | http ]

Peng Yuan, Carlo Condello, C. Dirk Keene, Yaming Wang, Thomas D. Bird, Steven M. Paul, Wenjie Luo, Marco Colonna, David Baddeley, and Jaime Grutzendler. TREM2 Haplodeficiency in Mice and Humans Impairs the Microglia Barrier Function Leading to Decreased Amyloid Compaction and Severe Axonal Dystrophy. Neuron, 90(4):724--739, 2016. [ DOI | http ]

Michelle L. Munro, Isuru D. Jayasinghe, Qiongling Wang, Ann Quick, Wei Wang, David Baddeley, Xander H.T. Wehrens, and Christian Soeller. Junctophilin-2 in the nanoscale organisation and functional signalling of ryanodine receptor clusters in cardiomyocytes. Journal of Cell Science, 129(23):4388--4398, 2016. [ DOI ]

Benjamin S. Stratton, Jason M. Warner, Zhenyong Wu, Joerg Nikolaus, George Wei, Emma Wagnon, David Baddeley, Erdem Karatekin, and Ben O'Shaughnessy. Cholesterol Increases the Openness of SNARE-Mediated Flickering Fusion Pores. Biophysical Journal, 110(7):1538--1550, 2016. [ DOI | http ]

Lucy Goodman, David Baddeley, Wojciech Ambroziak, Clarissa L. Waites, Craig C. Garner, Christian Soeller, and Johanna M. Montgomery. N-terminal SAP97 isoforms differentially regulate synaptic structure and postsynaptic surface pools of AMPA receptors. Hippocampus, 27(6):668--682, 2017. [ DOI ]

David J. Crossman, Xin Shen, Mia Jüllig, Michelle Munro, Yufeng Hou, Martin Middleditch, Darshan Shrestha, Amy Li, Sean Lal, Cristobal G. Dos Remedios, David Baddeley, Peter N. Ruygrok, and Christian Soeller. Increased collagen within the transverse tubules in human heart failure. Cardiovascular Research, 113(8):879--891, 2017. [ DOI ]

Ruisheng Lin, Alexander H. Clowsley, Isuru D. Jayasinghe, David Baddeley, and Christian Soeller. Algorithmic corrections for localization microscopy with sCMOS cameras - characterisation of a computationally efficient localization approach. Optics Express, 25(10):11701, 2017. [ DOI | http ]

Isuru Jayasinghe, Alexander H. Clowsley, Ruisheng Lin, Tobias Lutz, Carl Harrison, Ellen Green, David Baddeley, Lorenzo Di Michele, and Christian Soeller. True Molecular Scale Visualization of Variable Clustering Properties of Ryanodine Receptors. Cell Reports, 22(2):557--567, 2018. [ DOI | http ]

Andrew E S Barentine, Lena K Schroeder, Michael Graff, David Baddeley, and Joerg Bewersdorf. Simultaneously Measuring Image Features and Resolution in Live-Cell STED Images. Biophysj, pages 1--6, 2018. [ DOI | http ]

Andreas M. Ernst, Saad A. Syed, Omar Zaki, Francesca Bottanelli, Hong Zheng, Moritz Hacke, Zhiqun Xi, Felix Rivera-Molina, Morven Graham, Aleksander A. Rebane, Patrik Björkholm, David Baddeley, Derek Toomre, Frederic Pincet, and James E. Rothman. S-Palmitoylation Sorts Membrane Cargo for Anterograde Transport in the Golgi. Developmental Cell, 47(4):479--493.e7, 2018. [ DOI ]

Lorena Benedetti, Andrew E.S. Barentine, Mirko Messa, Heather Wheeler, Joerg Bewersdorf, and Pietro De Camilli. Light-activated protein interaction with high spatial subcellular confinement. Proceedings of the National Academy of Sciences of the United States of America, 115(10):E2238--E2245, 2018. [ DOI ]

Tobias MP Hartwich, Kenny KH Chung, Lena Schroeder, Joerg Bewersdorf, Christian Soeller, and David Baddeley. A stable, high refractive index, switching buffer for super-resolution imaging. bioRxiv, page 465492, 2018. [ DOI | http ]

Patrick D.Ellis Fisher, Qi Shen, Bernice Akpinar, Luke K. Davis, Kenny Kwok Hin Chung, David Baddeley, Andela Šarić, Thomas J. Melia, Bart W. Hoogenboom, Chenxiang Lin, and C. Patrick Lusk. A Programmable DNA Origami Platform for Organizing Intrinsically Disordered Nucleoporins within Nanopore Confinement. ACS Nano, 12(2):1508--1518, 2018. [ DOI ]

Thomas M.D. Sheard, Miriam E. Hurley, John Colyer, Ed White, Ruth Norman, Eleftheria Pervolaraki, Kaarjel K. Narayanasamy, Yufeng Hou, Hannah M. Kirton, Zhaokang Yang, Liam Hunter, Jung Uk Shim, Alexander H. Clowsley, Andrew J. Smith, David Baddeley, Christian Soeller, Michael A. Colman, and Izzy Jayasinghe. Three-dimensional and chemical mapping of intracellular signaling nanodomains in health and disease with enhanced expansion microscopy. ACS Nano, 13(2):2143--2157, 2019. [ DOI ]

Juliette E. Cheyne, Nawal Zabouri, David Baddeley, and Christian Lohmann. Spontaneous Activity Patterns Are Altered in the Developing Visual Cortex of the Fmr1 Knockout Mouse. Frontiers in Neural Circuits, 13(September):1--8, 2019. [ DOI ]

Michael M. Lacy, David Baddeley, and Julien Berro. Single-molecule turnover dynamics of actin and membrane coat proteins in clathrin-mediated endocytosis. eLife, 8:1--24, 2019. [ DOI ]

Lena K. Schroeder, Andrew E.S. Barentine, Holly Merta, Sarah Schweighofer, Yongdeng Zhang, David Baddeley, Joerg Bewersdorf, and Shirin Bahmanyar. Dynamic nanoscale morphology of the ER surveyed by STED microscopy. Journal of Cell Biology, 218(1):83--96, 2019. [ DOI ]

Mary Grace M. Velasco, Mengyang Zhang, Jacopo Antonello, Peng Yuan, Edward S Allgeyer, Dennis May, Ons M'Saad, Phylicia Kidd, Andrew E. S. Barentine, Valentina Greco, Jaime Grutzendler, Martin J. Booth, and Joerg Bewersdorf. 3D super-resolution deep-tissue imaging in living mice. bioRxiv Biophysics, 2019. [ DOI | http ]

Andrew E S Barentine, Yu Lin, Miao Liu, Phylicia Kidd, Leonhard Balduf, Michael R Grace, Siyuan Wang, Joerg Bewersdorf, and David Baddeley. 3D Multicolor Nanoscopy at 10,000 Cells a Day. bioRxiv, pages 1--12, 2019. [ DOI ]

James Jonkman, Claire M. Brown, Graham D. Wright, Kurt I. Anderson, and Alison J. North. Tutorial: guidance for quantitative confocal microscopy. Nature Protocols, pages 1--27, 2020. [ DOI | http ]

Anna Oliveras, Clara Serrano-Novillo, Cristina Moreno, Alicia de la Cruz, Carmen Valenzuela, Christian Soeller, Núria Comes, and Antonio Felipe. The unconventional biogenesis of Kv7.1-KCNE1 complexes. Science Advances, 6(14):1--13, 2020. [ DOI ]

Mengyuan Sun, Kevin Hu, Joerg Bewersdorf, and Thomas D Pollard. Running Title: mEos3.2 photophysics in cells Optimizing imaging conditions for photoconvertible protein mEos3.2 in live and fixed cells. bioRxiv, page 2020.05.28.119735, 2020. [ DOI | arXiv | http ]

Alexander H Clowsley, William T Kaufhold, Tobias Lutz, Anna Meletiou, Lorenzo Di Michele, and Christian Soeller. Repeat DNA-PAINT suppresses background and non-specific signals in optical nanoscopy. bioRxiv Molecular Biology, pages 6--10, 2020. [ DOI | http ]

Kenny Kwok Hin Chung, Zhao Zhang, Phylicia Kidd, Yongdeng Zhang, Nathan D Williams, Bennett Rollins, Yang Yang, Chenxiang Lin, David Baddeley, and Joerg Bewersdorf. Fluorogenic probe for fast 3D whole-cell DNA-PAINT. bioRxiv, page 2020.04.29.066886, 2020. [ DOI | http ]

Ruisheng Lin, Alexander H. Clowsley, Tobias Lutz, David Baddeley, and Christian Soeller. 3D super-resolution microscopy performance and quantitative analysis assessment using DNA-PAINT and DNA origami test samples. Methods, 174(March 2019):56--71, 2020. [ DOI | http ]