This is an incomplete list of publications which have used PYME (or what would later become PYME). If you have used PYME in your work, please let us know and we'll add your publication here. Publications which describe algorithms or their implementations in PYME are highlighted in blue. Publications decribing plugins are highlighted in cyan.
Andrew E. S. Barentine, Yu Lin, Edward M. Courvan, Phylicia Kidd, Miao Liu, Leonhard Balduf, Timy Phan, Felix Rivera-Molina, Michael R. Grace, Zach Marin, Mark Lessard, Juliana Rios Chen, Siyuan Wang, Karla M. Neugebauer, Joerg Bewersdorf and David Baddeley, “An Integrated Platform for High-Throughput Nanoscopy,” Nature Biotechnology (2023). [ DOI | html ]
Lukas A. Fuentes, Zach Marin, Jonathan Tyson, David Baddeley, Joerg Bewersdorf; "The nanoscale organization of reticulon 4 shapes local endoplasmic reticulum structure in situ." Journal of Cell Biology 2023; 222 (10): e202301112. [DOI]
Florian Schueder, Felix Rivera-Molina, Maohan Su, Phylicia Kidd, James E. Rothman, Derek Toomre, Joerg Bewersdorf "Unraveling cellular complexity with unlimited multiplexed super-resolution imaging" BioRxiv 2023 [DOI]
Clowsley AH, Meletiou A, Lučinskaitė E, Jansen I, Jones PP, Louch WE, Soeller C, "Analysis of RyR2 distribution in HEK293 cells and mouse cardiac myocytes using 3D MINFLUX microscopy", bioRxiv, 2023, [DOI|URL]
Jin X, Meletiou A, Chung J, Tilunaite A, Demydenko K, Dries E, Puertas RD, Amoni M, Tomar A, Claus P, Soeller C, Rajagopal V, Sipido K, Roderick HL, "InsP3R-RyR channel crosstalk augments sarcoplasmic reticulum Ca2+ release and arrhythmogenic activity in post-MI pig cardiomyocytes", Journal of Molecular and Cellular Cardiology, 2023, [DOI|URL]
Hou Y, Laasmaa M, Li J, Shen X, Manfra O, Nordén ES, Le C, Zhang L, Sjaastad I, Jones PP, Soeller C, Louch WE, "Live-cell photoactivated localization microscopy correlates nanoscale ryanodine receptor configuration to calcium sparks in cardiomyocytes", Nature Cardiovascular Research, 2023, [DOI|URL]
Alexander H Clowsley, Anna Meletiou, Evelina Lucinskaite, Isabelle Jansen, Peter P Jones, William E Louch, Christian Soeller, "Analysis of RyR2 distribution in HEK293 cells and mouse cardiac myocytes using 3D MINFLUX microscopy" BioRxiv 2023 [DOI]
Marin, Z., L.A. Fuentes, J. Bewersdorf, and D. Baddeley. 2023. "Extracting nanoscale membrane morphology from single-molecule localizations." Biophysical Journal, 2023:S0006-3495(23)00398-3. [DOI]
Parveen S, Cheah PHS, Worthington LPI, Smither RA, Munro ML, Bussey CT, Lamberts RR, Jones PP, "Depressed HCN4 function in the type 2 diabetic sinoatrial node", Molecular and Cellular Biochemistry, 2022 [DOI]
Zach Marin, Michael Graff, Andrew E. S. Barentine, Christian Soeller, Kenny Kwok Hin Chung, Lukas A. Fuentes and David Baddeley. "PYMEVisualize: an open-source tool for exploring 3D super-resolution data" Nature Methods, 18(May 2021):582--584, 2021. [ DOI | http ]
Eerqing N, Subramanian S, Rubio J, Lutz T, Wu H, Anders J, Soeller C, Vollmer F, "Comparing Transient Oligonucleotide Hybridization Kinetics Using DNA-PAINT and Optoplasmonic Single-Molecule Sensing on Gold Nanorods", ACS Photonics, 2021,
Munro ML, van Hout I, Aitken-Buck HM, Sugunesegran R, Bhagwat K, Davis PJ, Lamberts RR, Coffey S, Soeller C, Jones PP, "Human Atrial Fibrillation Is Not Associated With Remodeling of Ryanodine Receptor Clusters", Frontiers in Cell and Developmental Biology, 2021, [DOI|URL]
Hou Y, Bai J, Shen X, de Langen O, Li A, Lal S, dos Remedios CG, Baddeley D, Ruygrok PN, Soeller C, Crossman DJ, "Nanoscale Organisation of Ryanodine Receptors and Junctophilin-2 in the Failing Human Heart", Frontiers in Physiology, 2021, [DOI|URL]
Clowsley AH, Kaufhold WT, Lutz T, Meletiou A, Di Michele L, Soeller C, "Repeat DNA-PAINT suppresses background and non-specific signals in optical nanoscopy", Nature Communications, 2021, [DOI|URL]
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 ]
Clowsley AH, Kaufhold WT, Lutz T, Meletiou A, Di Michele L, Soeller C, "Detecting nanoscale distribution of protein pairs by proximity dependent super-resolution microscopy", Journal of the American Chemical Society, 2020, [DOI|URL]
Oliveras A, Serrano-Novillo C, Moreno C, Cruz Adl, Valenzuela C, Soeller C, Comes N, Felipe A, "The unconventional biogenesis of Kv7.1-KCNE1 complexes", Science Advances, 2020, [DOI|URL]
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 ]
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 ]
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 ]
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 ]
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 ]
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 ]
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 ]
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 ]
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 ]
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 ]
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 ]
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 ]
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 ]
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 ]
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 ]
Lutz T, Clowsley AH, Lin R, Pagliara S, Di Michele L, Soeller C, "Versatile multiplexed super-resolution imaging of nanostructures by Quencher-Exchange-PAINT", Nano Research, 2018, [DOI|URL]<\p>
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 ]
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 ]
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 ]
Jeynes JCG, Geraki K, Jeynes C, Zhaohong M, Bettiol AA, Latorre E, Harries LW, Soeller C, "Nanoscale Properties of Human Telomeres Measured with a Dual Purpose X-ray Fluorescence and Super Resolution Microscopy Gold Nanoparticle Probe.", ACS nano, 2017, [DOI|URL]<\p>
Jones RA, Harrison C, Eaton SL, Llavero Hurtado M, Graham LC, Alkhammash L, Oladiran OA, Gale A, Lamont DJ, Simpson H, Simmen MW, Soeller C, Wishart TM, Gillingwater TH, "Cellular and Molecular Anatomy of the Human Neuromuscular Junction", Cell Reports, 2017, [DOI|URL]<\p>
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 ]
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 ]
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 ]
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 ]
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 ]
Makoto Sakai and Masaaki Fujii. Super- Resolution Microscopy Methods and Protocols, volume 64. Humana Press, 2015. [ DOI ]
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 ]
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 ]
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 ]
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 ]
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, 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 ]
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 ]
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 ]
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. Visualization of localization microscopy data. Microscopy and ..., 16(01):64--72, 2010. [ DOI | http ]
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, 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 ]
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 ]
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, 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 ]
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 ]
David Baddeley. Precision measurements with SMI and 4Pi Microscopy. PhD thesis, Ruperto-Carola University of Heidelberg, Germany, 2007. [ DOI ]