Cool papers that develop or use new microscopy approaches
Editors Christophe Leterrier Philip R Nicovich Ricardo Henriques
Daniel Sage, Thanh-An Pham, Hazen Babcock, Tomas Lukes, Thomas Pengo, Ramraj Velmurugan, Alex Herbert, Anurag Agarwal, Silvia Colabrese, Ann Wheeler, Anna Archetti, Bernd Rieger, Raimund Ober, Guy M. Hagen, Jean-Baptiste Sibarita, Jonas Ries, Ricardo Henriques, Michael Unser, Seamus Holden
http://dx.doi.org/10.1101/362517
Jul 05, 2018
Adam K Glaser, Ye Chen, Chengbo Yin, Linpeng Wei, Lindsey Barner, Nicholas Reder, Jonathan Liu
http://dx.doi.org/10.1101/270207
Jun 25, 2018
BigStitcher: Reconstructing high-resolution image datasets of cleared and expanded samples (2018)
David Hörl, Fabio Rojas Rusak, Friedrich Preusser, Paul Tillberg, Nadine Randel, Raghav K. Chhetri, Albert Cardona, Philipp J. Keller, Hartmann Harz, Heinrich Leonhardt, Mathias Treier, Stephan Preibisch
http://dx.doi.org/10.1101/343954
Jun 11, 2018 - Open-source and in Fiji, #BigStitcher merges multi-tile and multi-view acquisitions, allowing massive datasets to be explored and mined.
Content-Aware Image Restoration: Pushing the Limits of Fluorescence Microscopy (2017)
Martin Weigert, Uwe Schmidt, Tobias Boothe, Andreas Müller, Alexandr Dibrov, Akanksha Jain, Benjamin Wilhelm, Deborah Schmidt, Coleman Broaddus, Siân Culley, Maurício Rocha-Martins, Fabián Segovia-Miranda, Caren Norden, Ricardo Henriques, Marino Zerial, Michele Solimena, Jochen Rink, Pavel Tomancak, Loic Royer, Florian Jug, Eugene W. Myers
http://dx.doi.org/10.1101/236463
Jun 06, 2018 - CARE - deep learning by the guys that develop Fiji, to massively enhance microscopy images. It features the capacity to denoise, super-resolve and enhance deep imaging. Now with code made available in https://github.com/csbdeep/csbdeep.
The Rényi divergence enables accurate and precise cluster analysis for localization microscopy (2018)
Adela D Staszowska, Patrick Fox-Roberts, Liisa M Hirvonen, Christopher J Peddie, Lucy M Collinson, Gareth E Jones, Susan Cox
http://dx.doi.org/10.1093/bioinformatics/bty403
Jun 06, 2018
Three dimensional live-cell STED microscopy at increased depth using a water immersion objective (2018)
Jörn Heine, Christian A. Wurm, Jan Keller-Findeisen, Andreas Schönle, Benjamin Harke, Matthias Reuss, Franziska R. Winter, Gerald Donnert
http://www.ncbi.nlm.nih.gov/pubmed/29864829
Jun 06, 2018
Correlative live and super-resolution imaging reveals the dynamic structure of replication domains (2018)
Wanqing Xiang, M. Julia Roberti, Jean-Karim Hériché, Sébastien Huet, Stephanie Alexander, Jan Ellenberg
http://dx.doi.org/10.1083/jcb.201709074
Jun 06, 2018
Breaking the Axial Diffraction Limit: A Guide to Axial Super‐Resolution Fluorescence Microscopy (2018)
Wenjie Liu, Kimani C. Toussaint, Chukwuemeka Okoro, Dazhao Zhu, Youhua Chen, Cuifang Kuang, Xu Liu
http://dx.doi.org/10.1002/lpor.201700333
Jun 06, 2018
Dynamic Bayesian Cluster Analysis of Live‐Cell Single Molecule Localization Microscopy Datasets (2018)
Juliette Griffié, Garth L. Burn, David J. Williamson, Ruby Peters, Patrick Rubin-Delanchy, Dylan M. Owen
http://dx.doi.org/10.1002/smtd.201800008
Jun 05, 2018 - A novel cluster analysis algorithm / strategy to characterise molecular assemblies in living-cells imaged by SMLM. An excellent follow up to the author's extensive development of Bayesian cluster identification analysis (https://doi.org/10.1038/nmeth.3612).
SRRF: Universal live-cell super-resolution microscopy (2018)
Siân Culley, Kalina L. Tosheva, Pedro Matos Pereira, Ricardo Henriques
http://www.ncbi.nlm.nih.gov/pubmed/29852248
Jun 04, 2018 - The authors show that SRRF (https://doi.org/10.1038/ncomms12471) imaging can be optimised by SQUIRREL (https://doi.org/10.1038/nmeth.4605) to achieve high-quality super-resolution imaging in almost any microscope.
T. TAKESHIMA, T. TAKAHASHI, J. YAMASHITA, Y. OKADA, S. WATANABE
http://www.ncbi.nlm.nih.gov/pubmed/29797718
Jun 04, 2018
Expansion Microscopy for Brain Imaging (2019)
Jae-Byum Chang
http://dx.doi.org/10.1007/978-981-10-9020-2_13
Jun 04, 2018
Quantum dot conjugated nanobodies for multiplex imaging of protein dynamics at synapses (2018)
Souvik Modi, Nathalie F. Higgs, David Sheehan, Lewis D. Griffin, Josef T. Kittler
http://dx.doi.org/10.1039/c7nr09130c
Jun 04, 2018
MINFLUX monitors rapid molecular jumps with superior spatiotemporal resolution (2018)
Yvan Eilers, Haisen Ta, Klaus C. Gwosch, Francisco Balzarotti, Stefan W. Hell
http://www.ncbi.nlm.nih.gov/pubmed/29844182
Jun 04, 2018
http://dx.doi.org/10.1038/s41598-018-19981-z
Jun 04, 2018 - Why buy an expensive sCMOS camera when a cheap one will do. See also a related recent article by Diekmann et al.
Glyoxal as an alternative fixative to formaldehyde in immunostaining and super‐resolution microscopy (2018)
Katharina N Richter, Natalia H Revelo, Katharina J Seitz, Martin S Helm, Deblina Sarkar, Rebecca S Saleeb, Elisa D'Este, Jessica Eberle, Eva Wagner, Christian Vogl, Diana F Lazaro, Frank Richter, Javier Coy‐Vergara, Giovanna Coceano, Edward S Boyden, Rory R Duncan, Stefan W Hell, Marcel A Lauterbach, Stephan E Lehnart, Tobias Moser, Tiago F Outeiro, Peter Rehling, Blanche Schwappach, Ilaria Testa, Bolek Zapiec, Silvio O Rizzoli
http://www.ncbi.nlm.nih.gov/pubmed/29146773
Jun 04, 2018 - In a world full of cell fixation artefacts, glyoxal may give an alternative closer to nature. People trying glyoxal fixation have been reporting their results on Twitter, check the hashtag #glyoxal.
Memoir on inventing the confocal scanning microscope (1988)
M. Minsky
http://dx.doi.org/10.1002/sca.4950100403
May 29, 2018
Yu Li, Fan Xu, Fa Zhang, Pingyong Xu, Mingshu Zhang, Ming Fan, Lihua Li, Xin Gao, Renmin Han
http://arxiv.org/abs/1805.07777v2
May 29, 2018
Deep-STORM: super-resolution single-molecule microscopy by deep learning (2018)
Elias Nehme, Lucien E. Weiss, Tomer Michaeli, Yoav Shechtman
http://dx.doi.org/10.1364/optica.5.000458
May 29, 2018
High-throughput, high-resolution Generated Adversarial Network Microscopy (2018)
Hao Zhang, Xinlin Xie, Chunyu Fang, Yicong Yang, Di Jin, Peng Fei
http://arxiv.org/abs/1801.07330v1
May 29, 2018
DeepLoco: Fast 3D Localization Microscopy Using Neural Networks (2018)
Nicholas Boyd, Eric Jonas, Hazen P Babcock, Benjamin Recht
http://dx.doi.org/10.1101/267096
May 29, 2018
Observing the cell in its native state: Imaging subcellular dynamics in multicellular organisms (2018)
Tsung-Li Liu, Srigokul Upadhyayula, Daniel E. Milkie, Ved Singh, Kai Wang, Ian A. Swinburne, Kishore R. Mosaliganti, Zach M. Collins, Tom W. Hiscock, Jamien Shea, Abraham Q. Kohrman, Taylor N. Medwig, Daphne Dambournet, Ryan Forster, Brian Cunniff, Yuan Ruan, Hanako Yashiro, Steffen Scholpp, Elliot M. Meyerowitz, Dirk Hockemeyer, David G. Drubin, Benjamin L. Martin, David Q. Matus, Minoru Koyama, Sean G. Megason, Tom Kirchhausen, Eric Betzig
http://www.ncbi.nlm.nih.gov/pubmed/29674564
May 29, 2018
Christopher H. Bohrer, Xinxing Yang, Zhixin Lyu, Shih-Chin Wang, Jie Xiao
http://dx.doi.org/10.1101/304816
May 29, 2018
Expansion Stimulated Emission Depletion Microscopy (ExSTED) (2018)
Mengfei Gao, Riccardo Maraspini, Oliver Beutel, Amin Zehtabian, Britta Eickholt, Alf Honigmann, Helge Ewers
http://www.ncbi.nlm.nih.gov/pubmed/29672025
May 29, 2018
Imaging beyond the super-resolution limits using ultrastructure expansion microscopy (UltraExM) (2018)
Davide Gambarotto, Fabian Zwettler, Marketa Cernohorska, Denis Fortun, Susanne Borgers, Jorn Heine, Jan-Gero Schloetel, Matthias Reuss, Michael Unser, Edward Boyden, Markus Sauer, Virginie Hamel, Paul Guichard
http://dx.doi.org/10.1101/308270
May 29, 2018
Nurmohammed Patwary, Ana Doblas, Chrysanthe Preza
http://dx.doi.org/10.1364/boe.9.001630
May 29, 2018
Deep learning achieves super-resolution in fluorescence microscopy (2018)
Hongda Wang, Yair Rivenson, Yiyin Jin, Zhensong Wei, Ronald Gao, Harun Gunaydin, Laurent Bentolila, Aydogan Ozcan
http://dx.doi.org/10.1101/309641
May 29, 2018
Self-interference 3D super-resolution microscopy for deep tissue investigations (2018)
Pierre Bon, Jeanne Linarès-Loyez, Maxime Feyeux, Kevin Alessandri, Brahim Lounis, Pierre Nassoy, Laurent Cognet
http://www.ncbi.nlm.nih.gov/pubmed/29713082
May 29, 2018
Anna-Karin Gustavsson, Petar N. Petrov, W. E. Moerner
http://www.ncbi.nlm.nih.gov/pubmed/29801343
May 29, 2018
cellSTORM - Cost-effective Super-Resolution on a Cellphone using dSTORM (2018)
Benedict Diederich, Patrick Then, Alexander Jügler, Ronny Förster, Rainer Heintzmann
http://arxiv.org/abs/1804.06244v1
May 29, 2018
Spatial orchestration of mitochondrial translation and OXPHOS complex assembly (2018)
Stefan Stoldt, Dirk Wenzel, Kirsten Kehrein, Dietmar Riedel, Martin Ott, Stefan Jakobs
http://www.ncbi.nlm.nih.gov/pubmed/29662179
May 29, 2018
Fast, long-term, super-resolution imaging with Hessian structured illumination microscopy (2018)
Xiaoshuai Huang, Junchao Fan, Liuju Li, Haosen Liu, Runlong Wu, Yi Wu, Lisi Wei, Heng Mao, Amit Lal, Peng Xi, Liqiang Tang, Yunfeng Zhang, Yanmei Liu, Shan Tan, Liangyi Chen
http://www.ncbi.nlm.nih.gov/pubmed/29644998
May 29, 2018
Using the NoiSee workflow to measure signal-to-noise ratios of confocal microscopes: (2018)
Alexia Ferrand, Kai D Schleicher, Nikolaus Ehrenfeuchter, Wolf Heusermann, Oliver Biehlmaier
http://dx.doi.org/10.1101/291500
May 29, 2018
Super-long single-molecule tracking reveals dynamic-anchorage-induced integrin function (2018)
Taka A. Tsunoyama, Yusuke Watanabe, Junri Goto, Kazuma Naito, Rinshi S. Kasai, Kenichi G. N. Suzuki, Takahiro K. Fujiwara, Akihiro Kusumi
http://www.ncbi.nlm.nih.gov/pubmed/29610485
May 29, 2018
Quantitative mapping and minimization of super-resolution optical imaging artifacts (2018)
Siân Culley, David Albrecht, Caron Jacobs, Pedro Matos Pereira, Christophe Leterrier, Jason Mercer, Ricardo Henriques
http://dx.doi.org/10.1038/nmeth.4605
May 29, 2018
Automating multimodal microscopy with NanoJ-Fluidics (2018)
Pedro Almada, Pedro Pereira, Siân Culley, Ghislaine Caillol, Fanny Boroni-Rueda, Christina L. Dix, Romain F. Laine, Guillaume Charras, Buzz Baum, Christophe Leterrier, Ricardo Henriques
http://dx.doi.org/10.1101/320416
May 29, 2018
Deep learning massively accelerates super-resolution localization microscopy (2018)
Wei Ouyang, Andrey Aristov, Mickaël Lelek, Xian Hao, Christophe Zimmer
http://www.ncbi.nlm.nih.gov/pubmed/29658943
May 29, 2018
Atsushi Matsuda, Lothar Schermelleh, Yasuhiro Hirano, Tokuko Haraguchi, Yasushi Hiraoka
http://www.ncbi.nlm.nih.gov/pubmed/29765093
May 29, 2018