Neubias Academy 2020

A guided tour for analyzing and quantifying single-molecule localization microscopy data

Part two: quantification strikes back

Webinar

• Slides: slides.pdf

• Main project page/ C++ code / Windows installer: https://github.com/flevet/SR-Tesseler

• Forum: https://forum.image.sc (tag "tesseler")

• Slides of Part one by Siân Culley: slides.pdf

Contact

Florian Levet

Reference to papers presented in the slides

Slide 3

Rossier, O., Octeau, V., Sibarita, J. et al. Integrins β1 and β3 exhibit distinct dynamic nanoscale organizations inside focal adhesions. Nat Cell Biol 14, 1057–1067 (2012). https://doi.org/10.1038/ncb2588

Slide 4

Charlotte Mariani-Floderer, Jean-Baptiste Sibarita, Cyril Favard, and Delphine M. Muriaux.AIDS Research and Human Retroviruses.Jul 2016.658-659. http://doi.org/10.1089/aid.2016.0052

Rossier, O., Octeau, V., Sibarita, J. et al. Integrins β1 and β3 exhibit distinct dynamic nanoscale organizations inside focal adhesions. Nat Cell Biol 14, 1057–1067 (2012). https://doi.org/10.1038/ncb2588

Deepak Nair, Eric Hosy, Jennifer D. Petersen, Audrey Constals, Gregory Giannone, Daniel Choquet, Jean-Baptiste Sibarita. Super-Resolution Imaging Reveals That AMPA Receptors Inside Synapses Are Dynamically Organized in Nanodomains Regulated by PSD95. Journal of Neuroscience 7 August 2013, 33 (32) 13204-13224. https://doi.org/10.1523/JNEUROSCI.2381-12.2013

Levet, F., Hosy, E., Kechkar, A. et al. SR-Tesseler: a method to segment and quantify localization-based super-resolution microscopy data. Nat Methods 12, 1065–1071 (2015). https://doi.org/10.1038/nmeth.3579

Slide 7

Baddeley, D., Cannell, M., & Soeller, C. (2010). Visualization of Localization Microscopy Data. Microscopy and Microanalysis, 16(1), 64-72. https://doi.org/10.1017/S143192760999122X

Slide 10

Deschout, H., Zanacchi, F., Mlodzianoski, M. et al. Precisely and accurately localizing single emitters in fluorescence microscopy. Nat Methods 11, 253–266 (2014). https://doi.org/10.1038/nmeth.2843

Nicovich, P., Owen, D. & Gaus, K. Turning single-molecule localization microscopy into a quantitative bioanalytical tool. Nat Protoc 12, 453–460 (2017). https://doi.org/10.1038/nprot.2016.166

Slide 11

B. D. Ripley, J ApplProbability13, 255-66 (1976).

Lagache T, Lang G, Sauvonnet N, Olivo-Marin JC (2013) Analysis of the Spatial Organization of Molecules with Robust Statistics. PLOS ONE 8(12): e80914. https://doi.org/10.1371/journal.pone.0080914

Slide 13

Truan Z, Tarancón Díez L, Bönsch C, et al. Quantitative morphological analysis of arrestin2 clustering upon G protein-coupled receptor stimulation by super-resolution microscopy. J Struct Biol. 2013;184(2):329‐334. https://doi.org/10.1016/j.jsb.2013.09.019

Slide 16

Sengupta, P., Jovanovic-Talisman, T., Skoko, D. et al. Probing protein heterogeneity in the plasma membrane using PALM and pair correlation analysis. Nat Methods 8, 969–975 (2011). https://doi.org/10.1038/nmeth.1704

Veatch SL, Machta BB, Shelby SA, Chiang EN, Holowka DA, et al. (2012) Correlation Functions Quantify Super-Resolution Images and Estimate Apparent Clustering Due to Over-Counting. PLOS ONE 7(2): e31457. https://doi.org/10.1371/journal.pone.0031457

Slide 18

Rubin-Delanchy, P., Burn, G., Griffié, J. et al. Bayesian cluster identification in single-molecule localization microscopy data. Nat Methods 12, 1072–1076 (2015). https://doi.org/10.1038/nmeth.3612

Slide 19

Williamson, D.J., Burn, G.L., Simoncelli, S. et al. Machine learning for cluster analysis of localization microscopy data. Nat Commun 11, 1493 (2020). https://doi.org/10.1038/s41467-020-15293-x

Slide 20

Martin Ester, Hans-Peter Kriegel, Jörg Sander, and Xiaowei Xu. 1996. A density-based algorithm for discovering clusters in large spatial databases with noise. In Proceedings of the Second International Conference on Knowledge Discovery and Data Mining (KDD’96). AAAI Press, 226–231.

Slide 26

Endesfelder, Ulrike et al . Multiscale Spatial Organization of RNA Polymerase in Escherichia coli. Biophysical Journal, Volume 105, Issue 1, 172 – 181. https://doi.org/10.1016/j.bpj.2013.05.048

Slide 31

Optical single-channel resolution imaging of the ryanodine receptor distribution in rat cardiac myocytes. David Baddeley, Isuru D. Jayasinghe, Leo Lam, Sabrina Rossberger, Mark B. Cannell, Christian Soeller. Proceedings of the National Academy of Sciences Dec 2009, 106 (52) 22275-22280. https://doi.org/10.1073/pnas.0908971106

Slide 41

Levet, F., Hosy, E., Kechkar, A. et al. SR-Tesseler: a method to segment and quantify localization-based super-resolution microscopy data. Nat Methods 12, 1065–1071 (2015). https://doi.org/10.1038/nmeth.3579

Andronov, L., Orlov, I., Lutz, Y. et al. ClusterViSu, a method for clustering of protein complexes by Voronoi tessellation in super-resolution microscopy. Sci Rep 6, 24084 (2016). https://doi.org/10.1038/srep24084

Slide 45

Levet, F., Hosy, E., Kechkar, A. et al. SR-Tesseler: a method to segment and quantify localization-based super-resolution microscopy data. Nat Methods 12, 1065–1071 (2015). https://doi.org/10.1038/nmeth.3579

Slide 51

Annibale P, Vanni S, Scarselli M, Rothlisberger U, Radenovic A (2011) Quantitative Photo Activated Localization Microscopy: Unraveling the Effects of Photoblinking. PLOS ONE 6(7): e22678. https://doi.org/10.1371/journal.pone.0022678

Slide 55

Jungmann, R., Avendaño, M., Woehrstein, J. et al. Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT. Nat Methods 11, 313–318 (2014). https://doi.org/10.1038/nmeth.2835

Jungmann, R., Avendaño, M., Dai, M. et al. Quantitative super-resolution imaging with qPAINT. Nat Methods 13, 439–442 (2016). https://doi.org/10.1038/nmeth.3804

Slide 56

Optical single-channel resolution imaging of the ryanodine receptor distribution in rat cardiac myocytes. David Baddeley, Isuru D. Jayasinghe, Leo Lam, Sabrina Rossberger, Mark B. Cannell, Christian Soeller. Proceedings of the National Academy of Sciences Dec 2009, 106 (52) 22275-22280. https://doi.org/10.1073/pnas.0908971106

Asghari P, Scriven DR, Sanatani S, Gandhi SK, Campbell AI, Moore ED. Nonuniform and variable arrangements of ryanodine receptors within mammalian ventricular couplons. Circ Res. 2014;115(2):252‐262. https://doi.org/10.1161/CIRCRESAHA.115.303897

Jayasinghe, Isuru et al. True Molecular Scale Visualization of Variable Clustering Properties of Ryanodine Receptors. Cell Reports, Volume 22, Issue 2, 557 – 567. https://doi.org/10.1016/j.celrep.2017.12.045