6. References

Below you'll find a short (and by no means exhaustive) collection of papers to get you started on the different topics.

Super-resolution microscopy (reviews)

1. Schermelleh, Lothar, et al. "Super-resolution microscopy demystified." (2019) Nature Cell Biology 21(1) 72. link
2. Sahl, Steffen J., Stefan W. Hell, and Stefan Jakobs. "Fluorescence nanoscopy in cell biology." (2017) Nature Reviews Molecular Cell Biology ** 18(11)685 link
3. Schermelleh, Lothar, Rainer Heintzmann, and Heinrich Leonhardt. "A guide to super-resolution fluorescence microscopy." (2010) The Journal of Cell Biology 190(2)165-175 link
4. Huang, Bo, Mark Bates, and Xiaowei Zhuang. "Super-resolution fluorescence microscopy." (2009) Annual Review of Biochemistry 78:993-1016 link

SMLM (reviews)

1. Baddeley, David, and Joerg Bewersdorf. "Biological insight from super-resolution microscopy: what we can learn from localization-based images." (2018) Annual Review of Biochemistry 87:965-989 link
2. Sigal, Yaron M., Ruobo Zhou, and Xiaowei Zhuang. "Visualizing and discovering cellular structures with super-resolution microscopy." (2018) Science 361(6405)880-887 link
3. Sauer, Markus, and Mike Heilemann. "Single-molecule localization microscopy in eukaryotes."(2017) Chemical Reviews 117(11)7478-7509. link
4. Liu, Zhe, Luke D. Lavis, and Eric Betzig. "Imaging live-cell dynamics and structure at the single-molecule level." (2015) Molecular Cell 58(4) 644-659. link
5. Choquet, D., Sainlos, M. & Sibarita, JB. "Advanced imaging and labelling methods to decipher brain cell organization and function." (2021) Nat Rev Neurosci 22, 237–255. link

Resolution

1. Descloux, Adrien Charles, Kristin Stefanie Grussmayer, and Aleksandra Radenovic. "Parameter-free image resolution estimation based on decorrelation analysis." (2019) Nature Methods 16 918-924 link
2. Nieuwenhuizen, Robert PJ, et al. "Measuring image resolution in optical nanoscopy." (2013) Nature Methods 10(6):557 link
3. Banterle, Niccolò, et al. "Fourier ring correlation as a resolution criterion for super-resolution microscopy." (2013) Journal of Structural Biology 183(3):363-367 link

Spatial analysis, quantification, clustering (Background)

1. Nicovich, Philip R., Dylan M. Owen, and Katharina Gaus. "Turning single-molecule localization microscopy into a quantitative bioanalytical tool." (2017) Nature Protocols 12(3):453 link
2. Durisic, Nela, Lara Laparra Cuervo, and Melike Lakadamyali. "Quantitative super-resolution microscopy: pitfalls and strategies for image analysis." (2014) Current Opinion in Chemical Biology 20:22-28 link
3. Coltharp, Carla, Xinxing Yang, and Jie Xiao. "Quantitative analysis of single-molecule superresolution images." (2014) Current Opinion in Structural Biology 28:112-121 link

Clustering (Software)

1. Griffié, Juliette, et al. "A Bayesian cluster analysis method for single-molecule localization microscopy data." (2016) Nature Protocols 11(12):2499 link
2. Levet, Florian, et al. "SR-Tesseler: a method to segment and quantify localization-based super-resolution microscopy data." (2015) Nature Methods 12(11):1065 link
3. Sengupta, Prabuddha, et al. "Probing protein heterogeneity in the plasma membrane using PALM and pair correlation analysis." (2011) Nature Methods 8(11):969.link

Tracking

1. Manley, Suliana, et al. "High-density mapping of single-molecule trajectories with photoactivated localization microscopy." (2008) Nature Methods 5(2):155-157. link
2. Giannone, G. et al. "Dynamic superresolution imaging of endogenous proteins on living cells at ultra-high density." (2010) Biophys. J. 99, 1303–1310. link
3. Hoze, Nathanael, et al. "Heterogeneity of AMPA receptor trafficking and molecular interactions revealed by superresolution analysis of live cell imaging." (2012) PNAS 109.42:17052-17057. link

Counting

1. Hummer, Gerhard, Franziska Fricke, and Mike Heilemann. "Model-independent counting of molecules in single-molecule localization microscopy." (2016) Molecular Biology of the Cell 27.22: 3637-3644. link
2. Puchner, Elias M., et al. "Counting molecules in single organelles with superresolution microscopy allows tracking of the endosome maturation trajectory." (2013) PNAS 110.40:16015-16020. link
3. Jungmann, Ralf, et al. "Quantitative super-resolution imaging with qPAINT." (2016) Nature Methods 13.5: 439-442. link