SR-SamplePreparation

Resources:

Flurophors:

• FPBase.org

• Sarmento, M.J., Fernandes, F. Fluorescence Spectroscopy and Microscopy in Biology (2022). "Choosing the Right Fluorescent Probe"

• Lelek, M., et al. Nat Rev Methods Primers (2021) "Single-molecule localization microscopy"

• Organic dyes:

  • Grimm, J.B., et al. Nat Methods (2022) "Caveat fluorophore: an insiders’ guide to small-molecule fluorescent labels"
  • Dempsey, G., et al. Nat Methods (2011) "Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging"
  • Demmerle, J., et al. Nat Protoc (2017) "Strategic and practical guidelines for successful structured illumination microscopy"
  • Luke Lavis: "Janelia dyes"
  • Mayeul Collot and Andrey Klymchenko: "Membright"
  • HM-SiR: Uno, S. N. et al. Nat Chem (2014) "Spontaneously Blinking Fluorophore Based on Intramolecular Spirocyclization for Live-Cell Super-Resolution Imaging" and Takakura, H. et al. Nat Biotechnol (2017) "Long Time-Lapse Nanoscopy with Spontaneously Blinking Mem- brane Probes"
  • HM-JF526: Zheng et al. ACS Central Science (2019) "Rational Design of Fluorogenic and Spontaneously Blinking Labels for Super-Resolution Imaging"
  • Abberior FLIP 565: Grußmayer, K. et al. ACS Nano (2020) "Self-Blinking Dyes Unlock High-Order and Multiplane Super-Resolution Optical Fluctuation Imaging"
  • Thevathasan, J.V. et al. Nat Methods (2019) "Nuclear pores as versatile reference standards for quantitative superresolution microscopy."
  • Schnitzbauer, J. et al. Nat Protoc (2017) "Super-resolution microscopy with DNA-PAINT"

• Fluorescent proteins:

  • Goedhart, J. & Mastop, M., Addgene blog post (2017) "A Practical Approach to Choosing the B(right)est Fluorescent Protein"
  • “Fluorescent Proteins 101” eBook from Addgene
  • Chudakov, D.M. et al. Physiol Rev (2010) "Fluorescent Proteins and Their Applications in Imaging Living Cells and Tissues"
  • Wu, B. et al. Current Opinion in Cell Biology (2011) "Modern fluorescent proteins and imaging technologies to study gene expression, nuclear localization, and dynamics"
  • Shaner, N.C. et al. Meth Cell Bio (2014) "Chapter 6 - Fluorescent proteins for quantitative microscopy: Important properties and practical evaluation"
  • Turkowyd, B. et al. Angew. Chem. Int. Ed. (2017) "A General Mechanism of Photoconversion of Green-to-Red Fluorescent Proteins Based on Blue and Infrared Light Reduces Phototoxicity in Live-Cell Single-Molecule Imaging"
  • Durisic, N. et al. Nat Methods (2014) "Single-molecule evaluation of fluorescent protein photoactivation efficiency using an in vivo nanotemplate."

Refractive index:

• Refractive index database: refractiveindex.info
• Khan et al., Photodiagnosis and Photodynamic Therapy 33 (2021) 102192 "Refractive index of biological tissues: Review, measurement techniques, and applications"

Tissue clearing:

• Weiss, K.R. et al., Nat Protoc 16, 2732–2748 (2021) "Tutorial: practical considerations for tissue clearing and imaging."
• Molbay, M. et al. Molecular Systems Biology, 17:e9807 (2021) "A guidebook for DISCO tissue clearing"
• Richardson, D.S. et al. Nat Rev Methods Primers 1, 84 (2021) "Tissue clearing."

Sample preparation for Super-resolution Microscopy:

• Jimenez et al., Methods (2020) "About samples, giving examples: Optimized Single Molecule Localization Microscopy"
• Jacquemet et al., J Cell Sci (2020) "The cell biologist's guide to super-resolution microscopy"
• Pereira, et al., Methods Cell Biol (2015) "High-content 3D multicolor super-resolution localization microscopy" DOI:10.1016/bs.mcb.2014.10.004
• Whelan et al., J Phys Chem Lett (2015) Super-Resolution Single-Molecule Localization Microscopy: Tricks of the Trade
• Whelan et al., Sci Rep (2015) "Image artifacts in Single Molecule Localization Microscopy: why optimization of sample preparation protocols matters"
• Richter et al., EMBO J (2018) "Glyoxal as an alternative fixative to formaldehyde in immunostaining and super‐resolution microscopy"
• Channel registration with bUnwarpJ: "Thisis of Sven Proppert: Design, implementation and characterization of a microscope capable of three-dimensional two color super-resolution fluorescence imaging"
• Blinking buffers: Olivier et al., Biomed. Opt. Express (2013) "Simple buffers for 3D STORM microscopy"