Learn More — Reading List and External Resources

Vendor learning hubs

The big microscopy companies have built genuinely good educational sites. Pretend the marketing isn’t there and the content is excellent.

Nikon MicroscopyU — the deepest of the four. Optical theory, fluorescence, super-resolution, image processing.
Zeiss Campus — interactive Java-era classics; aged but useful.
Leica Science Lab — application-focused articles.
Olympus / Evident Microscopy Resource Center — the original online microscopy reference.

iBiology microscopy series — lectures from Hell, Betzig, Zhuang, and other founders. Free.
Bio-Image Analysis Notebooks — Python notebooks from BiAPoL. Pragmatic.
BioImage Archive — public reference image data.
ImageJ / Fiji Learn — official tutorials.
image.sc forum — when you’re stuck on analysis at midnight, this is where you ask.

Grouped by technique. Cite if you use the technique.

Hell, S. W. & Wichmann, J. (1994). Breaking the diffraction resolution limit by stimulated emission: stimulated-emission-depletion fluorescence microscopy. Optics Letters, 19(11), 780–782. https://doi.org/10.1364/OL.19.000780 — the original proposal.
Klar, T. A. & Hell, S. W. (1999). Subdiffraction resolution in far-field fluorescence microscopy. Optics Letters, 24(14), 954–956. https://doi.org/10.1364/OL.24.000954 — first experimental demonstration.
Hell, S. W. (2007). Far-field optical nanoscopy. Science, 316(5828), 1153–1158. https://doi.org/10.1126/science.1137395 — the canonical review.

Betzig, E. et al. (2006). Imaging intracellular fluorescent proteins at nanometer resolution. Science, 313(5793), 1642–1645. https://doi.org/10.1126/science.1127344 — PALM.
Rust, M. J., Bates, M. & Zhuang, X. (2006). Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nature Methods, 3(10), 793–795. https://doi.org/10.1038/nmeth929 — STORM.
Hess, S. T., Girirajan, T. P. K. & Mason, M. D. (2006). Ultra-high resolution imaging by fluorescence photoactivation localization microscopy. Biophysical Journal, 91(11), 4258–4272. https://doi.org/10.1529/biophysj.106.091116 — fPALM.
Heilemann, M. et al. (2008). Subdiffraction-resolution fluorescence imaging with conventional fluorescent probes. Angewandte Chemie International Edition, 47(33), 6172–6176. https://doi.org/10.1002/anie.200802376 — dSTORM.

Jungmann, R. et al. (2014). Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT. Nature Methods, 11(3), 313–318. https://doi.org/10.1038/nmeth.2835
Schnitzbauer, J., Strauss, M. T., Schlichthaerle, T., Schueder, F. & Jungmann, R. (2017). Super-resolution microscopy with DNA-PAINT. Nature Protocols, 12(6), 1198–1228. https://doi.org/10.1038/nprot.2017.024 — the implementation guide.

Balzarotti, F. et al. (2017). Nanometer resolution imaging and tracking of fluorescent molecules with minimal photon fluxes. Science, 355(6325), 606–612. https://doi.org/10.1126/science.aak9913

Heintzmann, R. & Cremer, C. G. (1999). Laterally modulated excitation microscopy: improvement of resolution by using a diffraction grating. Proc. SPIE, 3568, 185–196. https://doi.org/10.1117/12.336833
Gustafsson, M. G. L. (2000). Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy. Journal of Microscopy, 198(2), 82–87. https://doi.org/10.1046/j.1365-2818.2000.00710.x

Pawley, J. (ed.) (2006). Handbook of Biological Confocal Microscopy, 3rd edition. Springer. The reference, even decades on.
Lakowicz, J. R. (2006). Principles of Fluorescence Spectroscopy, 3rd edition. Springer. For the photons-and-electrons fundamentals.
Diaspro, A. (ed.) (2010). Optical Fluorescence Microscopy: From the Spectral to the Nano Dimension. Springer. Modern super-resolution treatment.