This is where documents regarding training will reside as they are developed.
last updated 2021-12-23

Are you a new confocal user? Go here.

Recommended reading:

Sadly, some of these are behind paywalls.

This article is comprehensive.
Wait EC, Reiche MA, Chew TL. Hypothesis-driven quantitative fluorescence microscopy - the importance of reverse-thinking in experimental design. J Cell Sci. 2020 Nov 5;133(21):jcs250027. doi: 10.1242/jcs.250027. PMID: 33154172

A key slide in my standard lecture on confocal is how it relied on a confluence of many technologies. This article reviews one of these key technologies, fluorescent chemistry. Much of it is a good technical introduction, but it also covers many practical aspects of fluorescent molecule use in microscopy; the non-chemist can skip over the chemical minutae and learn a lot too. [not behind paywall] [behind paywall] Grimm, J.B., Lavis, L.D. Caveat fluorophore: an insiders’ guide to small-molecule fluorescent labels. Nat Methods (2021). https://doi.org/10.1038/s41592-021-01338-6
(And Mauve: How One Man Invented a Color That Changed the World by Simon Garfield is also a fun read about how absorptive and fluorescent dyes critical to microscopy began.)

I especially recommend heeding the advice in the later sections regarding figure presentation. Easier to read than Wait et al above.
(Extra points if you find the minor math error in the paper.)
Jen-Yi Lee and Maiko Kitaoka, A beginner’s guide to rigor and reproducibility in fluorescence imaging experiments, https://doi.org/10.1091/mbc.E17-05-0276

Although I disagree with the section later in the paper regarding quantification of transmitted light images, I assign this article when I teach because the earlier sections are important guides to what images are and accessible to people at all levels.
Cromey DW. Avoiding twisted pixels: ethical guidelines for the appropriate use and manipulation of scientific digital images. Sci Eng Ethics. 2010 Dec;16(4):639-67. doi: 10.1007/s11948-010-9201-y. Epub 2010 Jun 22. PMID: 20567932

Great coverage of topics in light microscopy for biologists.
North, AJ, Seeing is believing? A beginners' guide to practical pitfalls in image acquisition. J Cell Biol. 2006 Jan 2; 172(1): 9–18. doi: 10.1083/jcb.200507103

A follow-up to North's paper above which focuses on confocal microscopy with more details on how to achieve results including non-confocal techniques.
Annoying that another important paper is behind a paywall.
Jonkman, J., Brown, C.M., Wright, G.D. Anderson KI, North AJ. Tutorial: guidance for quantitative confocal microscopy. Nat Protoc 15, 1585–1611 (2020). https://doi.org/10.1038/s41596-020-0313-9

Many technical details that need to be addressed for valid microscopy. Also, like Wait et al above, this paper discusses, "When thinking about how best to avoid bias in an experiment, it is important to consider whether the experiment is intended for hypothesis generation (“learning”) or hypothesis testing (“confirming”)."
Jost AP, Waters JC. Designing a rigorous microscopy experiment: Validating methods and avoiding bias. J Cell Biol. 2019 May 6;218(5):1452-1466. doi: 10.1083/jcb.201812109. Epub 2019 Mar 20. PMID: 30894402
I also recommend the associated YouTube Microcourses channel.

There is a general problem of researchers not providing enough methods details for reproducibility. Although I am not as dogmatic as these authors, sometimes a micrograph is merely a documentation or illustration and deep description of its methodology does not add useful knowledge, the main messages should be heeded. And as you can see by the references above, doing the microscopy correctly is critical regardless of reported methods.
Marqués G, Pengo T, Sanders MA. Imaging methods are vastly underreported in biomedical research. Elife. 2020 Aug 11;9:e55133. doi: 10.7554/eLife.55133. PMID: 32780019

This article presumes knoweldge of a lot of terminology already, but is an excellent expansion of the Elife article above. Paula Montero Llopis, Rebecca A. Senft, Tim J. Ross-Elliott, Ryan Stephansky, Daniel P. Keeley, Preman Koshar, Guillermo Marqués, Ya-Sheng Gao, Benjamin R. Carlson, Thomas Pengo, Mark A. Sanders, Lisa A. Cameron & Michelle S. Itano. Best practices and tools for reporting reproducible fluorescence microscopy methods. Nat Methods (2021). https://doi.org/10.1038/s41592-021-01156-w https://www.nature.com/articles/s41592-021-01156-w

Prescriptions of aspects of microscopy to be aware of. QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy https://onlinelibrary.wiley.com/doi/10.1111/jmi.13041 And a related a related article stressing the importance of metadata including biological information for the omics era. https://www.nature.com/articles/s41592-021-01166-8.pdf

For a thorough history of the confocal: Confocal_microscopy_Amos_McConnell_Wilson.pdf