• A beginner’s guide to rigor and reproducibility in fluorescence imaging experiments by Jen-Yi Leea, and Maiko Kitaokab. Mol Biol Cell.  Jul 1;29(13):1519-1525 2018
• Quickstart Guide to Good imaging practice (PDF) - some background information on experiment planning, fluorophor choice, sample preparation, image acquisition, gain/offset settings, and how they affect image quantification
• Tutorial: guidance for quantitative confocal microscopy by James Jonkman, Claire M. Brown, Graham D. Wright, Kurt I. Anderson and Alison J. North. Nature Protocols 2020.
• Zeiss Online Campus
• Microscopy Primer - just about everything you ever want to know about microscopes, including many useful interactive flash animations
• Nikon MicroscopyU
• iBiology Microscopy Course
• MyScope microscopy training tool

• Semrock Searchlight - an essential tool to set up the excitation and emission of fluorophore
• Spectraviewer - an essential tool to set up a fluorescent microscope
• Fluorescent dye spectra (University of Arizona; contains many fluorescent proteins)
• Fluorophores.org (TU Graz) - very detailed and complete spectral information of fluorophores, with browsing by application (eg. pH indicators, DNA dyes, ion sensors)
• Spectrum Viewer hosted by Becton Dickinson
  
• Two-photon cross sections of common fluorophores (Cornell University)
• Interactive lists at UCSF:
  • Fluorescent proteins
  • Photoswitchable proteins

• Nyquist Calculator - calculates the optimal sampling rate for microscopic image acquisition (Nyquist rate = 2x maximal resolution) Scientific Volume Imaging

• Leica objective database
• Zeiss objective database

Tutorial: guidance for quantitative confocal microscopy by James Jonkman, Claire M. Brown, Graham D. Wright, Kurt I. Anderson and Alison J. North. Nature Protocols 2020

See our Software Pages - Software

• FigureJ FIJI/ImageJ plugin
• Scientifig FIJI/ImageJ plugin or stand alone
• QuickFigures FIJI/ImageJ plugin

This is a growing collection of methods and techniques used in the facility, representing the enormous range of expertise of our microscopists. Everybody is very much invited to contribute with their own protocols. Protocols are provided as Word files, so they can be downloaded and edited as required.

• Method to prepare paraformaldehyde (PDF)
• ‌Fixation protocol (PDF)‌ Standard protocol for fixation and mounting on coverslips
• DNA staining for Fluorescence
• Antigen Retrieval Methods
• Staining protocol (PDF)‌ Staining of fixed cells
• Staining Jurkat Cells (PDF) Imaging immunological synapses, including transient transfection of Jurkat cells, FACS sorting, superantigen-loading of Raji B cells‌
• Invitrogen's information on chemical stability and quenching of Q-Dots (PDF)
• for an excellent description introduction to experiment planning, fluorophore selection and image acquisition techniques for FRET and FRET-Flim, see the article "Detecting Protein-Protein Interactions In Vivo with FRET using Multiphoton Fluorescence Lifetime Imaging Microscopy (Flim)" by Lleres et al., Current Protocols in Cytometry 12.10.1-12.10.19, October 2007
• Optical clearing (PDF) of samples, i.e. adjusting the refractive index with TDE to minimise optical aberrations
• Eric Dubuis: Cell labelling with Di‐8‐ANEPPS, Fura-2 or Fluo4-AM (for Ca2+ measurements) or DiI (e.g. retrograde labelling of neurons) Cell Labelling - Eric Dubuis (PDF).

• Basics of microscopy (PDF)‌ (Martin Spitaler, Microscopy Day)
• Fluorophores (PDF) Fluorophores, autofluorescence, phototoxicity etc ( Martin Spitaler, Microscopy Day)
• Fixation techniques (PDF)  Fixation techniques (Martin Spitaler, FILM Club)
• Image data (PDF) Understanding image data: Formats, visualisation, handling, analysis (Martin Spitaler, Microscopy Day)
• Special techniques I (PDF) (Microscopy Day 2012)
• Special techniques II (PDF)‌ (Microscopy Day 2012)
• A Walkthrough the Zoo (PDF) of microscopy techniques (Microscopy Day 2013) - indirect microscopy tools for molecular measurements
• Deconvolution training (PDF)