• 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
• 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

• ImageJ (open source) - general image handling and analysis and a large range of available plugins -  NIH (available for Windows 32 and 64 bit, Linux 32 and 64 bit, Mac)
• FIJI (FIJI is just ImageJ) (open source) - a maintained version of ImageJ (available for Windows 32 and 64 bit, Linux 32 and 64 bit, Mac). Some helpful macros and more information.
• ICY (open source) - general imageing,  good for cell segmentation and tracking (available for Windows 32 and 64 bit, Linux 32 and 64 bit, Mac).  Pasteur Institute
• Cell Profiler (open source) - A very powerful open-source software tool for batch-processing of large numbers of images. Easy to set up and use, since it comes with a very detailed manual (hidden in the download section), describing all the algorithms used, and a collection of examples. A point by point quickstart guide has also been published, and you can even watch a demo movie online. For advanced problems, there is an extensive user forum/help page. Based on compiled Matlab, available for Windows 32 and 64 bit, Linux 32 and 64 bit, Mac
• FLIMfit (open source) - Fluorescent lifetime analysis software
• Volocity - Good for 3D visualisation/rendering and movie contruction (see our equipment pages) (PC and MAC)
• Huygens - Deconvolution software, 3D rendering and analysis (see our equipment pages) (PC and MAC)
• Omero - Image database - view, organise, analyse and share your data

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

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)