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•  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
•  by James Jonkman, Claire M. Brown, Graham D. Wright, Kurt I. Anderson and Alison J. North. Nature Protocols 2020.
• - just about everything you ever want to know about microscopes, including many useful interactive flash animations 
•  microscopy training tool
• by Montero Llopis P, van Oostende-Triplet C, Gaudreault N, Strambio De Castillia C, Fernandez-Rodriguez J, Martins G, North A, Acevedo L, Avilov S, Bertocchi C, Boehm U, Cameron L, Cammer M, Cleret-Buhot A, Dietzel S, Faklaris O, Gaboriau D, Guilbert T, Grunwald D, Gu T, Halidi N, Hammer M, Hartmann H, Heller J, Jambor H, Koksoy AA, Lacoste J, Larsen D, Le Dévédec SE, Liu P, Moore J, Nelson G, Nelson M, Norlin N, Parslow A, Payne-Dwyer AL, Peterson J, Podder S, Ravasio A, Rosa-Molinar E, Schroth-Diez B, Selchow O, Srinivasan S, Taatjes D, Vonderstein K, Walther C, Nitschke R. Journal of Cell Biology 2026. 

• - an essential tool to set up the excitation and emission of fluorophore
•  - an essential tool to set up a fluorescent microscope
• (University of Arizona; contains many fluorescent proteins)
• (TU Graz) - very detailed and complete spectral information of fluorophores, with browsing by application (eg. pH indicators, DNA dyes, ion sensors)
• hosted by Becton Dickinson
  
• (Cornell University)
• Interactive lists at :

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

by James Jonkman, Claire M. Brown, Graham D. Wright, Kurt I. Anderson and Alison J. North. Nature Protocols 2020

See our Software Pages - Software

•  FIJI/ImageJ plugin
•  FIJI/ImageJ plugin or stand alone
•  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
• 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 (PDF)
• for an excellent description introduction to experiment planning, fluorophore selection and image acquisition techniques for FRET and FRET-Flim, see the article  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)