Microscopic image of mitochondriaThis page contains a list of useful web links and documents relating to sample preparation, fluorophores (dyes) and other imaging requirements


General information

Spectral information on fluorophores, filters and lamps


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

General imaging and analysis software

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

  • 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

Whole figure preparation

Protocols, tips and tricks - sample preparation

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.