Confocal and Advanced Light Microscopy (CALM) Facility

Experimental design - planning your experiment

This page provides basic information and links to help with your experimental design.

We not only provide the infrastructure to acquire and analyse microscopy images, but also have extensive expertise to give you advice on your imaging experiments or on help with your experimental design. The following gives you a brief ‘check list’ on the essential steps in standard imaging experiments that we can advise on:



The largest part of the CALM infrastructure is designed for image acquisition based on fluorescent labels. We can assist with planning your experiments by recommending fluorescent labels or advise on the optimal spectral recording of your fluorophores. On request, this could include extra training on spectral unmixing, if the experiment involves several fluorescent labels with strongly overlapping emission spectra. For general planning and selection of fluorescent labels, you can refer to the following interactive online tools:

Chroma SpectraViewer

Semrock Searchlight

Thermofisher Fluorescence SpectraViewer


Sample processing

This is a very important step in any imaging experiment, and has a critical effect on the quality of the image data. The following list is just a brief overview over the most important steps we can advise on:

  • sample preparation
  • fixation and permeabilization
  • immunodetection
  • mounting


Live specimen maintenance and handling

Image acquisition from live specimens such as clonal cell cultures, primary cells and Zebrafish embryos adds a lot of complexity to an imaging experiment and requires additional microscope components to maintain optimal sample conditions. We can assist with:

  • operating microscope enclosures and their controllers
  • handling gases (carbon dioxide, oxygen, nitrogen)
  • the choice of sample vessels (POC mini chamber, glass-bottom plates, etc)
  • the embedding of specimens 


Choice of microscope

If you are not sure about which microscope system to use for your experiment, you can use the equipment finder on this website or ask CALM facility staff.

Go to Equipment finder


Image acquisition

Training on all our equipment is mandatory and will provide you with the basic skills necessary for acquiring your images. Beyond this, we are happy to deliver additional and advanced training via one-to-one sessions, to help you to optimise your image acquisition, and this training can be tailored to your individual experimental requirements.


Image analysis and quantitation

The final step of your imaging experiment is usually the analysis and visualisation of your image data and a separate section on this website introduces you to the infrastructure we provide to do so.  Go to Data analysis

If you are not sure during the planning of your experiments how you want to analyse the image data you will be generating, we can assist with this and explain all options available.


Collaborative approaches

 Should your experimental design need a significant amount of expertise, which we provide to help with any of your imaging requirements, you should consider a collaborative approach. In this case, we can deliver a wide range of assistance, from planning your experimental strategy, carrying out image acquisition and optimising technical applications to analysing your image data. You find more details in our facility guidelines


Requirements beyond the local infrastructure

Should you require light microscopy infrastructure that is not available locally, we can assist you in finding and contacting other facilities that might be able to provide you with the technology you require for special applications. Please send your query to