Guides & Tutorials

We have compiled a range of guide and tutorials for our most commonly asked questions regarding use of facility microscopes, image software and equipment.

Introduction to Microscopy

This is a very brief introduction to the concepts and principles behind the microscopy that you can do in LMCF. The facility has a broad range of imaging equipment and this overview covers most of the imaging systems and techniques available. There are links throughout for more detailed information.

Choose Best Microscope for your Sample

This flow chart may help you select the best microscope. It certainly doesn't cover every factor in the choice and LMCF can help you if decide if you are not sure. Browsing the simple introduction to microscopy may help you better understand the different types of microscopes.

Introduction to Sample Preparation: Immunofluorescence

This is an overview of immunofluorescence (IF) protocols. Unfortunately, there isn't one protocol that is best for everything, so some testing and optimization is often necessary. If you can find out conditions that work well for your antibody-protein-specimen (eg from papers, companies selling the antibodies, lab web pages) that can save some time.

Safe Imaging of Live Samples

Live sample imaging is a powerful technique and is commonly performed on many of the LMCF systems. The guidelines presented below will ensure you and all other users of the facility are safe when such experiments are carried out.

Laser Lines and Filters

The facility has a large variety of laser lines, excitiation and emission filters available across a wide range of microscopes. This page provides a table to help you quickly find the microscopes able to image a specific fluorophore.

Count Nuclear Foci - ImageJ

Simple instruction for counting  nuclear foci - relatively easy as nuclei tend to be fairly well separated, similar in size and brightly stained.

Overlay Images in ImageJ

Simple instructions for overlaying images using ImageJ software.


This is an overview of some common tasks that might be carried out using Photoshop. Always work with a copy of your image, never the original, as some actions lose information and are irreversible.

Control Motorized Stage in MetaMorph

The stage can be controlled directly with MetaMorph bypassing the rotary controller next to the LCD touch screen.

Kohler Illumination Procedure

If you want to accurately observe or capture transmitted light images, you will need to establish Kohler illumination each time you change the objective. This ensures the illumination is even and is essential for optimal image quality.

Clean an Objective

Guidance for safely cleaning an objective to get optimal image quality.

File Formats for Microscopy

In general, using TIFF is a safe and wise choice for saving scientific images. TIFF is by default a lossless format and all data are preserved. See additional information from .jpeg and .png.


Critical resources for microscopy, including manufacturer sites, tutorials, guidelines, etc.