What microscopes do you have?  

Click here to find out.

Which softwares do you have? 

Check here to find out.

How can I learn how to use the microscopes?

You would need to register for AIR on PPMS our booking software and fill in a Training request form (Training Tab in PPMS)

How can I learn how to use an image analysis software?

Fill in the Informatics Support Request Form in PPMS or email the Imaging Helpdesk

How do I turn this microscope on/off?

Find the manual for the microscope you are using here. The manuals are a link at the bottom System start up and shutdown procedures will be the first contents of each manual. Additionally, there are start up and shut down instructions on the walls by the microscopes. If you haven't been trained to use the microscope then please fill in the Microscope Training Request Form.

Where's the manual? I can't find it!

These should be found next to each microscope, however, if you can't find one there they are also on our equipment page here.

Its out of hours and the microscope isn’t working

This is quite stressful but if you can’t find a Super-user to help the best thing to do is turn off the microscope and log an incident report. The AIR team will look at it first thing the next day. Most of the confocals and epifluorescence systems have ‘duplicates’ so try a different microscope.

There is no light, I can't see my sample! (widefield microscope)

Troubleshoot flowchart

Which microscope do I need/ should I use?

The imaging facility team is happy to discuss the best system for your experiment and how to optimise your protocols to get the best results. Come and see them in the facility or e-mail the helpdesk.

I forgot to calibrate

You can check the calibrations for the facility epifluorescence microscopes here. You will need to know the objective and whether your set the camera to bin. 

Images taken using the confocal and super-resolution systems are already calibrated.

Where do I find information for publications/ my thesis?

Check here.

Where should I store my data?

The policy of the IGMM is that users should be storing imaging data on the Datastore network share of their group . If you are about to start collecting a lot of imaging data (for example, from long time-lapse experiments) you should talk to your Group Leader/ PI to check that there is sufficient space for the resultant files. It is not safe or wise to leave your data on the computers attached to the microscope or the imaging workstations. 

How do I access the Datastore?

On a Windows computer

  • The path to get to the your network share is \\cmvm.datastore.ed.ac.uk\igmm\<your-group-area>

  • If you are asked for your username enter your username in this form ed\UNN e.g. ed\s1257503, using your normal log-in UUN and password

On a Mac computer

  • Select Go in the taskbar at the top of the desktop and then select Connect to Server...

  • In the window type the path of the folder you wish to connect in the form below


  • When you are asked for your username enter your username in this form ed/UNN e.g. ed/s1257503, using your normal log-in UUN and password

How do I add scale bars to my images? 

Try to follow the instructions here

Where's the script/macro I used before?

Have you checked the Scripts and Macros folder on our Github?

What can I do about fluorescence bleed-through (cross-talk)?

  • Ensure you are using dyes / fluorescent proteins that can be imaged in the core facility. Not sure please follow this link.

  • When you set up your samples ensure you have biological and technical controls. You will need:

    • Primary only and no secondary antibodies.

    • Each Primary antibody labelled individually with a secondary. Not sure what this means, please speak to Ann.

    • To have titrated your dye labelled antibodies correctly.

  • Bleed-through can often be seen when viewing down the eyepieces due to the quad filter set in use, which can only offer a certain amount of spectral separation. The camera offers better separationdue to an extra filter wheel just before the camera which has single band emission filters. (Not sure what this means, see talks)

  • A very bright fluorophore can cause bleed-through. If you see bleed through first titrate the dye down (yes that means you need to repeat the experiment, best practice involves titrating any reagents before using them for experiments). Using dyes which are well spectrally separated, e.g. AF488 and AF647, will help. As will minimising intensity and exposure. Please see Ann or Matt for help with this.