Sample prep FAQs

Success at the microscope starts with your sample! If you are trying something new in our core, here are some tips to help you get good results.

Sample Dimensions: Each microscopes has its own unique stage insert. Before you use a microscope for the first time, check with Andrea or Jasmine to see if the sample you're bringing will fit on that particular stage.

Coverslips: Most of our objective lenses are designed to image your specimen through a #1.5 (0.17 mm) thickness coverslip.

  • For best results, tissue sections should be mounted directly on #1.5 coverslips after sectioning, not on a thick slide. This video from the Live Cell Imaging Facility at the Karolinska Institute in Sweden shows how that can be done (the relevant portion starts at 3:58 but the whole video is very helpful). Whether you mount your sections this way or the traditional way (directly onto a 1" x 3" slide, then topped with a coverslip), you should take care when adding mounting medium so that there are no bubbles and the layer is uniform. 
  • For best results cells that are fixed and stained should be grown directly on acid-washed #1.5 coverslips, then mounted on a slide using a suitable mounting medium.  This is an example of a protocol for growing adherent cells on coverslips for immunofluorescence microscopy.
  • Petri dishes and multi-well vessels must have coverglass bottoms for any confocal or high-resolution widefield imaging.  If you are unfamiliar with these, check out these companies:

Live cell (or organism) imaging poses many challenges, one of them being high background fluorescence (especially in the green part of the spectrum) due to components in the surrounding media. Phototoxicity and bleaching can also be problematic. To avoid these issues you may want to try media specifically designed to protect cells and reduce background fluorescence during long periods of light exposure

Stains and Dyes: Before you prepare your samples, make sure the dyes you have chosen are compatible with the microscope you plan to use.  If you're not sure about this, contact Andrea or Jasmine for advice.