Finding Dirt and Debris in your Microscope

Technical Note: 431
Reads: 8316
Creation Date: 24/11/2006
Modification Date: 24/11/2006

Introduction

Dirt or debris on a microscope can cause artefacts in your images. This note describes how to locate debris or dirt and remove it.

Locating the Problem

To locate the dirt or debris, we need to find the optical surface that the debris is on. The most common surfaces that will cause problems are the front window of the camera, the sample itself and the epi-fluorescence condenser as these components are at or near the in-focus planes of the system.

  1. Set up the microscope so you can see an image on the computer screen that includes the dirt or debris
  2. Rotate the camera - if the debris does not rotate then the debris is on the front-window of the camera. Clean the front window using a puffer bulb (not a compressed-air blower - compressed air may scratch the glass). If this does not remove the debris, contact the camera manufacturer for cleaning instructions
  3. Rotate or move other components between the camera and the sample. These might include:
    • C-mount adapter (if it has a lens)
    • Emission filter
    • Optovar or other zoom lens
    • Filter cube
    • Objective
  4. If the dirt or debris moves when a surface is moved then the dirt is on that surface. For filters and c-mounts, the dirt can be removed with a puffer bulb. Objectives should be cleaned according to the manufacturer's instructions. For internal components the microscope will need to be serviced by the manufacturer.
  5. Move the sample using the XY stage. If the dirt or debris moves then the dirt must be on the sample coverslip or slide. Clean the coverslip.
  6. Continue to follow the light path back to the TL or fluorescence source (depending on whether you are using transmitted light or fluorescence imaging). Again, move each optical component to see if the dirt moves with it. Components may include:
    • Emission filter
    • Optigrid paddle
    • EXFO or similar fluorescence condenser
    • Light guide or fibre-optic
    • Fluorescence lamp house
    • DIC slider insert
    • TL condenser filter
    • TL lamp house
    Again, if the dirt or debris moves when a surface is moved then the dirt is on that surface. For most components, the dirt can be removed with a puffer bulb. For badly soiled surfaces, contact the manufacturer as different optical coatings require different cleaning regimes. For internal components the microscope will need to be serviced by the manufacturer.

Cleaning

To remove dirt or debris, use a photographer's puffer bulb to blow the debris away. Avoid compressed-air cleaners as these can scratch optical surfaces and may deposit propellents, making the problem worse.

If you are not able to blow the dirt away, contact the manufacturer for cleaning instructions as different optical surfaces will need different cleaning regimes. Many surfaces have coatings that are sensitive to solvents and are easily scratched.

Keeping your Microscope Clean

Prevention is better than cure - keep your microscope clean! Optical surfaces attract dust. In particular:

  • Always put the cover on your microscope when it is not in use
  • Never leave a port uncovered, not even for a few seconds
  • Always put a lens cap on your camera when it is not attached to the microscope
  • Never lean over any port or surface - it is very easy for skin particles to fall onto optical surfaces
  • Always clean oil objectives after use
  • Never mix different makes or types of immersion oil (they can react and form crystals)
  • Never use powdered gloves
  • Keep the microscope room free of dust