PhD Optics Course

During our PhD optics course students learn how microscopes work from the ground up. Starting with the basics of image formation with a single lens, we will build up to more complex lens systems, fluorescence, and two photon imaging. By the end of course we build a two photon microscope and use it to image Calcium activity.

Lectures

• Light, Image Formation, and Lenses
• Resolution
• Noise [Slides]
• Fluorescence
• Confocal and Scanning
• DAQ intro
• Scanning tute

Practicals

• Basic optics
  • Single lenses and image formation. Magnification. Virtual images.
  • Pairs of lenses: finite and infinite conjugate. Beam expanders and telescopes.
  • Aligning lenses on a rail using a laser.
  • Compound optical systems demo.
• Sample illumination.
• Fluorescence imaging: build a fluorescence microscope and image brain slices. Characterize the resolution of your microscope
• Routing and aligning laser beams.
• Scanner control with Python (or MATLAB). Build a simple scanning microscope with a laser pointer and a photodiode.
• Laser safety.
• Build a two-photon microscope and image calcium activity in zebrafish larvae.

Laser Safety

During the second week of the course you will be working with Class 4 pulsed lasers. The beam from these devices may be invisible and can blind you instantly. You will use these lasers under supervision and will receive verbal and practical instruction. The safe operating procedures are summarised below.

• Wear eye protection and use IR viewing cards as appropriate.
• Always be aware of the location of the beam and ensure everyone else in the room is also aware.
• Remove watches, jewellery, etc. Avoid directing the beam at shiny surfaces which could reflect it at unpredictable angles.
• Reduce laser power during alignment and tune the laser to visible wavelengths when possible.
• Shutter the beam when not in use and do not leave an open beam unattended.
• Take particular care where the beam is directed upwards, such as at a periscope.
• Use caution when routing the beam into the scanners: they can potentially deflect the beam by large angles.
• Use black foil, protective screens, and beam dumps as appropriate to keep the beam within your work area.