Thorlabs, Newton NJ
Practical Light Microscopy:
Abbe theory, phase contrast, and fluorescence using student-built microscopes
June 9, 2025 to June 11, 2025
Number of setups
available: 2
Maximum
number of participants: 4
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We have built many, many light microscopy systems, in both industry and academia, and this is the lab class we wished we had had as students. There is a strong emphasis on building physical intuition, and on the simple rules of thumb that practicing scientists and engineers use to understand optical systems. The use of actual cameras and lenses allow you to see (literally!) what is being discussed, from illumination sources imaged onto the condenser front focal plane to diffracted orders in the objective back focal plane. This makes what once took hours of drawing tedious diagrams to understand obvious in seconds as students look firsthand at where the light actually goes, or how the image changes when an iris is moved. Learning optics this way is also a lot more fun for both students and instructors – a regular favorite is the moment when students first set up imaging with their cameras: even when three groups in a class have just done the same thing, the fourth still finds it exciting.
A set of ten 3-hour lab modules have been designed to support a semester-long course, with all required materials. However, subsets of the labs can also be done as part of an Advanced Lab class that has students rotate through various different lab set-ups, or to emphasize the Fourier optics components of the labs for more advanced students.
Pedagogically, the course starts with lenses and moves quickly (in Lab 2) to actual imaging on real CMOS cameras. Labs 3 and 4 introduce resolution, aberrations and the importance of illumination, setting the stage for setting up a complete microscope (with Kohler illumination) in Lab 5. The following three labs, 6 – 8, are the theoretical heart of the course and make use of a second camera imaging the objective back focal plane to Inexpensive image sensors (in webcams, and now cellphones) have changed the possibilities for undergraduate and graduate optics labs: suddenly the real power and elegance of optical imaging is accessible to students at all levels through exciting and useful hands-on imaging labs. Since it is now commonplace to build custom microscopes for research projects – especially those involving fluorescence microscopy, a technique at the vanguard of the current revolution in biology and biomedicine (and subject of 2008 and 2014 Nobel prizes) – the skills taught in these labs can be immediately put to useintroduce the Abbe theory of image formation in substantial detail, including deeper investigations of resolution and contrast, including the MTF, darkfield and phase contrast. The final two Labs, 9 and 10, involve fluorescence imaging and include a quantitative introduction to filter selection using Excel – a critical skill for those working with fluorescence, and simple enough that there is no reason not to include it at even the undergraduate level.
The Immersion will be three days long. The intent is to make it tractable for participants to introduce lab modules or the entire class at their home campuses; total equipment cost is $11,221.63 for a single lab set-up. The materials are available as a single kit through Thorlabs, making it easier to both set up and support the lab. Course and Lab Notes, (as well as Instructor Tips documents for faculty) for all ten lab modules – over 300 pages total – are provided as free PDFs to reduce student costs. We will address set-up and alignment of the optical system; imaging, image analysis, and go through several of the most exciting lab modules, including Abbe theory and spatial filtering, phase contrast, and fluorescence imaging. Reading from the Lab and Course Notes will be assigned beforehand; participants should bring their course materials (provided in advance), a notebook, and a laptop.
Schedule:
Day 1:
- Morning: Digital imaging; introduction to rail system
- Afternoon: System alignment; Kohler illumination and conjugate planes
Day 2:
- Morning: Darkfield imaging; introduction to Abbe theory of image formation
- Afternoon: Adding a back focal plane camera; imaging and the back focal plane.
Day 3:
- Morning: Fluorescence imaging
- Afternoon: Contrast mechanisms (brightfield, darkfield, fluorescence; phase if time allows).
Hosts and Mentors:
Neil
Switz received his B.S. in physics from Stanford, his M.S. in applied &
engineering physics from Cornell, and his Ph.D. in biophysics from UC Berkeley.
He has industry experience as an engineer making safety-critical medical gas
monitoring systems and helping launch a publicly listed microfluidics and
fluorescence imaging-based biotechnology company. He taught broadly in the
upper and lower-division physics curriculum at The Evergreen State College in
Washington state, and (since 2016) the physics department at San Jose State
University. Currently his research focuses on optics-based medical diagnostics
for deployment in low-resource areas. Devices he has helped design have been
deployed in Vietnam, Thailand, and Cameroon. Neil won awards for teaching the
material in this Immersion at UC Berkeley, and now teaches it as part of his
upper division advanced optics lab course at SJSU as well as in a summer
bootcamp at the (Woods Hole) Marine Biological Laboratory.
Jonathan Adams is a Photonics Support Laboratory Supervisor at Thorlabs,
overseeing various laboratory projects and customer requests across Thorlabs'
product portfolio. He also provides hands-on product trainings, covering
laboratory techniques and product applications. Jonathan Adams received his
B.S. in Physics from Grove City College with a minor in Medical Physics.
Please note that the Jonathan F. Reichert Foundation has established a grant program to help purchase apparatus used in Laboratory Immersions. Limitations and exclusions apply, but generally speaking the Foundation may support up to 50% of the cost of the required equipment.