Optics/Microscopy Resources

Most of my career has involved optics, most often as part of biomedical devices. It was evident from the outset that something was missing in optics education – the usual optics classes were far from sufficient to prepare me for working in an optics lab, and especially doing microscopy. Years in industry convinced me there had to be a better way to prepare students (and eventual design engineers and scientists).

My colleague at UC Berkeley, Dan Fletcher, had arrived at similar conclusions. Together we put together a semester-long lab course (n.b.: can also be run in a quarter-long system) designed to give students practical experience building optical imaging systems using standard optomechanical parts. Emphasis was (and remains) on use of rules of thumb for rapid design decisions, and developing an intuitive understanding of how optical systems work – including experience with fluorescence imaging and Abbe theory (the gateway to understanding Fourier optics).

The class won awards at UC Berkeley, and has proven popular over many years, and we wanted to make our materials available to others. Because we know the difficulty of supporting lab classes in the college/university environment, we approached Thorlabs about assembling a simple bill of materials that could be easily ordered. Instead, Alex Cable and others at Thorlabs joined forces with us to produce a vastly better system that is both easier to use and easier to support long-term, and also supported professional preparation of all of our teaching materials (including ample instructor notes and assembly instructions). All of our written materials are provided free of charge, simplifying teaching of the class – students can just download the PDFs, though we suggest printing them for people as a course reader (or obtaining the very nicely printed versions from Thorlabs, quite likely actually cheaper than the local printers) to avoid students trying to read lab procedures on their 5” diagonal phones…

It is important to point out that Dan Fletcher and I have no financial interest in this – our (very substantial) efforts have been in service of our students and the wider optics community, as we have benefited from those before us.

The following links are intended to assist those either teaching the class or interested in doing so; I will add to them over time.

Course, course materials, and video introductions:

Thorlabs OMC1 Optical Microscopy course Kit

From that page, I will highlight a few items. There is vastly more there – fully supported by one of the world’s largest optics companies – I encourage you to investigate.


Kit Overview

Kohler Illumination

Abbe Theory

Course Materials:

Course Notes (for students, but also of interest for faculty)
Lab Notes

Lab Notes for older (DCC1545/1645) camera kits

The Course Materials tab at the kit website has links for additional materials:
Instructor Notes (partial; complete available from Thorlabs to instructors only)

CVI / IDEX / Melles Griot Fundamental Optics Guide

Note: those in the field know what an amazing pedagogical resource this Guide is. At our request, IDEX/Semrock has very kindly again made it available. It is a free download, but one must enter an email address to get the download. I assign parts of the Fundamental Optics Guide to all students; those Melles Griot engineers who wrote this guide – and those at IDEX who have again made it available – did a huge service to the optics community. I am putting it here just so there is one more link to it for people to find on the web.

3-day training Immersion for faculty interested in teaching the material

We teach (every summer) a 3-day workshop to introduce the system to US and international faculty. Emphasis is on comfort aligning the system and with how to productively teach the lab materials. Offered under the aegis of the NSF-funded Advanced Physics Laboratory Association (ALPhA):

N.b.: I will not update this link every year, but you can find the current year from this link.

Lecture slides:

I have often been asked for my slides; here are links. I have broken them into the three main parts of the class. The main slides for each lab are straight from the Course Notes; all are our own. Additional Materials are other slides I use when teaching the materials; I have cited (in slide notes section) images that are not my own, but not procured any commercial rights to them, since I am providing these materials free for fair-use educational purposes. Anything not otherwise cited is copyright by myself and Dan Fletcher, and we provide permission to use in any not-for-profit educational context. A portion of the effort to make my class materials available was kindly funded by a NASA CASGC grant.


All slides are available in a single folder, here.
Files contained include:

    • Introduction, Aberrations, Kohler Illumination, Labs 1-5 (20 MB; 107 slides)
    • Abbe Theory, MTF, and Phase Contrast, Labs 6-8        (62 MB; 169 slides)
    • Fluorescence, Spectra and Filters, Labs 9-10               (12 MB; 95 slides)

Note: these slides are intended for use by instructors familiar with the material. The main slides are from the kit materials and are thus well-supported by the documentation. The ‘Additional Materials’ slides are those I use for supplementary discussions depending on where and to whom I am teaching, and are not fully supported by the kit documentation (though they are directly relevant).

In-class Exercises:

I also have some in-class design exercises (on designing a TIRF microscope, and doing a photon budget for DNA imaging or PALM). I am willing to share these with faculty; email me from your university address if you would like these, and I will provide them on the condition you do not post them online / provide any electronic copies to students.