Introductory Biomedical Imaging

Course Materials

Lecture Notes

Lecture Notes

This page includes links to a complete set of lecture notes from Biomedical Imaging. The course was taught by Bethe Scalettar in Spring 2026 at Lewis & Clark College. The notes were taken live by James Abney and recopied after class to improve legibility. The notes are organized chronologically, by lecture number. Each lecture was a full 60 minutes. The notes provide an alternative path to learning material in the book. They also should provide instructors with insight into how Bethe selects and presents material from the book. The students were given a take-home midterm covering microscopy (lectures 1-23) and an in-class final covering medical imaging and digital image processing (lectures 24-39). The amount of time spent on each subject, and the content of the corresponding lectures, varies somewhat from year-to-year, depending in part on class composition. For example, the class typically spends a lot of time on microscopy, especially fluorescence microscopy, because many of the students are biology majors working with those techniques. Click on the lecture number to view the associated notes.

Lecture Date Key Words and Topics Chapter
11/21/26Course mechanics, overview of course subject matter1
21/23/26Light waves and rays, ray bending at interfaces, Snell’s law, lens function, ray diagrams2
31/26/26Image quality, geometrical optics versus wave optics, diffraction3
41/28/26Ray tracing, real and virtual images, minification and magnification, lens equations, Activity 13
51/30/26Simple microscope, ray diagram, eyepiece, objective, critical and Kohler illumination3
62/2/26Resolution, diffraction, Rayleigh theory, Activity 2, numerical aperture4
72/4/26Abbe theory (start)4
82/6/26Abbe theory (finish), Activity 3, introduction to contrast4,5
92/9/26Amplitude and phase specimens, brightfield microscopy, tricks to enhance contrast, Kohler ray trace, conjugate planes, Activity 4, darkfield microscopy (start)5
102/11/26Darkfield microscopy (finish), phase contrast microscopy (start)5
112/13/26Phase contrast microscopy (continued)5
122/16/26Phase contrast microscopy (finish), Activity 5, introduction to fluorescence, overview of fluorescence microscopy, Jablonski diagram5,6
132/18/26Fluorescence excitation and emission, photons, quantification of light energy6
142/20/26Excitation, emission, spectra, fluorescence microscope (light source, emission filter, dichromatic mirror, stage, emission filter, detector), Activity 6, multi-color imaging6
152/23/26Dichromatic mirrors for multi-color imaging, 3D imaging, optical sectioning, blur problem, introduction to confocal microscopy6
162/25/26Blur problem, point spread function (PSF), laser scanning confocal microscopy (LSCM), pinhole size6
172/27/26Spinning disk confocal microscopy (SDCM), Nipkow disk, camera, comparison of LSCM and SDCM6
183/2/26Widefield fluorescence microscopy, deconvolution, polarization microscopy, Activity 7, crossed polarizers5,6
193/4/26Specialized fluorescence techniques (overview), two-photon microscopy (start)7
203/6/26Two-photon microscopy (finish), total internal reflection fluorescence microscopy (TIRFM) (start)7
213/9/26Total internal reflection fluorescence microscopy (finish), super-resolution fluorescence microscopy (overview), structured illumination microscopy (SIM) (start), moiré patterns7,8
223/11/26Structured illumination microscopy (finish), beats, photoactivatable localization microscopy (PALM) (start)8
233/13/26Photoactivatable localization microscopy (finish), stimulated emission depletion (STED) microscopy8
243/16/26
253/18/26
263/20/26
273/30/26
284/1/26
294/3/26
304/6/26
314/8/26
324/13/26
334/15/26
344/17/26
354/20/26
364/22/26
374/24/26
384/27/26
394/29/26