| Lecture | Date | Key Words and Topics | Chapter |
|---|---|---|---|
| 1 | 1/21/26 | Course mechanics, overview of course subject matter | 1 |
| 2 | 1/23/26 | Light waves and rays, ray bending at interfaces, Snell’s law, lens function, ray diagrams | 2 |
| 3 | 1/26/26 | Image quality, geometrical optics versus wave optics, diffraction | 3 |
| 4 | 1/28/26 | Ray tracing, real and virtual images, minification and magnification, lens equations, Activity 1 | 3 |
| 5 | 1/30/26 | Simple microscope, ray diagram, eyepiece, objective, critical and Kohler illumination | 3 |
| 6 | 2/2/26 | Resolution, diffraction, Rayleigh theory, Activity 2, numerical aperture | 4 |
| 7 | 2/4/26 | Abbe theory (start) | 4 |
| 8 | 2/6/26 | Abbe theory (finish), Activity 3, introduction to contrast | 4,5 |
| 9 | 2/9/26 | Amplitude and phase specimens, brightfield microscopy, tricks to enhance contrast, Kohler ray trace, conjugate planes, Activity 4, darkfield microscopy (start) | 5 |
| 10 | 2/11/26 | Darkfield microscopy (finish), phase contrast microscopy (start) | 5 |
| 11 | 2/13/26 | Phase contrast microscopy (continued) | 5 |
| 12 | 2/16/26 | Phase contrast microscopy (finish), Activity 5, introduction to fluorescence, overview of fluorescence microscopy, Jablonski diagram | 5,6 |
| 13 | 2/18/26 | Fluorescence excitation and emission, photons, quantification of light energy | 6 |
| 14 | 2/20/26 | Excitation, emission, spectra, fluorescence microscope (light source, emission filter, dichromatic mirror, stage, emission filter, detector), Activity 6, multi-color imaging | 6 |
| 15 | 2/23/26 | Dichromatic mirrors for multi-color imaging, 3D imaging, optical sectioning, blur problem, introduction to confocal microscopy | 6 |
| 16 | 2/25/26 | Blur problem, point spread function (PSF), laser scanning confocal microscopy (LSCM), pinhole size | 6 |
| 17 | 2/27/26 | Spinning disk confocal microscopy (SDCM), Nipkow disk, camera, comparison of LSCM and SDCM | 6 |
| 18 | 3/2/26 | Widefield fluorescence microscopy, deconvolution, polarization microscopy, Activity 7, crossed polarizers | 5,6 |
| 19 | 3/4/26 | Specialized fluorescence techniques (overview), two-photon microscopy (start) | 7 |
| 20 | 3/6/26 | Two-photon microscopy (finish), total internal reflection fluorescence microscopy (TIRFM) (start) | 7 |
| 21 | 3/9/26 | Total internal reflection fluorescence microscopy (finish), super-resolution fluorescence microscopy (overview), structured illumination microscopy (SIM) (start), moiré patterns | 7,8 |
| 22 | 3/11/26 | Structured illumination microscopy (finish), beats, photoactivatable localization microscopy (PALM) (start) | 8 |
| 23 | 3/13/26 | Photoactivatable localization microscopy (finish), stimulated emission depletion (STED) microscopy | 8 |
| 24 | 3/16/26 | Activity 8 (Microscopy Review) – Problems 1-5 Ultrasound (start) – introduction (essence of ultrasound) | 2-8 10 |
| 25 | 3/18/26 | Activity 8 (Microscopy Review) – Problems 6-11 Ultrasound (continued) – choice of US frequency, quantifying contrast, types of reflection (specular, diffuse, scattering), quantification of specular reflection | 2-8 10 |
| 26 | 3/20/26 | Ultrasound (continued) – contrast, 13-microsecond rule, imaging modalities (A-Mode, M-Mode, B-Mode), resolution (lateral and axial) (start), Activity 9 | 10 |
| 27 | 3/30/26 | Ultrasound (continued) – resolution (finish), interplay between frequency and penetration depth, attenuation, time gain compensation (TGC) | 10 |
| 28 | 4/1/26 | Ultrasound (finish) – Doppler ultrasound Radiography (start) – introduction (essence of radiography), diagnostic X-rays, basis of image formation, overview of imaging modes (projection vs. computed tomography) | 10,11 |
| 29 | 4/3/26 | Radiography (continued) – interactions of X-rays with matter (photoelectric effect (good), Compton scattering (bad)), contrast agents, anti-scatter grids, local contrast (start), Activity 10 | 11 |
| 30 | 4/6/26 | Radiography (continued) – local contrast (finish), Beer’s law, attenuation coefficients, resolution, computed tomography (CT) (start) | 11 |
| 31 | 4/8/26 | Radiography (finish) – CT (continued), single- vs multi-slice detectors, scanning modes, reconstruction algorithms, simple vs filtered back projection, Activity 11 Nuclear imaging (start) – comparison of X-ray and radionuclide imaging | 11,12 |
| 32 | 4/13/26 | Nuclear imaging (continued) – nuclear instability, radioactivity, decay mechanisms, common radionuclides (e.g., Tc-99m and 18-fluorine), radioactive half-lives, projection imaging, collimators (start) | 12 |
| 33 | 4/15/26 | Nuclear imaging (continued) – collimators (finish), resolution, tomographic nuclear imaging (SPECT and PET) (start) | 12 |
| 34 | 4/17/26 | Nuclear imaging (finish) – tomographic nuclear imaging (SPECT and PET) (finish), time-of-flight (TOF) PET, iterative reconstruction, Activity 12 MRI (start) – brief introduction | 12,13 |
| 35 | 4/20/26 | MRI (continued) – expanded introduction, nuclear magnetism, resonance (Larmor) frequency, slice selection (start) | 13 |
| 36 | 4/22/26 | MRI (continued) – slice selection (finish), Activity 13, phase encoding, frequency encoding | 13 |
| 37 | 4/24/26 | MRI (continued) – localization (recap), contrast (T1, T2, and density weighting) (start) | 13 |
| 38 | 4/27/26 | MRI (finish) – contrast (finish), Activity 14 Digital image processing (start) – analog vs digital signals, digitization, overview of restoration and enhancement | 13,9 |
| 39 | 4/29/26 | Digital image processing (finish) – restoration scheme, brightness and contrast restoration (histogram stretching, lookup tables), gamma correction, noise reduction (mean and median filters), Fourier filters | 9 |