VIBS 627

VIBS 627: Optical Microscopy & Live Cell Imaging

  • Prerequisites: Graduate status & permission of instructor
  • Meeting times:
    • Lecture: Monday 9:00–10:40 a.m.
    • Labs*: Monday 11:00 a.m.–2:00 p.m. or 2:00 p.m.–5:00 p.m.
    • *Laboratory schedule with learning outcomes and assignments will be distributed to registered students.
  • Instructor: Robert C. Burghardt, Ph.D.Professor & Image Analysis Laboratory (IAL) Director
WeekLecture TopicsLab Topics
1Introduction to optical microscopy: visual perception, resolution of eye and magnification; the magnifying lens; description of optical phenomena; geometrical optics; Koehler illuminationInstruments and safety; Axioplan 2 microscope, Axiocam HR and Axiovision software; Koehler illumination on multiple instruments
2Applications of geometrical optics; basics of objectives, condensers, and light sourcesIntroduction to ZEN software. Acquire and process czi files; Stage micrometer; C-mounts, optivar settings
3Applications of wave optics, diffraction, and interference; the diffraction apparatus and image formation in a microscope; brightfield microscopyAbbe diffraction apparatus; brightfield microscopy/achieving theoretical limit of resolution
4Contrast in optical microscopy; compare brightfield, darkfield, phase contrast, and differential interference contrast microscopy; compare contrast generation in optical vs. transmission electron microscopy (TEM)Darkfield and phase contrast imaging; TEM brightfield and diffraction imaging
5Basics of digital images; digital imaging ethicsDIC imaging on Axioplan 2 and inverted live cell workstations
6Introduction to widefield fluorescence microscopyIntroduction to Axio Imager.M2 Motorized Upright Microscope.  BF, DF, Phase, DIC, z-stacks, tiling
7Written Examination
Submit project proposal
Laboratory Practical Examination
8Fluorescence probes of cellular function; steady state and kinetic analysis for live cell imagingTraining on ZEN software on AxioImager.M2 automated widefield microscope
9Confocal microscopyIntro to ZEN Software for Zeiss 780 and Zeiss CellDiscoverer 7 instruments
10Confocal and multiphoton microscopyImage acquisition of fixed samples on Zeiss 780
11Confocal microscopy & Automated live cell imagingImage acquisition of live samples on Zeiss 780 and Celldiscoverer 7
12Breaking the diffraction limit: Super-resolution microscopy-Intro to Airyscan superresolutionIntroduction to Airyscan imaging on Zeiss 780
13TIRF and Correlation CoefficientsData acquisition using high-end instruments
14Data acquisitionData acquisition using high-end instruments
15Final presentations & written project reports are duePresentation of research projects