Introduction
- Historical Contributions from Light Microscopy: What Can You Learn with a Light Microscope? (Ron Vale, HHMI/UCSF)
- History of Early Microscopes (Joseph Gall, Carnegie Institution)
Image Formation
- Refractive Lenses and Image Formation (Daniel Fletcher, UC Berkeley)
- Microscope Imaging and Koehler Illumination (Ron Vale, HHMI/UCSF)
- Objectives and Eyepieces (Stephen Ross, Nikon )
- Huygens Wavelets Constructive/Destructive Interference, and Diffraction (Jeff Lichtman, Harvard University)
- Point Spread Function (Jeff Lichtman, Harvard University)
- Resolution of a Microscope (Jeff Lichtman, Harvard University)
- Bonus: Photons: What is Light? (Bo Huang, UCSF)
- Bonus: Fourier Space: Fourier Transform (Bo Huang, UCSF)
- Lab: How to Focus: The Focal Plane (Ron Vale, HHMI/UCSF)
- Lab: How to Set Up Koehler Illumination (Ron Vale, HHMI/UCSF)
- Lab: Abbe Diffraction Demonstration (Kurt Thorn, UCSF)
- Lab: Measuring a Point Spread Function (Nico Stuurman, UCSF)
- Tip: Eyepieces (Stephen Ross, Nikon)
- Tip: Features of an Objective (Stephen Ross, Nikon)
- Tip: How to Clean Objective Lenses and Filters (Kurt Thorn, UCSF)
- Tip: Cleaning a Microscope: How to Find Dirt in Your Optical System (Stephen Ross, Nikon)
- Tip: Light Sources for Microscopy (Nico Stuurman, UCSF/HHMI)
- Tip: Adjusting the Eyepiece and Camera (Nico Stuurman, UCSF/HHMI)
- Tip: Correcting for Spherical Aberration with a Correction Collar (Stephen Ross, Nikon)
Contrast Generation for Transmitted Light
- Darkfield and Phase Contrast Microscopy (Edward Salmon, University of North Carolina)
- Polarized Light and its Interaction with Material (Shinya Inoue, Marine Biological Laboratory)
- Polarization Microscopy (Edward Salmon, University of North Carolina)
- Differential Interference Contrast (DIC) Microscopy (Edward Salmon, University of North Carolina)
- Bonus: Examples of Using Polarization Microscopy (Shinya Inoue, Marine Biological Laboratory)
- Bonus: Pragmatics of DIC and Video-Enhanced Contrast Microscopy (Edward Salmon, University of North Carolina)
- Lab: Phase, Polarization and DIC Microscopy Lab (Stephen Ross, Nikon)
Fluorescence Microscopy
- Introduction to Fluorescence Microscopy (Nico Stuurman, UCSF/HHMI)
- Fluorescent Probes: Organic Dyes and Quantum Dots (Timothy Mitchison, Harvard University)
- Fluorescent Proteins and the Story Behind GFP (Roger Tsien, UCSD/HHMI)
- Fluorescent Protein Indicators (Roger Tsien, UCSD/HHMI)
- Optical Sectioning and Confocal Microscopy (Kurt Thorn, UCSF)
- Two Photon Microscopy (Kurt Thorn, UCSF)
- Light Sheet Sectioning (Ernst Stelzer, European Molecular Biology Laboratory)
- Dual-View Inverted Selective Plane Illumination (diSPIM) (Hari Shroff, NIBI and National Institutes of Health)
- Total Internal Reflection Fluorescence (TIRF) Microscopy (Daniel Axelrod, University of Michigan)
- Super-Resolution: Overview and Stimulated Emission Depletion (STED) Microscopy (Stefan Hell, Max Planck Institute)
- Super-Resolution: Localization Microscopy (Bo Huang, UCSF)
- Super-Resolution: Structured Illumination Microscopy (SIM) (David Agard, UCSF/HHMI)
- Measuring Dynamics: Photobleaching and Photoactivation (Jennifer Lippincott-Schwartz, NIH)
- Measuring Dynamics: Fluorescent Speckle Microscopy (Clare Waterman, NIH)
- Förster Resonance Energy Transfer (FRET) Microscopy (Philippe Bastiaens, Max Planck Institute)
- Lab: Fluorescence Lifetime Imaging Microscopy (Philippe Bastiaens, Max Planck Institute)
- Summary: Designing a Fluorescence Microscopy Experiment (Kurt Thorn, UCSF)
- Bonus: Labeling Proteins with Fluorescent Probes (Timothy Mitchison, Harvard University)
- Bonus: Correlating Fluorescence with Electron Microscopy (Roger Tsien, UCSD/HHMI)
- Bonus: Pushing the Boundaries of Light Microscopy (Steven Chu, Stanford)
- Demystifying Microscopes: Disassembling a Nikon Ti Eclipse Microscope (Stephen Ross, Nikon)
- Tips: Demystifying Microscopes: Disassembling an ASI RAMM (Nico Stuurman, UCSF/HHMI)
- Tip: Optimizing Detection of GFP (Roger Tsien, UCSD/HHMI)
- Tip: Live Cell Imaging and Environmental Control (Kurt Thorn, UCSF)
- Tip: Minimizing Damage from Fluorescence (Ron Vale, UCSF/HHMI)
- Tip: Quantitative Analysis of Speckle Microscopy (Clare Waterman, NIH)
Robotics, Detection and Image Analysis
- Cameras and Detectors I: How Do They Work? (Nico Stuurman, UCSF/HHMI)
- Cameras and Detectors II: Specifications and Performance (Nico Stuurman, UCSF/HHMI)
- Introduction to Digital Images (Kurt Thorn, UCSF)
- Image Analysis (Kurt Thorn, UCSF)
- Deconvolution Microscopy (David Agard, UCSF/HHMI)
- Lab: Using Software to Control Microscopes (Nico Stuurman, UCSF/HHMI)
- Lab: Camera Calibration (Nico Stuurman, UCSF/HHMI)
- Tip: High Speed Synchronization (Nico Stuurman, UCSF/HHMI)
Specialized Microscopy
- Optical Traps (Carlos Bustamante,UC Berkeley/HHMI)
- High Throughput Microscopy (Jan Ellenberg, European Molecular Biology Laboratory)
- Array Tomography (Stephen Smith, Stanford University)
- Miniature Microscopes for Deep Tissue Imaging (Mark Schnitzer, Stanford University/HHMI)
- Optogenetics: The Use of Opsin Genes in Technique Development (Karl Deisseroth, Stanford University/HHMI)
- Mobile Microscopy (Daniel Fletcher, UC Berkeley)
- Lab: Demystifying Microscopes: Disassembling a Nikon Ti Eclipse Microscope (Stephen Ross, Nikon)
- Lab: Demystifying Microscopes: Disassembling an ASI RAMM (Nico Stuurman, UCSF/HHMI)