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Home » Courses » Microscopy Series » Microscopy Series Table of Contents

Microscopy Series Table of Contents

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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)
    • Optical Traps A: An Introduction
    • Optical Traps B: Building and Calibrating
    • Optical Traps C: Measuring Steps by Molecular Motors
  • 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)

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This material is based upon work supported by the National Science Foundation and the National Institute of General Medical Sciences under Grant No. 2122350 and 1 R25 GM139147. Any opinion, finding, conclusion, or recommendation expressed in these videos are solely those of the speakers and do not necessarily represent the views of the Science Communication Lab/iBiology, the National Science Foundation, the National Institutes of Health, or other Science Communication Lab funders.

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