Super-Resolution Microscopy: Xiaowei Zhuang

Super-Resolution Microscopy - Xiaowei Zhuang

Description: This lecture surveys a variety of recent methods that achieve higher resolution than is possible with conventional microscopy with diffraction-limited optics. These include different types of patterned illumination (e.g. STED and SIM microscopy) or techniques that build up an image by stochastically switching on single fluorescent molecules and localizing each molecule with high spatial precision (STORM, PALM, FPALM).

About the Speaker: Xiaowei Zhuang
Xiaowei Zhuang is Professor of Chemistry and Chemical Biology, and of Physics at Harvard University and a Howard Hughes Medical Institute Investigator.  Zhuang uses her background in physics to develop new super-resolution microscopy methods for use in cell and neurobiology.

For full tutorial & assessment go to iBiology

Choosing the Right Microscopy Technique: Ron Vale

Choosing the Right Microscopy Technique - Ron Vale


Description: This concluding lecture summarizes the main techniques covered in the short course and provides an overview of when a specific microscopy method might be advantageous for a particular sample or biological experiment.

About the Speaker: Ron Vale
Ron Vale is a Professor at the University of California, San Francisco, a Howard Hughes Medical Institute Investigator, and a member of the National Academy of Sciences. He has a long-standing interest in intracellular movement and his lab uses many types of microscopy to study this problem. Ron also founded, and continues to be very involved with, the iBiology program.

For full tutorial and assessment go to iBiology

Correlating Fluorescence with Electron Microscopy: Roger Tsien

Correlating Fluorescence with Electron Microscopy - Roger Tsien

Description: This lecture discusses a new protein, miniSOG, which can be imaged fluorescently but which can also produce an electron-dense deposit for visualization in electron microscopy, thus enabling correlated light and electron microscopy.

About the Speaker: Roger Tsien
Dr. Tsien is a Professor at the University of California, San Diego, a Howard Hughes Medical Institute Investigator and a member of the National Academy of Sciences. In 2008, Tsien shared the Nobel Prize in Chemistry for the discovery and development of green fluorescent protein, GFP. His lab continues to develop new fluorescent proteins as tools to study cell signaling.

For full tutorial & assessment go to iBiology

Optical Sectioning and Confocal Microscopy: Kurt Thorn

Optical Sectioning and Confocal Microscopy - Kurt Thorn

Description: This talk introduces confocal microscopy, and discusses optical sectioning, reconstruction of 3D images, and how the laser-scanning confocal microscope and spinning disk confocal microscope work.

About the Speaker: Kurt Thorn
Kurt Thorn is an Assistant Professor of Biochemistry and Biophysics at UCSF and Director of the Nikon Imaging Center – a facility that provides cutting-edge light microscopy equipment to UCSF researchers. Kurt can be followed on his blog at

Fir full tutorial & assessment go to iBiology

Cameras and Detectors How do they work?: Nico Stuurman

Cameras and Detectors How do they work

Description: Photosensitive detectors are used in microscopy to generate digital images. This lecture introduces the two main classes of detectors: single-point (Photo-multipliers and Photo-diodes) and multi-point detectors (cameras) and explains their basic principles.

About the Speaker: Nico Stuurman
Nico Stuurman is a Research Specialist at the University of California, San Francisco, in the lab of Ron Vale. Nico combines his expertise in computer programming and microscopy to advance many projects including the Open Source software, Micro Manager.

For full tutorial & assessment go to iBiology

Dual-View Inverted Selective Plane Illumination (diSPIM): Hari Shroff

Dual-View Inverted Selective Plane Illumination (diSPIM) - Hari Shroff

Description: Selective Plane Illumination Microscopy (SPIM) greatly reduces phototoxicity in comparison with other fluorescent imaging modalities and makes it possible to image living small animals in 3D over extended periods of time.  This talk describes an extension of SPIM such that it can be used with specimens on a coverslip rather than in a capillary (inverted SPIM or iSPIM), and a second modification that images the specimen using two perpendicular light sheets (Dual-View iSPIM or diSPIM), resulting in 3D datasets with the same resolution in X, Y, and Z (isotropic resolution)

About the Speaker: Hari Shroff 
Hari Shroff is an Investigator at the National Institute of Biomedical Imaging and Bioengineering at the National Institutes of Health. During his post-doc, which was with Eric Betzig at HHMI’s Janelia Farm Research Campus, he focused on the development of PALM (photoactivated localization microscopy) microscopy. Since then he has developed several microscopy techniques, such as diSPIM and instant structured illumination microscopy.

For full tutorial & assessment go to iBiology

Miniature Microscopes for Deep Tissue Imaging: Mark Schnitzer

Miniature Microscopes for Deep Tissue Imaging -Mark Schnitzer

Description: This lecture describes recent work on developing small microscopes for deep tissue imaging that can be surgically implemented into living and awake animals. Exciting applications are described for imaging the activity and long term shape changes of single neurons in the brain.

About the Speaker: Mark Schnitzer
Mark Schnitzer is an Associate Professor in the Departments of Biological Sciences and Applied Physics at Stanford University and an Investigator of the Howard Hughes Medical Institute. His research focuses on understanding learning and memory processes at the level of neural circuits. To this end, his lab has developed techniques capable of observing individual neurons and dendrites in live animals. Schnitzer will be a contributor to the BRAIN project recently announced by President Obama.

For full tutorial & assessment go to iBiology

Polarization Microscopy: Edward Salmon

Polarization Microscopy - Edward Salmon

Description: Polarization microscopy probes the interaction of molecules with polarized light and is particularly good for examining well-order structures composed of polymers, such as the mitotic spindle. This lecture describes the components of a polarization microscope (e.g. polarizer, analyzer), birefringence and how it is exploited to generate images, adjusting a polarization microscope, examples of images, and new methods such the LC-Polscope.

About the Speaker: Edward Salmon
Ted Salmon is a Distinguished Professor in the Biology Department at the University of North Carolina. His lab has pioneered techniques in video and digital imaging to study the assembly of spindle microtubules and the segregation of chromosomes during mitosis.

Fir full tutorial and assessment go to iBiology

Resolution in Microscopy: Jeff Lichtman

Resolution in Microscopy - Jeff Lichtman

Description: This lecture describes the diffraction of light, a key principle in image formation and a factor that limits the resolution of a conventional light microscope. The behavior of light traveling through an objective is described along with the concept of numerical aperture. The “point spread function” (or PSF) and Nyquist sampling are explained, which are critical concepts for understanding image resolution and detection of images.

About the Speaker: Jeff Lichtman
One of Dr. Lichtman’s research goals is to generate a complete map of all the neural connections in the brain- the “connectome”. His lab has developed several novel imaging techniques including the “Brainbow” mouse and serial electron microscopy reconstruction to reach this goal. Lichtman is the Jeremy R. Knowles Professor of Molecular and Cellular Biology and Santiago Ramón y Cajal Professor of Arts and Sciences at Harvard University.

For full tutorial & assessment go to iBiology

Super Resolution Localization Microscopy: Bo Huang

Super Resolution Localization Microscopy - Bo Huang

Description: A large family of techniques to achieve super-resolution imaging utilize single molecule switching and localization microscopy. In these techniques, such as STORM, PALM, FPALM, and GSDIM, super-resolution is achieved by first switching all the molecules in the sample to a non-fluorescent state. Individual molecules are then returned to the fluorescent state, imaged, and their position determined to much higher than the diffraction limit. This lecture describes these techniques, dye requirements (photoswitchable fluorescent proteins and small molecule dyes) and how to extend these techniques to 3 dimensional imaging.

About the Speaker: Bo Huang
Dr. Huang’s research focuses on using super-resolution microscopy and single-molecule imaging to understand how proteins form large complexes and how proteins interact to regulate signaling. Huang is an Assistant Professor in Pharmaceutical Chemistry and in Biochemistry and Biophysics at UC San Francisco.

For full tutorial and assessment go to iBiology

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