Difference: CemCourseMaterials15 ( vs. 1)

Detailed Syllabus:

Jan 11 : Introduction & SEMC tour

Welcome to the Simons Electron Microscopy Center and explanation of the course. A tour of NYSBC and SEMC will be given.

The trailer for the Jensen lab lectures will be played along with details on how to watch them.

Getting Started in Cryo-EM with Professor Grant Jensen
Time: 2:52
Link: https://youtu.be/gDgFbAqdM_c

Welcome to Cryo-EM
Time: 7:36
Link: https://youtu.be/q17nGZPCeoA

Jan 18 : No class - Martin Luther King

Jan 25 : Basic anatomy of the electron microscope

To prepare watch Jensen lectures part 1 before class.

Online video lectures

Introduction: Why Electrons?
Time: 8:39
Link: https://youtu.be/Z2U0pcNk1jo

Part 1: Basic Anatomy of the EM
Time: 0:43
Link: https://youtu.be/GBU1eA1PqeQ

Part 1: Electron Guns
Time: 19:00
Link: https://youtu.be/C6DSFK7zJo0

Part 1: EM Lenses
Time: 32:15
Link: https://youtu.be/SKjxp-al_UI

Part 1: The Column
Time: 26:09
Link: https://youtu.be/hc2s4uSbpyI

Part 1: Sample Chamber
Time: 14:05
Link: https://youtu.be/EaXbk9OQDHw

Part 1: Energy Filters
Time: 7:06
Link: https://youtu.be/UzKNE8ZZBxw

Part 1: Detectors
Time: 11:56
Link: https://youtu.be/-0bjbWgxH2k

Part 1: Vacuum Systems
Time: 9:50
Link: https://youtu.be/LUlM0kl6Lp0

Part 1: Summary and Safety
Time: 5:13
Link: https://youtu.be/2rC8nFMRW4I

Feb 1 : Fourier transforms and Image Formation

To prepare watch Jensen lectures part 2 & 3 before class

Online video lectures

Part 2: Fourier Transforms for Beginners
Time: 0:54
Link: https://youtu.be/-EAQm8wgLbc

Part 2: 1-D Sine Waves and Their Sums
Time: 32:55
Link: https://youtu.be/OESy_ltOCvI

Part 2: 1-D Reciprocal Space
Time: 20:07
Link: https://youtu.be/IUaqeoMK5y4

Part 2: 2-D Waves and Images
Time: 19:16
Link: https://youtu.be/nyk75ufbP74

Part 2: 2-D Transforms and Filters
Time: 32:56
Link: https://youtu.be/fEyLh9HqsWU

Part 2: 3-D Waves and Transforms
Time: 13:17
Link: https://youtu.be/INtehLmqfmA

Part 2: Convolution and Cross-Correlation
Time: 15:06
Link: https://youtu.be/MQm6ZP1F6ms

Part 3: Image Formation
Time: 0:49
Link: https://youtu.be/HTJsYTGAhYg

Part 3: Amplitude and Phase Contrast
Time: 30:14
Link: https://youtu.be/jhniWbY2Jhc

Part 3: Wave Propagation and Phase Shifts
Time: 30:06
Link: https://youtu.be/YXIvVCoHbp4

Part 3: The Contrast Transfer Function
Time: 33:49
Link: https://youtu.be/mPynoF2j6zc

Part 3: Defocus and Its Effects
Time: 21:29
Link: https://youtu.be/izLp5vpoFyQ

Part 3: Envelopes
Time: 16:21
Link: https://youtu.be/joNEW0Nb2no

Part 3: CTF Correction
Time: 31:45
Link: https://youtu.be/GYDLhg49UQA

Feb 8 : Challenges in biological EM & Sample Prep

To prepare watch Jensen lectures part 4 before class

Online video lectures

Part 4: Fundamental Challenges in Biological TEM
Time: 3:05
Link: https://youtu.be/jYhp4aLZEb4

Part 4: Sample Prep: Room Temperature Methods
Time: 20:27
Link: https://youtu.be/aXj9rCr2Imk

Part 4: Sample Prep: Methods Involving Freezing
Time: 27:47
Link: https://youtu.be/7HHdFBA-fDs

Part 4: Sample Prep: Grids
Time: 11:08
Link: https://youtu.be/uHbyk2_tZn4

Part 4: 3-D Reconstruction
Time: 11:18
Link: https://youtu.be/_Ngybc0Rjo0

Part 4: Dose Limitations
Time: 22:06
Link: https://youtu.be/4BEXfZo-zDs

Feb 15 : No class - President's Day

Feb 22 : Tomography (part I)

To prepare watch Jensen lectures part 5 before class.

Online video lectures

Part 5: Tomography
Time: 23:20
Link: https://youtu.be/tOnijBqdJ1E

Part 5: Tomography Data Collection and Reconstruction
Time: 40:56
Link: https://youtu.be/WHiVBQy2i-w

Feb 29 : Tomography (part II)

To prepare watch Jensen lectures part 5 before class

Online video lectures

Part 5: Tomography Identfying Objects of Interest
Time: 24:31
Link: https://youtu.be/pZr4fagyp84

Part 5: Tomography Limitations
Time: 29:48
Link: https://youtu.be/PHbqQKqJWbc

Part 5: Tomography Parameters and Handedness
Time: 12:03
Link: https://youtu.be/96bWLdetKMs

Mar 7 : Single-particle analysis (part I)

To prepare watch Jensen lectures part 6 before class.

Online video lectures

Part 6: Single Particle Analysis
Time: 21:59
Link: https://youtu.be/IwR3MmnIpJI

Part 6: SPA Sample Prep
Time: 22:50
Link: https://youtu.be/poJGBbRR64Y

Mar 14 : Single-particle analysis (part II)

To prepare watch Jensen lectures part 6 before class.

Online video lectures

Part 6: SPA Data Collection
Time: 21:03
Link: https://youtu.be/UEsC8Il6nCQ

Part 6: SPA Reconstruction Basic Workflow
Time: 31:53
Link: https://youtu.be/7Zt5Tu75gXk

Mar 21 : Single-particle analysis (part III)

To prepare watch Jensen lectures part 6 before class.

Online video lectures

Part 6: SPA Reconstruction Additional Topics
Time: 44:28
Link: https://youtu.be/djQ8JCvHs5k

Part 6: SPA Interpretation and Limitations
Time: 26:26
Link: https://youtu.be/yvXhdbaS_kU

Mar 28 : 2D crystallography (part I)

To prepare watch Jensen lectures part 7 before class.

Online video lectures

Part 7: 2D Crystallography Intro and Sample Prep
Time: 6:25
Link: https://youtu.be/Qn7aP-fRT5I

Part 7: FT of a 2D Crystal
Time: 24:32
Link: https://youtu.be/EZ08dXR4JaU

Part 7: 2D Crystallography Data Collection and Reconstruction
Time: 17:01
Link: https://youtu.be/ViDGSwMOjLQ

Apr 4 : 2D crystallography (part II)

To prepare watch Jensen lectures part 7 before class. Class will have an additional lecture on helical tubes.

Online video lectures

(repeat) Part 7: 2D Crystallography Data Collection and Reconstruction
Time: 17:01
Link: https://youtu.be/ViDGSwMOjLQ

Part 7: Helical Tubes
Time: 3:57
Link: https://youtu.be/GKcvGoD3jfg

Part 7: Farewell
Time: 2:58
Link: https://youtu.be/IyDanBwRcs8

Apr 11 : Validation methods & Fitting Atomic Models

Lecture and discussion on Structure Validation & Fitting Atomic Models

Apr 18 : Practical: Appion tutorial (part I)

Apr 25 : Practical: Appion tutorial (part II)

May 2 : Conclusion & additional Appion help

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