Difference: CemCourseSyllabus13 (1 vs. 3)

Revision 330 Oct 2013 - Main.BillRice

   META TOPICPARENT   name="CemCourseGroup" 

Contents
 
 
 
 Instructors
  Useful Textbooks
  Requirements
 
  Syllabus 
 Intro to EM, Optics, image formation and Diffraction -  David Stokes (NYU)
  Diffraction, Fourier transforms, CTF, cross-correlation - Bill Rice (NYSBC)
  Tomography I - David Stokes (NYU)
  Tomography II -  David Stokes (NYU)
  Crystallography  I  - Iban Ubarretxena (Mt. Sinai)
  Crystallography II -  Iban Ubarretxena (Mt. Sinai)
  Helical reconstruction - - Hernando Sosa (Einstein)
 
 


 Instructors 
 
 DavidStokes: stokes@saturn.med.nyu.edu
  BillRice: rice@nysbc.org
  IbanUbarretxena: iu@sci.ccny.cuny.edu
  HernandoJoseSosa: hsosa@aecom.yu.edu
  JoachimFrank: jf2192@columbia.edu
  WillyWriggers: wrw@biomachina.org
 

 Useful Textbooks 

Glaeser, Downing, DeRosier, Chiu, Frank: 
 "Electron Crystallography of Biological Macromolecules" 

Frank: 
 "Three Dimensional Electron Microscopy of Macromolecular Assemblies" 

Michael Moody, 1990, Biophysical Electron Microscopy: Basic Concepts and Modern Techniques, in Biophysical Electron Microscopy. ed. Hawkes & Valdre, Academic Press. p 145-287. 

Steward: 
 "Fourier Optics:  An Introduction"

Reimer: 
 "Transmission Electron Microscopy: 
 Physics of Image Formation and Microanalysis" 

Bozzola & Russell: 
 "Electron Microscopy: Principles and Techniques for Biologists" 

Harris: 
 "Negative Staining and Cryoelectron Microscopy" 

Williams & Carter: 
 "Transmission Electron Microscopy: A Textbook for Materials Science" 

 Requirements 

The following will be required for students desiring credit for this course:
 

 complete homework assignments during the class
  present a paper at one of the discussion sessions^?
  attend all of the practical sessions
  write a final paper at the end of the class
 



 Syllabus 

 Intro to EM, Optics, image formation and Diffraction -  David Stokes (NYU) 
 
 Basic EM techniques (TEM, SEM, STEM)
  Interaction of electrons with matter
  Image formation
  overview of 3D reconstruction strategies 
 2D crystallography
  helical reconstruction (Fourier-Bessel)
  single particle analysis
  tomography
 
  Physics of electrons 
 Faraday's Law and Lorenz force
  Motion of an electron in a magnetic field
  electrostatic and magnetic lenses
  deflectors
 
  electron-specimen interactions 
 particle-wave duality
  scattering cross-section
  elastic scattering
  inelastic scattering 
 energy filter and zero-loss imaging
  EELS
 
  secondary electrons
  backscattered electrons
  x-rays
 
  microscope column 
 condenser, objective, intermediate, projector lenses
  gun, beam, image deflector coils
  condensor, objective, selected area apertures
 
  optics 
 focal length, magnification
  ray path diagram
  resolution
  aberrations
  coherence
 
  Radiation damage 
 low dose imaging
 
  Electron diffraction
  Diffraction of waves - Frauenhofer vs. Fresnel
  Sum of cosines -> Fourier transform
 


 Diffraction, Fourier transforms, CTF, cross-correlation - Bill Rice (NYSBC) 
 
 Sum of cosines -> Fourier transform
  Example functions (Gaussian, box, delta fcn, cosine)
  Friedel's Law
  Convolution fcn
  Correlation fcn & Convolution Thm
  Projection Thm
  relative importance of amplitude and phase
  Nyquist limit
  Convolution and convolution theorem
  Correlation
  Effect of aperture in diffraction plane; point spread function
  image formation in the microscope
  weak phase approximation
  lens aberrations, defocus : CTF function
  Envelope functions
  Effect of CTF on images
  CTF correction
 

 Tomography I - David Stokes (NYU) 
 
 imaging considerations 
 dose fractionation
  automated imaging and strategies for tracking
  equal tilt increments/cosine rule
  dual/single axis
 
  Alignment of images (fiducial vs. correlation)
  distortion correction (optical and mechanical)
  R-weighted backprojection vs. other reconstruction algorithms
  denoising (non-linear anisotropic diffusion vs. median filter)
  segmentation (automatic vs. manual)
  template matching and real-space averaging of subvolumes
  applications
 


 Tomography II -  David Stokes (NYU) 
 
 Cryoelectron tomography
  Zero-loss imaging
  Resolution assessment
  Motif averaging
  Missing wedge compensation
 



 Crystallography  I  - Iban Ubarretxena (Mt. Sinai) 
 Crystallography II -  Iban Ubarretxena (Mt. Sinai) 
 
 Braggs law
  real/reciprocal lattice 
 unit cell
  symmetry
  Miller indices 
  reciprocal lattice symmetry (ampl and phase)
  lattice lines
 
  convolution fcn -> crystal
  Projection Thm and radius of Ewald Sphere
  strategy for 3D recontruction 
 missing cone
 
  imaging considerations 
 electron diffraction
  spot-scan for images 
 
  Unbending of 2D crystals
  electron diffraction for amplitudes
  imaging for phases 
 unbending
 
  merging data in 3D (lattice lines)
  temperature factor compensation
  resolution criteria (point-spread fcn)
 


 Helical reconstruction - - Hernando Sosa (Einstein) 
 
 Fourier transfor in cylindrical coord
  Bessel functions
  continuous helix
  discontinuous helix 
 selection rule
  n,l plot
  layer lines
  G(n,l) -> g(n,l)
 
  geometrical corrections 
 in-plane tilt
  out-of-plane tilt
  repeat distance
 
  averaging of G(n,l) 
 weighting
  CTF correction
  filtering
  temp factor compensation
  resolution criteria
  symmetry groups
-  META TOPICPARENT
+ name="CemCourseGroup"
-<
<
+ Practical Exercises in Tomography and Crystallography 
 
 Day 1: Tomography 1
->
>
+ Practical Exercises in Tomography and Crystallography Nov. 4-8 
 
 Day 1: Processing individual images of 2D crystals
->
>
+       *2dx software package 
 Day 2: Processing individual images of Helical Crystals  
 EMIP software package     
 
  Day 3 - Merging of data from Helical Crystals and 3D reconstruction 
 EMIP software package
 
  Day 4 - Tomography 1
  Generation of tomograms with eTomo
-<
<
+ Day 2: Tomography 2
->
>
+ Day 5 - Tomography 2
  Joining of serial sections with eTomo
-<
<
+ Day 3 - Processing individual images of 2D crystals 
 2dx software package
 
  Day 4 - Processing individual images of Helical Crystals 
 EMIP software package
 
  Day 5 - Merging of data from Helical Crystals and 3D reconstruction     * EMIP software package
  Single Particle Analysis I - Joachim Frank (Columbia University) 
 Single Particle Analysis II - Joachim Frank (Columbia University) 
 Single Particle Analysis III - Joachim Frank (Columbia University) 
 
 alignment
  classification and class-averages
  how to get the initial model  
 random conical tilt with defined orientations
  orientation determination using common lines
  3D projection matching
 
  model bias
  refinement
  multivariable statistical analysis (MSA)
  defocus groups and CTF correction (Weiner filter)
  weighted backprojection, ART and direct Fourier reconstruction
  symmetry
  resolution criteria (Fourier Shell Correlation)
 


 Practical Exercises in Tomography and Single Particle Analysis 
 
 Day 1: single particle analysis 1  
 Generation of initial model by Random Conical Tilt     * use SPIDER
 
 
 

 Day 2: single particle analysis 2
->
>
+d analysis / particle picking
   Generation of initial model by Common Lines
  use both SPIDER and EMAN
 
 
 

 Day 3: single particle analysis 3 
 Model generation and refinement using Projection Matching
  SPIDER
->
>
+ Day 4: Fitting of atomic coordinates into EM models
->
>
+ Day 5: Makeup
  Molecular fitting -  Willy Wriggers (Weil Cornell Medical College) 
 
 Boundary determination 
 isodensity contour
  segmentation
 
  Automated strategies 
 Situs
  helix hunter
 
  Criteria for fit
 

 

 Set ALLOWTOPICVIEW = 
 

-- DavidStokes - 07 Aug 2013
->
>
   META FILEATTACHMENT   attachment="Moody-Book-1990.pdf" attr="" comment="Moody chapter" date="1375915138" name="Moody-Book-1990.pdf" path="Moody-Book-1990.pdf" size="7354367" stream="Moody-Book-1990.pdf" user="Main.DavidStokes" version="1"
-  META FILEATTACHMENT
+ attachment="Moody-Book-1990.pdf" attr="" comment="Moody chapter" date="1375915138" name="Moody-Book-1990.pdf" path="Moody-Book-1990.pdf" size="7354367" stream="Moody-Book-1990.pdf" user="Main.DavidStokes" version="1"

Revision 207 Aug 2013 - Main.DavidStokes

META TOPICPARENT	name="CemCourseGroup"

Contents

Syllabus

Instructors

Useful Textbooks

Glaeser, Downing, DeRosier, Chiu, Frank:
"Electron Crystallography of Biological Macromolecules"

Frank:
"Three Dimensional Electron Microscopy of Macromolecular Assemblies"

Michael Moody, 1990, Biophysical Electron Microscopy: Basic Concepts and Modern Techniques, in Biophysical Electron Microscopy. ed. Hawkes & Valdre, Academic Press. p 145-287.

Steward:
"Fourier Optics: An Introduction"

Reimer:
"Transmission Electron Microscopy:
Physics of Image Formation and Microanalysis"

Bozzola & Russell:
"Electron Microscopy: Principles and Techniques for Biologists"

Harris:
"Negative Staining and Cryoelectron Microscopy"

Williams & Carter:
"Transmission Electron Microscopy: A Textbook for Materials Science"

Requirements

The following will be required for students desiring credit for this course:

complete homework assignments during the class
present a paper at one of the discussion sessions^?
attend all of the practical sessions
write a final paper at the end of the class

Syllabus

Intro to EM, Optics, image formation and Diffraction - David Stokes (NYU)

Basic EM techniques (TEM, SEM, STEM)
Interaction of electrons with matter
Image formation
overview of 3D reconstruction strategies
- 2D crystallography
- helical reconstruction (Fourier-Bessel)
- single particle analysis
- tomography
Physics of electrons
- Faraday's Law and Lorenz force
- Motion of an electron in a magnetic field
- electrostatic and magnetic lenses
- deflectors
electron-specimen interactions
- particle-wave duality
- scattering cross-section
- elastic scattering
- inelastic scattering
  - energy filter and zero-loss imaging
  - EELS
- secondary electrons
- backscattered electrons
- x-rays
microscope column
- condenser, objective, intermediate, projector lenses
- gun, beam, image deflector coils
- condensor, objective, selected area apertures
optics
- focal length, magnification
- ray path diagram
- resolution
- aberrations
- coherence
Radiation damage
- low dose imaging
Electron diffraction
Diffraction of waves - Frauenhofer vs. Fresnel
Sum of cosines -> Fourier transform

Diffraction, Fourier transforms, CTF, cross-correlation - Bill Rice (NYSBC)

Sum of cosines -> Fourier transform
Example functions (Gaussian, box, delta fcn, cosine)
Friedel's Law
Convolution fcn
Correlation fcn & Convolution Thm
Projection Thm
relative importance of amplitude and phase
Nyquist limit
Convolution and convolution theorem
Correlation
Effect of aperture in diffraction plane; point spread function
image formation in the microscope
weak phase approximation
lens aberrations, defocus : CTF function
Envelope functions
Effect of CTF on images
CTF correction

Tomography I - David Stokes (NYU)

imaging considerations
- dose fractionation
- automated imaging and strategies for tracking
- equal tilt increments/cosine rule
- dual/single axis
Alignment of images (fiducial vs. correlation)
distortion correction (optical and mechanical)
R-weighted backprojection vs. other reconstruction algorithms
denoising (non-linear anisotropic diffusion vs. median filter)
segmentation (automatic vs. manual)
template matching and real-space averaging of subvolumes
applications

Tomography II - David Stokes (NYU)

Cryoelectron tomography
Zero-loss imaging
Resolution assessment
Motif averaging
Missing wedge compensation

Crystallography I - Iban Ubarretxena (Mt. Sinai)

Crystallography II - Iban Ubarretxena (Mt. Sinai)

Braggs law
real/reciprocal lattice
- unit cell
- symmetry
- Miller indices
- reciprocal lattice symmetry (ampl and phase)
- lattice lines
convolution fcn -> crystal
Projection Thm and radius of Ewald Sphere
strategy for 3D recontruction
- missing cone
imaging considerations
- electron diffraction
- spot-scan for images
Unbending of 2D crystals
electron diffraction for amplitudes
imaging for phases
- unbending
merging data in 3D (lattice lines)
temperature factor compensation
resolution criteria (point-spread fcn)

Helical reconstruction - - Hernando Sosa (Einstein)

Fourier transfor in cylindrical coord
Bessel functions
continuous helix
discontinuous helix
- selection rule
- n,l plot
- layer lines
- G(n,l) -> g(n,l)
geometrical corrections
- in-plane tilt
- out-of-plane tilt
- repeat distance
averaging of G(n,l)
- weighting
- CTF correction
- filtering
- temp factor compensation
- resolution criteria
- symmetry groups

Practical Exercises in Tomography and Crystallography

Day 1: Tomography 1
- Generation of tomograms with eTomo
Day 2: Tomography 2
- Joining of serial sections with eTomo
Day 3 - Processing individual images of 2D crystals
- 2dx software package
Day 4 - Processing individual images of Helical Crystals
- EMIP software package
Day 5 - Merging of data from Helical Crystals and 3D reconstruction * EMIP software package

Single Particle Analysis I - Joachim Frank (Columbia University)

Single Particle Analysis II - Joachim Frank (Columbia University)

Single Particle Analysis III - Joachim Frank (Columbia University)

alignment
classification and class-averages
how to get the initial model
- random conical tilt with defined orientations
- orientation determination using common lines
- 3D projection matching
model bias
refinement
multivariable statistical analysis (MSA)
defocus groups and CTF correction (Weiner filter)
weighted backprojection, ART and direct Fourier reconstruction
symmetry
resolution criteria (Fourier Shell Correlation)

Practical Exercises in Tomography and Single Particle Analysis

Day 1: single particle analysis 1
- Generation of initial model by Random Conical Tilt * use SPIDER

Day 2: single particle analysis 2
- Generation of initial model by Common Lines
- use both SPIDER and EMAN

Day 3: single particle analysis 3
- Model generation and refinement using Projection Matching
- SPIDER

Molecular fitting - Willy Wriggers (Weil Cornell Medical College)

Boundary determination
- isodensity contour
- segmentation
Automated strategies
- Situs
- helix hunter
Criteria for fit

Set ALLOWTOPICVIEW =

-- DavidStokes - 07 Aug 2013

Added:

>
>

META FILEATTACHMENT	attachment="Moody-Book-1990.pdf" attr="" comment="Moody chapter" date="1375915138" name="Moody-Book-1990.pdf" path="Moody-Book-1990.pdf" size="7354367" stream="Moody-Book-1990.pdf" user="Main.DavidStokes" version="1"

Revision 107 Aug 2013 - Main.DavidStokes

META TOPICPARENT	name="CemCourseGroup"