(1 vs. 16) CemCourseSyllabus06 < Main

Revision 1613 Mar 2009 - Main.DavidCowburn

META TOPICPARENT	name="CemCourseGroup"

Cryoelectron Microscopy of Macromolecular Assemblies - 2006

NYU course # G16.4408 - 3 credits

Contents

Instructors

Instructors

David Stokes: stokes@saturn.med.nyu.edu
John Berriman: berriman@nysbc.org
Bill Rice: rice@nysbc.org
Iban Ubarretxena: iu@sci.ccny.cuny.edu
Hernando Sosa: hsosa@aecom.yu.edu

Changed:

<
<

Joachim Frank: joachim@wadsworth.org

>
>

Joachim Frank: joachim AT wadsworth.org

Carmen Mannella: carmen@wadsworth.org

Useful Textbooks

Frank: "Three Dimensional Electron Microscopy of Macromolecular Assemblies"
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"

Syllabus

Intro to EM and History of 3D Reconstruction - Sept 12 - David Stokes (NYSBC/NYU)

Basic EM techniques
- TEM
- SEM
- STEM
- Types of specimens
Electron sources
- tips (W, LaB6^?, FEG)
Physics of electrons
- Faraday's Law
- influence of a B field
- electrostatic and electromagnetic lens
Interaction of electrons with matter
- elastic scattering
- inelastic scattering
- secondary electrons
- backscattered electrons
- x-rays
- EELS
overview of 3D reconstruction strategies
- 2D crystallography
- helical reconstruction (Fourier-Bessel)
- single particle analysis
- tomography
negative stain of viruses
- model of negative stain
- matching of projection images
- quasiequivalence & icosahedral viruses
optical diffraction
- optical filtering
bacteriorhodopsin
acetylcholine receptor
ribosomes
insect flight muscle tomography

Sample preparation - Sept 19 - John Berriman (NYSBC)

Discussion leaders (Sept 26):

tissue -> sections
- positive stain
- immunolabeling
molecules -> negative stain
- single particles
- 2D crystals
cryo -> no stain
- frozen sections
- suspensions of molecules or 2D crystals

Diffraction and Fourier transforms - Sep 26 - Iban Ubarretxena (CCNY)

Discussion Leaders (Oct 3): Jaime Llodra

Diffraction of waves - Frauenhofer vs. Fresnel
Sum of cosines -> Fourier transform
Example functions (Gaussian, box, delta fcn, cosine)
Friedel's Law
Convolution fcn
Correlation fcn & Convolution Thm
Projection Thm

Single Particle Analysis I - Oct 3 - Joachim Frank (Wadsworth Ctr)

Discussion Leader (Oct 10): Jaclyn Greimann & David Grandy

philosophy of single-particle reconstruction
imaging considerations
- solid/perforated carbon
- automated data collection
how to get the initial model
- random conical tilt with defined orientations
- orientation determination using common lines
- 3D projection matching
model bias
correspondence analysis
classification and class-averages
refinement
defocus groups and CTF correction (Weiner filter)
weighted backprojection, ART and direct Fourier reconstruction
symmetry
resolution criteria (Fourier Shell Correlation)
overview of programs (Spider, Eman, Imagic)
applications

Single Particle Analysis II - Oct 10 - Joachim Frank (Wadsworth Ctr)

SPA practical (Oct 17):

Crystallography - Oct 17 - Iban Ubarretxena (CCNY)

Discussion Leaders (Oct 24): Allyson Bunbury

Braggs law
real/reciprocal lattice
- unit cell
  - asymmetric unit
  - fractional coordinates
- symmetry
  - symmetry operators
  - plane groups & space groups
- Miller indices
- reciprocal lattice symmetry (ampl and phase)
- lattice lines
convolution fcn -> crystal
- convolution Thm -> reciprocal lattice
Projection Thm and radius of Ewald Sphere
strategy for 3D recontruction
- missing cone
imaging considerations
- electron diffraction
- spot-scan for images
electron diffraction for amplitudes
- radial background subtraction
- lattice refinement
- tilt angle/axis
- local background sub and spot integration
- merging
- refinement
- curve fitting
imaging for phases
- unbending
- defocus determination
- tilt angle/axis
- merging, weighting
- temperature factor compensation
resolution criteria (point-spread fcn)

Helical reconstruction - Oct 24 - Hernando Sosa (Einstein)

Discussion Leaders (Oct 31): Vikas Jain

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
Hybrid methods - unbending
- separately refining small segments against average
- Egelman's spider implementation for helical structures
- real-space averaging of symmetry groups

Electron Optics - Oct 31 - David Stokes

Discussion Leaders (Nov 7): Jinrang Kim

Physics of electrons
- Faraday's Law
- influence of a B field
- electrostatic and electromagnetic lens
- deflectors
electron scattering
- scattering cross-section
- elastic scattering
- inelastic scattering
- secondary electrons
- backscattered electrons
- x-rays
- EELS
microscope column
- condensor, objective, intermediate, projector lenses
- gun, beam, image deflector coils
- condensor, objective, selected area apertures
optics
- focal length, magnification
- ray path diagram
- resolution
- aberrations
- coherency

Imaging strategies and Media - Nov 7 - David Stokes

Discussion Leaders (Nov 14): Jorge Mansilla-Soto

Radiation damage
- low dose imaging
Electron diffraction
Inelastic scattering
- energy filter and zero-loss imaging
Review of diffraction and Fourier transforms
- scattering - Fresnel and Frauenhofer
- sum of sines -> Fourier transform
- Friedel's Law
- Convolution Thm
- Correlation function
effect of sampling
- discrete Fourier transform
- box function and lattice function
- Nyquist sampling frequency
- boxing and floating
- aliasing
transfer functions and detectors (CCD and film)
- CTF: phase vs amplitude contrast (cryo vs neg stain)
- DQE, MTF, NTF

Tomography - Nov 14 - Carmen Mannella (Wadsworth Ctr)

Discussion Leader (Nov 28): W. Nicholson Price

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

Hybrid Methods - Nov 28 - David Stokes (NYSBC/NYU)

Discussion Leader (Dec 5): Shyam Vaidya

Unbending of 2D crystals
patch averaging of 2D crystals
Real-space averaging of helical reconstructions
SPA of helical assemblies
SPA of tomographic volumes
tomography of 2D crystals

Molecular fitting - Dec 5 - Hernando Sosa (Einstein)

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

Visit Cryo EM website at http://www.nysbc.org/facilities/CEM

Set ALLOWTOPICVIEW =

-- DavidStokes - 24 Jul 2006

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Revision 1501 Sep 2008 - Main.DavidStokes

META TOPICPARENT	name="CemCourseGroup"

Changed:

<
<

Cryoelectron Microscopy of Macromolecular Assemblies

>
>

Cryoelectron Microscopy of Macromolecular Assemblies - 2006

NYU course # G16.4408 - 3 credits

Contents

Instructors

David Stokes: stokes@saturn.med.nyu.edu
John Berriman: berriman@nysbc.org
Bill Rice: rice@nysbc.org
Iban Ubarretxena: iu@sci.ccny.cuny.edu
Hernando Sosa: hsosa@aecom.yu.edu
Joachim Frank: joachim@wadsworth.org
Carmen Mannella: carmen@wadsworth.org

Useful Textbooks

Frank: "Three Dimensional Electron Microscopy of Macromolecular Assemblies"
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"

Syllabus

Intro to EM and History of 3D Reconstruction - Sept 12 - David Stokes (NYSBC/NYU)

Basic EM techniques
- TEM
- SEM
- STEM
- Types of specimens
Electron sources
- tips (W, LaB6^?, FEG)
Physics of electrons
- Faraday's Law
- influence of a B field
- electrostatic and electromagnetic lens
Interaction of electrons with matter
- elastic scattering
- inelastic scattering
- secondary electrons
- backscattered electrons
- x-rays
- EELS
overview of 3D reconstruction strategies
- 2D crystallography
- helical reconstruction (Fourier-Bessel)
- single particle analysis
- tomography
negative stain of viruses
- model of negative stain
- matching of projection images
- quasiequivalence & icosahedral viruses
optical diffraction
- optical filtering
bacteriorhodopsin
acetylcholine receptor
ribosomes
insect flight muscle tomography

Sample preparation - Sept 19 - John Berriman (NYSBC)

Discussion leaders (Sept 26):

tissue -> sections
- positive stain
- immunolabeling
molecules -> negative stain
- single particles
- 2D crystals
cryo -> no stain
- frozen sections
- suspensions of molecules or 2D crystals

Diffraction and Fourier transforms - Sep 26 - Iban Ubarretxena (CCNY)

Discussion Leaders (Oct 3): Jaime Llodra

Diffraction of waves - Frauenhofer vs. Fresnel
Sum of cosines -> Fourier transform
Example functions (Gaussian, box, delta fcn, cosine)
Friedel's Law
Convolution fcn
Correlation fcn & Convolution Thm
Projection Thm

Single Particle Analysis I - Oct 3 - Joachim Frank (Wadsworth Ctr)

Discussion Leader (Oct 10): Jaclyn Greimann & David Grandy

philosophy of single-particle reconstruction
imaging considerations
- solid/perforated carbon
- automated data collection
how to get the initial model
- random conical tilt with defined orientations
- orientation determination using common lines
- 3D projection matching
model bias
correspondence analysis
classification and class-averages
refinement
defocus groups and CTF correction (Weiner filter)
weighted backprojection, ART and direct Fourier reconstruction
symmetry
resolution criteria (Fourier Shell Correlation)
overview of programs (Spider, Eman, Imagic)
applications

Single Particle Analysis II - Oct 10 - Joachim Frank (Wadsworth Ctr)

SPA practical (Oct 17):

Crystallography - Oct 17 - Iban Ubarretxena (CCNY)

Discussion Leaders (Oct 24): Allyson Bunbury

Braggs law
real/reciprocal lattice
- unit cell
  - asymmetric unit
  - fractional coordinates
- symmetry
  - symmetry operators
  - plane groups & space groups
- Miller indices
- reciprocal lattice symmetry (ampl and phase)
- lattice lines
convolution fcn -> crystal
- convolution Thm -> reciprocal lattice
Projection Thm and radius of Ewald Sphere
strategy for 3D recontruction
- missing cone
imaging considerations
- electron diffraction
- spot-scan for images
electron diffraction for amplitudes
- radial background subtraction
- lattice refinement
- tilt angle/axis
- local background sub and spot integration
- merging
- refinement
- curve fitting
imaging for phases
- unbending
- defocus determination
- tilt angle/axis
- merging, weighting
- temperature factor compensation
resolution criteria (point-spread fcn)

Helical reconstruction - Oct 24 - Hernando Sosa (Einstein)

Discussion Leaders (Oct 31): Vikas Jain

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
Hybrid methods - unbending
- separately refining small segments against average
- Egelman's spider implementation for helical structures
- real-space averaging of symmetry groups

Electron Optics - Oct 31 - David Stokes

Discussion Leaders (Nov 7): Jinrang Kim

Physics of electrons
- Faraday's Law
- influence of a B field
- electrostatic and electromagnetic lens
- deflectors
electron scattering
- scattering cross-section
- elastic scattering
- inelastic scattering
- secondary electrons
- backscattered electrons
- x-rays
- EELS
microscope column
- condensor, objective, intermediate, projector lenses
- gun, beam, image deflector coils
- condensor, objective, selected area apertures
optics
- focal length, magnification
- ray path diagram
- resolution
- aberrations
- coherency

Imaging strategies and Media - Nov 7 - David Stokes

Discussion Leaders (Nov 14): Jorge Mansilla-Soto

Radiation damage
- low dose imaging
Electron diffraction
Inelastic scattering
- energy filter and zero-loss imaging
Review of diffraction and Fourier transforms
- scattering - Fresnel and Frauenhofer
- sum of sines -> Fourier transform
- Friedel's Law
- Convolution Thm
- Correlation function
effect of sampling
- discrete Fourier transform
- box function and lattice function
- Nyquist sampling frequency
- boxing and floating
- aliasing
transfer functions and detectors (CCD and film)
- CTF: phase vs amplitude contrast (cryo vs neg stain)
- DQE, MTF, NTF

Tomography - Nov 14 - Carmen Mannella (Wadsworth Ctr)

Discussion Leader (Nov 28): W. Nicholson Price

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

Hybrid Methods - Nov 28 - David Stokes (NYSBC/NYU)

Discussion Leader (Dec 5): Shyam Vaidya

Unbending of 2D crystals
patch averaging of 2D crystals
Real-space averaging of helical reconstructions
SPA of helical assemblies
SPA of tomographic volumes
tomography of 2D crystals

Molecular fitting - Dec 5 - Hernando Sosa (Einstein)

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

Visit Cryo EM website at http://www.nysbc.org/facilities/CEM

Set ALLOWTOPICVIEW =

-- DavidStokes - 24 Jul 2006

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Revision 1425 Sep 2006 - Main.DavidStokes

META TOPICPARENT	name="CemCourseGroup"

Cryoelectron Microscopy of Macromolecular Assemblies

NYU course # G16.4408 - 3 credits

Contents

Instructors

David Stokes: stokes@saturn.med.nyu.edu
John Berriman: berriman@nysbc.org
Bill Rice: rice@nysbc.org
Iban Ubarretxena: iu@sci.ccny.cuny.edu
Hernando Sosa: hsosa@aecom.yu.edu
Joachim Frank: joachim@wadsworth.org
Carmen Mannella: carmen@wadsworth.org

Useful Textbooks

Frank: "Three Dimensional Electron Microscopy of Macromolecular Assemblies"
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"

Syllabus

Intro to EM and History of 3D Reconstruction - Sept 12 - David Stokes (NYSBC/NYU)

Basic EM techniques
- TEM
- SEM
- STEM
- Types of specimens
Electron sources
- tips (W, LaB6^?, FEG)
Physics of electrons
- Faraday's Law
- influence of a B field
- electrostatic and electromagnetic lens
Interaction of electrons with matter
- elastic scattering
- inelastic scattering
- secondary electrons
- backscattered electrons
- x-rays
- EELS
overview of 3D reconstruction strategies
- 2D crystallography
- helical reconstruction (Fourier-Bessel)
- single particle analysis
- tomography
negative stain of viruses
- model of negative stain
- matching of projection images
- quasiequivalence & icosahedral viruses
optical diffraction
- optical filtering
bacteriorhodopsin
acetylcholine receptor
ribosomes
insect flight muscle tomography

Sample preparation - Sept 19 - John Berriman (NYSBC)

Discussion leaders (Sept 26):

tissue -> sections
- positive stain
- immunolabeling
molecules -> negative stain
- single particles
- 2D crystals
cryo -> no stain
- frozen sections
- suspensions of molecules or 2D crystals

Diffraction and Fourier transforms - Sep 26 - Iban Ubarretxena (CCNY)

Changed:

<
<

Discussion Leaders (Oct 3):

>
>

Discussion Leaders (Oct 3): Jaime Llodra

Diffraction of waves - Frauenhofer vs. Fresnel
Sum of cosines -> Fourier transform
Example functions (Gaussian, box, delta fcn, cosine)
Friedel's Law
Convolution fcn
Correlation fcn & Convolution Thm
Projection Thm

Single Particle Analysis I - Oct 3 - Joachim Frank (Wadsworth Ctr)

Changed:

<
<

Discussion Leader (Oct 10):

>
>

Discussion Leader (Oct 10): Jaclyn Greimann & David Grandy

philosophy of single-particle reconstruction
imaging considerations
- solid/perforated carbon
- automated data collection
how to get the initial model
- random conical tilt with defined orientations
- orientation determination using common lines
- 3D projection matching
model bias
correspondence analysis
classification and class-averages
refinement
defocus groups and CTF correction (Weiner filter)
weighted backprojection, ART and direct Fourier reconstruction
symmetry
resolution criteria (Fourier Shell Correlation)
overview of programs (Spider, Eman, Imagic)
applications

Single Particle Analysis II - Oct 10 - Joachim Frank (Wadsworth Ctr)

SPA practical (Oct 17):

Crystallography - Oct 17 - Iban Ubarretxena (CCNY)

Changed:

<
<

Discussion Leaders (Oct 24):

>
>

Discussion Leaders (Oct 24): Allyson Bunbury

Braggs law
real/reciprocal lattice
- unit cell
  - asymmetric unit
  - fractional coordinates
- symmetry
  - symmetry operators
  - plane groups & space groups
- Miller indices
- reciprocal lattice symmetry (ampl and phase)
- lattice lines
convolution fcn -> crystal
- convolution Thm -> reciprocal lattice
Projection Thm and radius of Ewald Sphere
strategy for 3D recontruction
- missing cone
imaging considerations
- electron diffraction
- spot-scan for images
electron diffraction for amplitudes
- radial background subtraction
- lattice refinement
- tilt angle/axis
- local background sub and spot integration
- merging
- refinement
- curve fitting
imaging for phases
- unbending
- defocus determination
- tilt angle/axis
- merging, weighting
- temperature factor compensation
resolution criteria (point-spread fcn)

Helical reconstruction - Oct 24 - Hernando Sosa (Einstein)

Changed:

<
<

Discussion Leaders (Oct 31):

>
>

Discussion Leaders (Oct 31): Vikas Jain

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
Hybrid methods - unbending
- separately refining small segments against average
- Egelman's spider implementation for helical structures
- real-space averaging of symmetry groups

Electron Optics - Oct 31 - David Stokes

Changed:

<
<

Discussion Leaders (Nov 7):

>
>

Discussion Leaders (Nov 7): Jinrang Kim

Physics of electrons
- Faraday's Law
- influence of a B field
- electrostatic and electromagnetic lens
- deflectors
electron scattering
- scattering cross-section
- elastic scattering
- inelastic scattering
- secondary electrons
- backscattered electrons
- x-rays
- EELS
microscope column
- condensor, objective, intermediate, projector lenses
- gun, beam, image deflector coils
- condensor, objective, selected area apertures
optics
- focal length, magnification
- ray path diagram
- resolution
- aberrations
- coherency

Imaging strategies and Media - Nov 7 - David Stokes

Changed:

<
<

Discussion Leaders (Nov 14):

>
>

Discussion Leaders (Nov 14): Jorge Mansilla-Soto

Radiation damage
- low dose imaging
Electron diffraction
Inelastic scattering
- energy filter and zero-loss imaging
Review of diffraction and Fourier transforms
- scattering - Fresnel and Frauenhofer
- sum of sines -> Fourier transform
- Friedel's Law
- Convolution Thm
- Correlation function
effect of sampling
- discrete Fourier transform
- box function and lattice function
- Nyquist sampling frequency
- boxing and floating
- aliasing
transfer functions and detectors (CCD and film)
- CTF: phase vs amplitude contrast (cryo vs neg stain)
- DQE, MTF, NTF

Tomography - Nov 14 - Carmen Mannella (Wadsworth Ctr)

Changed:

<
<

Discussion Leader (Nov 28):

>
>

Discussion Leader (Nov 28): W. Nicholson Price

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

Hybrid Methods - Nov 28 - David Stokes (NYSBC/NYU)

Changed:

<
<

Discussion Leader (Dec 5):

>
>

Discussion Leader (Dec 5): Shyam Vaidya

Unbending of 2D crystals
patch averaging of 2D crystals
Real-space averaging of helical reconstructions
SPA of helical assemblies
SPA of tomographic volumes
tomography of 2D crystals

Molecular fitting - Dec 5 - Hernando Sosa (Einstein)

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

Visit Cryo EM website at http://www.nysbc.org/facilities/CEM

Set ALLOWTOPICVIEW =

-- DavidStokes - 24 Jul 2006

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Revision 1304 Sep 2006 - Main.DavidStokes

Changed:

<
<

META TOPICPARENT	name="CemcourseGroup"

>
>

META TOPICPARENT	name="CemCourseGroup"

Cryoelectron Microscopy of Macromolecular Assemblies

NYU course # G16.4408 - 3 credits

Contents

Instructors

David Stokes: stokes@saturn.med.nyu.edu
John Berriman: berriman@nysbc.org
Bill Rice: rice@nysbc.org
Iban Ubarretxena: iu@sci.ccny.cuny.edu
Hernando Sosa: hsosa@aecom.yu.edu
Joachim Frank: joachim@wadsworth.org
Carmen Mannella: carmen@wadsworth.org

Useful Textbooks

Frank: "Three Dimensional Electron Microscopy of Macromolecular Assemblies"
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"

Syllabus

Intro to EM and History of 3D Reconstruction - Sept 12 - David Stokes (NYSBC/NYU)

Basic EM techniques
- TEM
- SEM
- STEM
- Types of specimens
Electron sources
- tips (W, LaB6^?, FEG)
Physics of electrons
- Faraday's Law
- influence of a B field
- electrostatic and electromagnetic lens
Interaction of electrons with matter
- elastic scattering
- inelastic scattering
- secondary electrons
- backscattered electrons
- x-rays
- EELS
overview of 3D reconstruction strategies
- 2D crystallography
- helical reconstruction (Fourier-Bessel)
- single particle analysis
- tomography
negative stain of viruses
- model of negative stain
- matching of projection images
- quasiequivalence & icosahedral viruses
optical diffraction
- optical filtering
bacteriorhodopsin
acetylcholine receptor
ribosomes
insect flight muscle tomography

Sample preparation - Sept 19 - John Berriman (NYSBC)

Discussion leaders (Sept 26):

tissue -> sections
- positive stain
- immunolabeling
molecules -> negative stain
- single particles
- 2D crystals
cryo -> no stain
- frozen sections
- suspensions of molecules or 2D crystals

Diffraction and Fourier transforms - Sep 26 - Iban Ubarretxena (CCNY)

Discussion Leaders (Oct 3):

Diffraction of waves - Frauenhofer vs. Fresnel
Sum of cosines -> Fourier transform
Example functions (Gaussian, box, delta fcn, cosine)
Friedel's Law
Convolution fcn
Correlation fcn & Convolution Thm
Projection Thm

Single Particle Analysis I - Oct 3 - Joachim Frank (Wadsworth Ctr)

Discussion Leader (Oct 10):

philosophy of single-particle reconstruction
imaging considerations
- solid/perforated carbon
- automated data collection
how to get the initial model
- random conical tilt with defined orientations
- orientation determination using common lines
- 3D projection matching
model bias
correspondence analysis
classification and class-averages
refinement
defocus groups and CTF correction (Weiner filter)
weighted backprojection, ART and direct Fourier reconstruction
symmetry
resolution criteria (Fourier Shell Correlation)
overview of programs (Spider, Eman, Imagic)
applications

Single Particle Analysis II - Oct 10 - Joachim Frank (Wadsworth Ctr)

SPA practical (Oct 17):

Crystallography - Oct 17 - Iban Ubarretxena (CCNY)

Discussion Leaders (Oct 24):

Braggs law
real/reciprocal lattice
- unit cell
  - asymmetric unit
  - fractional coordinates
- symmetry
  - symmetry operators
  - plane groups & space groups
- Miller indices
- reciprocal lattice symmetry (ampl and phase)
- lattice lines
convolution fcn -> crystal
- convolution Thm -> reciprocal lattice
Projection Thm and radius of Ewald Sphere
strategy for 3D recontruction
- missing cone
imaging considerations
- electron diffraction
- spot-scan for images
electron diffraction for amplitudes
- radial background subtraction
- lattice refinement
- tilt angle/axis
- local background sub and spot integration
- merging
- refinement
- curve fitting
imaging for phases
- unbending
- defocus determination
- tilt angle/axis
- merging, weighting
- temperature factor compensation
resolution criteria (point-spread fcn)

Helical reconstruction - Oct 24 - Hernando Sosa (Einstein)

Discussion Leaders (Oct 31):

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
Hybrid methods - unbending
- separately refining small segments against average
- Egelman's spider implementation for helical structures
- real-space averaging of symmetry groups

Electron Optics - Oct 31 - David Stokes

Discussion Leaders (Nov 7):

Physics of electrons
- Faraday's Law
- influence of a B field
- electrostatic and electromagnetic lens
- deflectors
electron scattering
- scattering cross-section
- elastic scattering
- inelastic scattering
- secondary electrons
- backscattered electrons
- x-rays
- EELS
microscope column
- condensor, objective, intermediate, projector lenses
- gun, beam, image deflector coils
- condensor, objective, selected area apertures
optics
- focal length, magnification
- ray path diagram
- resolution
- aberrations
- coherency

Imaging strategies and Media - Nov 7 - David Stokes

Discussion Leaders (Nov 14):

Radiation damage
- low dose imaging
Electron diffraction
Inelastic scattering
- energy filter and zero-loss imaging
Review of diffraction and Fourier transforms
- scattering - Fresnel and Frauenhofer
- sum of sines -> Fourier transform
- Friedel's Law
- Convolution Thm
- Correlation function
effect of sampling
- discrete Fourier transform
- box function and lattice function
- Nyquist sampling frequency
- boxing and floating
- aliasing
transfer functions and detectors (CCD and film)
- CTF: phase vs amplitude contrast (cryo vs neg stain)
- DQE, MTF, NTF

Tomography - Nov 14 - Carmen Mannella (Wadsworth Ctr)

Discussion Leader (Nov 28):

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

Hybrid Methods - Nov 28 - David Stokes (NYSBC/NYU)

Discussion Leader (Dec 5):

Unbending of 2D crystals
patch averaging of 2D crystals
Real-space averaging of helical reconstructions
SPA of helical assemblies
SPA of tomographic volumes
tomography of 2D crystals

Molecular fitting - Dec 5 - Hernando Sosa (Einstein)

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

Visit Cryo EM website at http://www.nysbc.org/facilities/CEM

Set ALLOWTOPICVIEW =

-- DavidStokes - 24 Jul 2006

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Revision 1204 Sep 2006 - Main.DavidStokes

Changed:

<
<

META TOPICPARENT	name="CemCourseGroup"

>
>

META TOPICPARENT	name="CemcourseGroup"

Cryoelectron Microscopy of Macromolecular Assemblies

NYU course # G16.4408 - 3 credits

Contents

Instructors

David Stokes: stokes@saturn.med.nyu.edu
John Berriman: berriman@nysbc.org
Bill Rice: rice@nysbc.org
Iban Ubarretxena: iu@sci.ccny.cuny.edu
Hernando Sosa: hsosa@aecom.yu.edu
Joachim Frank: joachim@wadsworth.org
Carmen Mannella: carmen@wadsworth.org

Useful Textbooks

Frank: "Three Dimensional Electron Microscopy of Macromolecular Assemblies"
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"

Syllabus

Intro to EM and History of 3D Reconstruction - Sept 12 - David Stokes (NYSBC/NYU)

Basic EM techniques
- TEM
- SEM
- STEM
- Types of specimens
Electron sources
- tips (W, LaB6^?, FEG)
Physics of electrons
- Faraday's Law
- influence of a B field
- electrostatic and electromagnetic lens
Interaction of electrons with matter
- elastic scattering
- inelastic scattering
- secondary electrons
- backscattered electrons
- x-rays
- EELS
overview of 3D reconstruction strategies
- 2D crystallography
- helical reconstruction (Fourier-Bessel)
- single particle analysis
- tomography
negative stain of viruses
- model of negative stain
- matching of projection images
- quasiequivalence & icosahedral viruses
optical diffraction
- optical filtering
bacteriorhodopsin
acetylcholine receptor
ribosomes
insect flight muscle tomography

Sample preparation - Sept 19 - John Berriman (NYSBC)

Discussion leaders (Sept 26):

tissue -> sections
- positive stain
- immunolabeling
molecules -> negative stain
- single particles
- 2D crystals
cryo -> no stain
- frozen sections
- suspensions of molecules or 2D crystals

Diffraction and Fourier transforms - Sep 26 - Iban Ubarretxena (CCNY)

Discussion Leaders (Oct 3):

Diffraction of waves - Frauenhofer vs. Fresnel
Sum of cosines -> Fourier transform
Example functions (Gaussian, box, delta fcn, cosine)
Friedel's Law
Convolution fcn
Correlation fcn & Convolution Thm
Projection Thm

Single Particle Analysis I - Oct 3 - Joachim Frank (Wadsworth Ctr)

Discussion Leader (Oct 10):

philosophy of single-particle reconstruction
imaging considerations
- solid/perforated carbon
- automated data collection
how to get the initial model
- random conical tilt with defined orientations
- orientation determination using common lines
- 3D projection matching
model bias
correspondence analysis
classification and class-averages
refinement
defocus groups and CTF correction (Weiner filter)
weighted backprojection, ART and direct Fourier reconstruction
symmetry
resolution criteria (Fourier Shell Correlation)
overview of programs (Spider, Eman, Imagic)
applications

Single Particle Analysis II - Oct 10 - Joachim Frank (Wadsworth Ctr)

SPA practical (Oct 17):

Crystallography - Oct 17 - Iban Ubarretxena (CCNY)

Discussion Leaders (Oct 24):

Braggs law
real/reciprocal lattice
- unit cell
  - asymmetric unit
  - fractional coordinates
- symmetry
  - symmetry operators
  - plane groups & space groups
- Miller indices
- reciprocal lattice symmetry (ampl and phase)
- lattice lines
convolution fcn -> crystal
- convolution Thm -> reciprocal lattice
Projection Thm and radius of Ewald Sphere
strategy for 3D recontruction
- missing cone
imaging considerations
- electron diffraction
- spot-scan for images
electron diffraction for amplitudes
- radial background subtraction
- lattice refinement
- tilt angle/axis
- local background sub and spot integration
- merging
- refinement
- curve fitting
imaging for phases
- unbending
- defocus determination
- tilt angle/axis
- merging, weighting
- temperature factor compensation
resolution criteria (point-spread fcn)

Helical reconstruction - Oct 24 - Hernando Sosa (Einstein)

Discussion Leaders (Oct 31):

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
Hybrid methods - unbending
- separately refining small segments against average
- Egelman's spider implementation for helical structures
- real-space averaging of symmetry groups

Electron Optics - Oct 31 - David Stokes

Discussion Leaders (Nov 7):

Physics of electrons
- Faraday's Law
- influence of a B field
- electrostatic and electromagnetic lens
- deflectors
electron scattering
- scattering cross-section
- elastic scattering
- inelastic scattering
- secondary electrons
- backscattered electrons
- x-rays
- EELS
microscope column
- condensor, objective, intermediate, projector lenses
- gun, beam, image deflector coils
- condensor, objective, selected area apertures
optics
- focal length, magnification
- ray path diagram
- resolution
- aberrations
- coherency

Imaging strategies and Media - Nov 7 - David Stokes

Discussion Leaders (Nov 14):

Radiation damage
- low dose imaging
Electron diffraction
Inelastic scattering
- energy filter and zero-loss imaging
Review of diffraction and Fourier transforms
- scattering - Fresnel and Frauenhofer
- sum of sines -> Fourier transform
- Friedel's Law
- Convolution Thm
- Correlation function
effect of sampling
- discrete Fourier transform
- box function and lattice function
- Nyquist sampling frequency
- boxing and floating
- aliasing
transfer functions and detectors (CCD and film)
- CTF: phase vs amplitude contrast (cryo vs neg stain)
- DQE, MTF, NTF

Tomography - Nov 14 - Carmen Mannella (Wadsworth Ctr)

Discussion Leader (Nov 28):

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

Hybrid Methods - Nov 28 - David Stokes (NYSBC/NYU)

Discussion Leader (Dec 5):

Unbending of 2D crystals
patch averaging of 2D crystals
Real-space averaging of helical reconstructions
SPA of helical assemblies
SPA of tomographic volumes
tomography of 2D crystals

Molecular fitting - Dec 5 - Hernando Sosa (Einstein)

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

Visit Cryo EM website at http://www.nysbc.org/facilities/CEM

Set ALLOWTOPICVIEW =

-- DavidStokes - 24 Jul 2006

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Revision 1124 Jul 2006 - Main.DavidStokes

META TOPICPARENT	name="CemCourseGroup"

Cryoelectron Microscopy of Macromolecular Assemblies

NYU course # G16.4408 - 3 credits

Contents

Instructors

David Stokes: stokes@saturn.med.nyu.edu
John Berriman: berriman@nysbc.org
Bill Rice: rice@nysbc.org
Iban Ubarretxena: iu@sci.ccny.cuny.edu
Hernando Sosa: hsosa@aecom.yu.edu
Joachim Frank: joachim@wadsworth.org
Carmen Mannella: carmen@wadsworth.org

Useful Textbooks

Frank: "Three Dimensional Electron Microscopy of Macromolecular Assemblies"
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"

Syllabus

Intro to EM and History of 3D Reconstruction - Sept 12 - David Stokes (NYSBC/NYU)

Basic EM techniques
- TEM
- SEM
- STEM
- Types of specimens
Electron sources
- tips (W, LaB6^?, FEG)
Physics of electrons
- Faraday's Law
- influence of a B field
- electrostatic and electromagnetic lens
Interaction of electrons with matter
- elastic scattering
- inelastic scattering
- secondary electrons
- backscattered electrons
- x-rays
- EELS
overview of 3D reconstruction strategies
- 2D crystallography
- helical reconstruction (Fourier-Bessel)
- single particle analysis
- tomography
negative stain of viruses
- model of negative stain
- matching of projection images
- quasiequivalence & icosahedral viruses
optical diffraction
- optical filtering
bacteriorhodopsin
acetylcholine receptor
ribosomes
insect flight muscle tomography

Sample preparation - Sept 19 - John Berriman (NYSBC)

Discussion leaders (Sept 26):

tissue -> sections
- positive stain
- immunolabeling
molecules -> negative stain
- single particles
- 2D crystals
cryo -> no stain
- frozen sections
- suspensions of molecules or 2D crystals

Diffraction and Fourier transforms - Sep 26 - Iban Ubarretxena (CCNY)

Discussion Leaders (Oct 3):

Diffraction of waves - Frauenhofer vs. Fresnel
Sum of cosines -> Fourier transform
Example functions (Gaussian, box, delta fcn, cosine)
Friedel's Law
Convolution fcn
Correlation fcn & Convolution Thm
Projection Thm

Single Particle Analysis I - Oct 3 - Joachim Frank (Wadsworth Ctr)

Discussion Leader (Oct 10):

philosophy of single-particle reconstruction
imaging considerations
- solid/perforated carbon
- automated data collection
how to get the initial model
- random conical tilt with defined orientations
- orientation determination using common lines
- 3D projection matching
model bias
correspondence analysis
classification and class-averages
refinement
defocus groups and CTF correction (Weiner filter)
weighted backprojection, ART and direct Fourier reconstruction
symmetry
resolution criteria (Fourier Shell Correlation)
overview of programs (Spider, Eman, Imagic)
applications

Single Particle Analysis II - Oct 10 - Joachim Frank (Wadsworth Ctr)

SPA practical (Oct 17):

Crystallography - Oct 17 - Iban Ubarretxena (CCNY)

Discussion Leaders (Oct 24):

Braggs law
real/reciprocal lattice
- unit cell
  - asymmetric unit
  - fractional coordinates
- symmetry
  - symmetry operators
  - plane groups & space groups
- Miller indices
- reciprocal lattice symmetry (ampl and phase)
- lattice lines
convolution fcn -> crystal
- convolution Thm -> reciprocal lattice
Projection Thm and radius of Ewald Sphere
strategy for 3D recontruction
- missing cone
imaging considerations
- electron diffraction
- spot-scan for images
electron diffraction for amplitudes
- radial background subtraction
- lattice refinement
- tilt angle/axis
- local background sub and spot integration
- merging
- refinement
- curve fitting
imaging for phases
- unbending
- defocus determination
- tilt angle/axis
- merging, weighting
- temperature factor compensation
resolution criteria (point-spread fcn)

Helical reconstruction - Oct 24 - Hernando Sosa (Einstein)

Discussion Leaders (Oct 31):

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
Hybrid methods - unbending
- separately refining small segments against average
- Egelman's spider implementation for helical structures
- real-space averaging of symmetry groups

Electron Optics - Oct 31 - David Stokes

Discussion Leaders (Nov 7):

Physics of electrons
- Faraday's Law
- influence of a B field
- electrostatic and electromagnetic lens
- deflectors
electron scattering
- scattering cross-section
- elastic scattering
- inelastic scattering
- secondary electrons
- backscattered electrons
- x-rays
- EELS
microscope column
- condensor, objective, intermediate, projector lenses
- gun, beam, image deflector coils
- condensor, objective, selected area apertures
optics
- focal length, magnification
- ray path diagram
- resolution
- aberrations
- coherency

Changed:

<
<

Imaging strategies - Nov 7 - David Stokes

>
>

Imaging strategies and Media - Nov 7 - David Stokes

Discussion Leaders (Nov 14):

Radiation damage
- low dose imaging
Electron diffraction
Inelastic scattering
- energy filter and zero-loss imaging
Review of diffraction and Fourier transforms
- scattering - Fresnel and Frauenhofer
- sum of sines -> Fourier transform
- Friedel's Law
- Convolution Thm
- Correlation function
effect of sampling
- discrete Fourier transform
- box function and lattice function
- Nyquist sampling frequency
- boxing and floating
- aliasing
transfer functions and detectors (CCD and film)
- CTF: phase vs amplitude contrast (cryo vs neg stain)
- DQE, MTF, NTF

Tomography - Nov 14 - Carmen Mannella (Wadsworth Ctr)

Discussion Leader (Nov 28):

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

Hybrid Methods - Nov 28 - David Stokes (NYSBC/NYU)

Discussion Leader (Dec 5):

Unbending of 2D crystals
patch averaging of 2D crystals
Real-space averaging of helical reconstructions
SPA of helical assemblies
SPA of tomographic volumes
tomography of 2D crystals

Molecular fitting - Dec 5 - Hernando Sosa (Einstein)

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

Visit Cryo EM website at http://www.nysbc.org/facilities/CEM

Set ALLOWTOPICVIEW =

-- DavidStokes - 24 Jul 2006

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Revision 1024 Jul 2006 - Main.DavidStokes

META TOPICPARENT	name="CemCourseGroup"

Cryoelectron Microscopy of Macromolecular Assemblies

NYU course # G16.4408 - 3 credits

Contents

Instructors

David Stokes: stokes@saturn.med.nyu.edu
John Berriman: berriman@nysbc.org
Bill Rice: rice@nysbc.org
Iban Ubarretxena: iu@sci.ccny.cuny.edu
Hernando Sosa: hsosa@aecom.yu.edu
Joachim Frank: joachim@wadsworth.org
Carmen Mannella: carmen@wadsworth.org

Useful Textbooks

Changed:

<
<

Frank:
"Three Dimensional Electron Microscopy of Macromolecular Assemblies"

>
>

Frank:
"Three Dimensional Electron Microscopy of Macromolecular Assemblies"

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"

Syllabus

Intro to EM and History of 3D Reconstruction - Sept 12 - David Stokes (NYSBC/NYU)

Basic EM techniques
- TEM
- SEM
- STEM
- Types of specimens
Electron sources
- tips (W, LaB6^?, FEG)
Physics of electrons
- Faraday's Law
- influence of a B field
- electrostatic and electromagnetic lens
Interaction of electrons with matter
- elastic scattering
- inelastic scattering
- secondary electrons
- backscattered electrons
- x-rays
- EELS
overview of 3D reconstruction strategies
- 2D crystallography
- helical reconstruction (Fourier-Bessel)
- single particle analysis
- tomography
negative stain of viruses
- model of negative stain
- matching of projection images
- quasiequivalence & icosahedral viruses
optical diffraction
- optical filtering
bacteriorhodopsin
acetylcholine receptor
ribosomes
insect flight muscle tomography

Sample preparation - Sept 19 - John Berriman (NYSBC)

Discussion leaders (Sept 26):

tissue -> sections
- positive stain
- immunolabeling
molecules -> negative stain
- single particles
- 2D crystals
cryo -> no stain
- frozen sections
- suspensions of molecules or 2D crystals

Diffraction and Fourier transforms - Sep 26 - Iban Ubarretxena (CCNY)

Discussion Leaders (Oct 3):

Diffraction of waves - Frauenhofer vs. Fresnel
Sum of cosines -> Fourier transform
Example functions (Gaussian, box, delta fcn, cosine)
Friedel's Law
Convolution fcn
Correlation fcn & Convolution Thm
Projection Thm

Single Particle Analysis I - Oct 3 - Joachim Frank (Wadsworth Ctr)

Discussion Leader (Oct 10):

philosophy of single-particle reconstruction
imaging considerations
- solid/perforated carbon
- automated data collection
how to get the initial model
- random conical tilt with defined orientations
- orientation determination using common lines
- 3D projection matching
model bias
correspondence analysis
classification and class-averages
refinement
defocus groups and CTF correction (Weiner filter)
weighted backprojection, ART and direct Fourier reconstruction
symmetry
resolution criteria (Fourier Shell Correlation)
overview of programs (Spider, Eman, Imagic)
applications

Single Particle Analysis II - Oct 10 - Joachim Frank (Wadsworth Ctr)

SPA practical (Oct 17):

Crystallography - Oct 17 - Iban Ubarretxena (CCNY)

Discussion Leaders (Oct 24):

Braggs law
real/reciprocal lattice
- unit cell
  - asymmetric unit
  - fractional coordinates
- symmetry
  - symmetry operators
  - plane groups & space groups
- Miller indices
- reciprocal lattice symmetry (ampl and phase)
- lattice lines
convolution fcn -> crystal
- convolution Thm -> reciprocal lattice
Projection Thm and radius of Ewald Sphere
strategy for 3D recontruction
- missing cone
imaging considerations
- electron diffraction
- spot-scan for images
electron diffraction for amplitudes
- radial background subtraction
- lattice refinement
- tilt angle/axis
- local background sub and spot integration
- merging
- refinement
- curve fitting
imaging for phases
- unbending
- defocus determination
- tilt angle/axis
- merging, weighting
- temperature factor compensation
resolution criteria (point-spread fcn)

Helical reconstruction - Oct 24 - Hernando Sosa (Einstein)

Discussion Leaders (Oct 31):

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
Hybrid methods - unbending
- separately refining small segments against average
- Egelman's spider implementation for helical structures
- real-space averaging of symmetry groups

Electron Optics - Oct 31 - David Stokes

Discussion Leaders (Nov 7):

Physics of electrons
- Faraday's Law
- influence of a B field
- electrostatic and electromagnetic lens
- deflectors
electron scattering
- scattering cross-section
- elastic scattering
- inelastic scattering
- secondary electrons
- backscattered electrons
- x-rays
- EELS
microscope column
- condensor, objective, intermediate, projector lenses
- gun, beam, image deflector coils
- condensor, objective, selected area apertures
optics
- focal length, magnification
- ray path diagram
- resolution
- aberrations
- coherency

Imaging strategies - Nov 7 - David Stokes

Discussion Leaders (Nov 14):

Radiation damage
- low dose imaging
Electron diffraction
Inelastic scattering
- energy filter and zero-loss imaging
Review of diffraction and Fourier transforms
- scattering - Fresnel and Frauenhofer
- sum of sines -> Fourier transform
- Friedel's Law
- Convolution Thm
- Correlation function
effect of sampling
- discrete Fourier transform
- box function and lattice function
- Nyquist sampling frequency
- boxing and floating
- aliasing
transfer functions and detectors (CCD and film)
- CTF: phase vs amplitude contrast (cryo vs neg stain)
- DQE, MTF, NTF

Tomography - Nov 14 - Carmen Mannella (Wadsworth Ctr)

Discussion Leader (Nov 28):

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

Hybrid Methods - Nov 28 - David Stokes (NYSBC/NYU)

Discussion Leader (Dec 5):

Unbending of 2D crystals
patch averaging of 2D crystals
Real-space averaging of helical reconstructions
SPA of helical assemblies
SPA of tomographic volumes
tomography of 2D crystals

Molecular fitting - Dec 5 - Hernando Sosa (Einstein)

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

Visit Cryo EM website at http://www.nysbc.org/facilities/CEM

Set ALLOWTOPICVIEW =

-- DavidStokes - 24 Jul 2006

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META FILEATTACHMENT	attr="" autoattached="1" comment="Bozzola" date="1153768165" name="Bozzola.jpg" path="Bozzola.jpg" size="22307" user="Main.DavidStokes" version=""
META FILEATTACHMENT	attr="" autoattached="1" comment="Frank" date="1153768121" name="frank.jpg" path="frank.jpg" size="23652" user="Main.DavidStokes" version=""
META FILEATTACHMENT	attr="" autoattached="1" comment="Williams & Carter" date="1153768186" name="WilliamsCarter.jpg" path="WilliamsCarter.jpg" size="45410" user="Main.DavidStokes" version=""
META FILEATTACHMENT	attr="" autoattached="1" comment="Harris" date="1153768146" name="harris.jpg" path="harris.jpg" size="31673" user="Main.DavidStokes" version=""

Revision 924 Jul 2006 - Main.DavidStokes

META TOPICPARENT	name="CemCourseGroup"

Cryoelectron Microscopy of Macromolecular Assemblies

NYU course # G16.4408 - 3 credits

Contents

Instructors

David Stokes: stokes@saturn.med.nyu.edu
John Berriman: berriman@nysbc.org
Bill Rice: rice@nysbc.org
Iban Ubarretxena: iu@sci.ccny.cuny.edu
Hernando Sosa: hsosa@aecom.yu.edu
Joachim Frank: joachim@wadsworth.org
Carmen Mannella: carmen@wadsworth.org

Useful Textbooks

Changed:

<
<

Frank:
"Three Dimensional Electron Microscopy of Macromolecular Assemblies"

>
>

Frank:
"Three Dimensional Electron Microscopy of Macromolecular Assemblies"

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"

Syllabus

Intro to EM and History of 3D Reconstruction - Sept 12 - David Stokes (NYSBC/NYU)

Basic EM techniques
- TEM
- SEM
- STEM
- Types of specimens
Electron sources
- tips (W, LaB6^?, FEG)
Physics of electrons
- Faraday's Law
- influence of a B field
- electrostatic and electromagnetic lens
Interaction of electrons with matter
- elastic scattering
- inelastic scattering
- secondary electrons
- backscattered electrons
- x-rays
- EELS
overview of 3D reconstruction strategies
- 2D crystallography
- helical reconstruction (Fourier-Bessel)
- single particle analysis
- tomography
negative stain of viruses
- model of negative stain
- matching of projection images
- quasiequivalence & icosahedral viruses
optical diffraction
- optical filtering
bacteriorhodopsin
acetylcholine receptor
ribosomes
insect flight muscle tomography

Sample preparation - Sept 19 - John Berriman (NYSBC)

Discussion leaders (Sept 26):

tissue -> sections
- positive stain
- immunolabeling
molecules -> negative stain
- single particles
- 2D crystals
cryo -> no stain
- frozen sections
- suspensions of molecules or 2D crystals

Diffraction and Fourier transforms - Sep 26 - Iban Ubarretxena (CCNY)

Discussion Leaders (Oct 3):

Diffraction of waves - Frauenhofer vs. Fresnel
Sum of cosines -> Fourier transform
Example functions (Gaussian, box, delta fcn, cosine)
Friedel's Law
Convolution fcn
Correlation fcn & Convolution Thm
Projection Thm

Single Particle Analysis I - Oct 3 - Joachim Frank (Wadsworth Ctr)

Discussion Leader (Oct 10):

philosophy of single-particle reconstruction
imaging considerations
- solid/perforated carbon
- automated data collection
how to get the initial model
- random conical tilt with defined orientations
- orientation determination using common lines
- 3D projection matching
model bias
correspondence analysis
classification and class-averages
refinement
defocus groups and CTF correction (Weiner filter)
weighted backprojection, ART and direct Fourier reconstruction
symmetry
resolution criteria (Fourier Shell Correlation)
overview of programs (Spider, Eman, Imagic)
applications

Single Particle Analysis II - Oct 10 - Joachim Frank (Wadsworth Ctr)

SPA practical (Oct 17):

Crystallography - Oct 17 - Iban Ubarretxena (CCNY)

Discussion Leaders (Oct 24):

Braggs law
real/reciprocal lattice
- unit cell
  - asymmetric unit
  - fractional coordinates
- symmetry
  - symmetry operators
  - plane groups & space groups
- Miller indices
- reciprocal lattice symmetry (ampl and phase)
- lattice lines
convolution fcn -> crystal
- convolution Thm -> reciprocal lattice
Projection Thm and radius of Ewald Sphere
strategy for 3D recontruction
- missing cone
imaging considerations
- electron diffraction
- spot-scan for images
electron diffraction for amplitudes
- radial background subtraction
- lattice refinement
- tilt angle/axis
- local background sub and spot integration
- merging
- refinement
- curve fitting
imaging for phases
- unbending
- defocus determination
- tilt angle/axis
- merging, weighting
- temperature factor compensation
resolution criteria (point-spread fcn)

Helical reconstruction - Oct 24 - Hernando Sosa (Einstein)

Discussion Leaders (Oct 31):

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
Hybrid methods - unbending
- separately refining small segments against average
- Egelman's spider implementation for helical structures
- real-space averaging of symmetry groups

Electron Optics - Oct 31 - David Stokes

Discussion Leaders (Nov 7):

Physics of electrons
- Faraday's Law
- influence of a B field
- electrostatic and electromagnetic lens
- deflectors
electron scattering
- scattering cross-section
- elastic scattering
- inelastic scattering
- secondary electrons
- backscattered electrons
- x-rays
- EELS
microscope column
- condensor, objective, intermediate, projector lenses
- gun, beam, image deflector coils
- condensor, objective, selected area apertures
optics
- focal length, magnification
- ray path diagram
- resolution
- aberrations
- coherency

Imaging strategies - Nov 7 - David Stokes

Discussion Leaders (Nov 14):

Radiation damage
- low dose imaging
Electron diffraction
Inelastic scattering
- energy filter and zero-loss imaging
Review of diffraction and Fourier transforms
- scattering - Fresnel and Frauenhofer
- sum of sines -> Fourier transform
- Friedel's Law
- Convolution Thm
- Correlation function
effect of sampling
- discrete Fourier transform
- box function and lattice function
- Nyquist sampling frequency
- boxing and floating
- aliasing
transfer functions and detectors (CCD and film)
- CTF: phase vs amplitude contrast (cryo vs neg stain)
- DQE, MTF, NTF

Tomography - Nov 14 - Carmen Mannella (Wadsworth Ctr)

Discussion Leader (Nov 28):

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

Hybrid Methods - Nov 28 - David Stokes (NYSBC/NYU)

Discussion Leader (Dec 5):

Unbending of 2D crystals
patch averaging of 2D crystals
Real-space averaging of helical reconstructions
SPA of helical assemblies
SPA of tomographic volumes
tomography of 2D crystals

Molecular fitting - Dec 5 - Hernando Sosa (Einstein)

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

Visit Cryo EM website at http://www.nysbc.org/facilities/CEM

Set ALLOWTOPICVIEW =

-- DavidStokes - 24 Jul 2006

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META FILEATTACHMENT	attr="" autoattached="1" comment="Bozzola" date="1153768165" name="Bozzola.jpg" path="Bozzola.jpg" size="22307" user="Main.DavidStokes" version=""
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Revision 824 Jul 2006 - Main.DavidStokes

META TOPICPARENT	name="CemCourseGroup"

Cryoelectron Microscopy of Macromolecular Assemblies

Changed:

<
<

NYU course G16.2617001 - Call #30137 - 3 credits

>
>

NYU course # G16.4408 - 3 credits

Contents

Instructors

David Stokes: stokes@saturn.med.nyu.edu
John Berriman: berriman@nysbc.org
Bill Rice: rice@nysbc.org
Iban Ubarretxena: iu@sci.ccny.cuny.edu
Hernando Sosa: hsosa@aecom.yu.edu
Joachim Frank: joachim@wadsworth.org
Carmen Mannella: carmen@wadsworth.org

Useful Textbooks

Added:

>
>

Frank:
"Three Dimensional Electron Microscopy of Macromolecular Assemblies"

Reimer: "Transmission Electron Microscopy: Physics of Image Formation and Microanalysis"
Bozzola & Russell: "Electron Microscopy: Principles and Techniques for Biologists"

Deleted:

<
<

Frank:
"Three Dimensional Electron Microscopy of Macromolecular Assemblies"

Harris: "Negative Staining and Cryoelectron Microscopy"
Williams & Carter: "Transmission Electron Microscopy: A Textbook for Materials Science"

Syllabus

Intro to EM and History of 3D Reconstruction - Sept 12 - David Stokes (NYSBC/NYU)

Basic EM techniques
- TEM
- SEM
- STEM
- Types of specimens
Electron sources
- tips (W, LaB6^?, FEG)
Physics of electrons
- Faraday's Law
- influence of a B field
- electrostatic and electromagnetic lens
Interaction of electrons with matter
- elastic scattering
- inelastic scattering
- secondary electrons
- backscattered electrons
- x-rays
- EELS
overview of 3D reconstruction strategies
- 2D crystallography
- helical reconstruction (Fourier-Bessel)
- single particle analysis
- tomography
negative stain of viruses
- model of negative stain
- matching of projection images
- quasiequivalence & icosahedral viruses
optical diffraction
- optical filtering
bacteriorhodopsin
acetylcholine receptor
ribosomes
insect flight muscle tomography

Sample preparation - Sept 19 - John Berriman (NYSBC)

Discussion leaders (Sept 26):

tissue -> sections
- positive stain
- immunolabeling
molecules -> negative stain
- single particles
- 2D crystals
cryo -> no stain
- frozen sections
- suspensions of molecules or 2D crystals

Diffraction and Fourier transforms - Sep 26 - Iban Ubarretxena (CCNY)

Discussion Leaders (Oct 3):

Diffraction of waves - Frauenhofer vs. Fresnel
Sum of cosines -> Fourier transform
Example functions (Gaussian, box, delta fcn, cosine)
Friedel's Law
Convolution fcn
Correlation fcn & Convolution Thm
Projection Thm

Single Particle Analysis I - Oct 3 - Joachim Frank (Wadsworth Ctr)

Discussion Leader (Oct 10):

philosophy of single-particle reconstruction
imaging considerations
- solid/perforated carbon
- automated data collection
how to get the initial model
- random conical tilt with defined orientations
- orientation determination using common lines
- 3D projection matching
model bias
correspondence analysis
classification and class-averages
refinement
defocus groups and CTF correction (Weiner filter)
weighted backprojection, ART and direct Fourier reconstruction
symmetry
resolution criteria (Fourier Shell Correlation)
overview of programs (Spider, Eman, Imagic)
applications

Single Particle Analysis II - Oct 10 - Joachim Frank (Wadsworth Ctr)

SPA practical (Oct 17):

Crystallography - Oct 17 - Iban Ubarretxena (CCNY)

Discussion Leaders (Oct 24):

Braggs law
real/reciprocal lattice
- unit cell
  - asymmetric unit
  - fractional coordinates
- symmetry
  - symmetry operators
  - plane groups & space groups
- Miller indices
- reciprocal lattice symmetry (ampl and phase)
- lattice lines
convolution fcn -> crystal
- convolution Thm -> reciprocal lattice
Projection Thm and radius of Ewald Sphere
strategy for 3D recontruction
- missing cone
imaging considerations
- electron diffraction
- spot-scan for images
electron diffraction for amplitudes
- radial background subtraction
- lattice refinement
- tilt angle/axis
- local background sub and spot integration
- merging
- refinement
- curve fitting
imaging for phases
- unbending
- defocus determination
- tilt angle/axis
- merging, weighting
- temperature factor compensation
resolution criteria (point-spread fcn)

Helical reconstruction - Oct 24 - Hernando Sosa (Einstein)

Discussion Leaders (Oct 31):

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
Hybrid methods - unbending
- separately refining small segments against average
- Egelman's spider implementation for helical structures
- real-space averaging of symmetry groups

Electron Optics - Oct 31 - David Stokes

Discussion Leaders (Nov 7):

Physics of electrons
- Faraday's Law
- influence of a B field
- electrostatic and electromagnetic lens
- deflectors
electron scattering
- scattering cross-section
- elastic scattering
- inelastic scattering
- secondary electrons
- backscattered electrons
- x-rays
- EELS
microscope column
- condensor, objective, intermediate, projector lenses
- gun, beam, image deflector coils
- condensor, objective, selected area apertures
optics
- focal length, magnification
- ray path diagram
- resolution
- aberrations
- coherency

Imaging strategies - Nov 7 - David Stokes

Discussion Leaders (Nov 14):

Radiation damage
- low dose imaging
Electron diffraction
Inelastic scattering
- energy filter and zero-loss imaging
Review of diffraction and Fourier transforms
- scattering - Fresnel and Frauenhofer
- sum of sines -> Fourier transform
- Friedel's Law
- Convolution Thm
- Correlation function
effect of sampling
- discrete Fourier transform
- box function and lattice function
- Nyquist sampling frequency
- boxing and floating
- aliasing
transfer functions and detectors (CCD and film)
- CTF: phase vs amplitude contrast (cryo vs neg stain)
- DQE, MTF, NTF

Tomography - Nov 14 - Carmen Mannella (Wadsworth Ctr)

Discussion Leader (Nov 28):

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

Hybrid Methods - Nov 28 - David Stokes (NYSBC/NYU)

Discussion Leader (Dec 5):

Unbending of 2D crystals
patch averaging of 2D crystals
Real-space averaging of helical reconstructions
SPA of helical assemblies
SPA of tomographic volumes
tomography of 2D crystals

Molecular fitting - Dec 5 - Hernando Sosa (Einstein)

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

Visit Cryo EM website at http://www.nysbc.org/facilities/CEM

Set ALLOWTOPICVIEW =

-- DavidStokes - 24 Jul 2006

Added:

>
>

META FILEATTACHMENT	attr="" autoattached="1" comment="Reimer" date="1153768095" name="Reimer.jpg" path="Reimer.jpg" size="23019" user="Main.DavidStokes" version=""
META FILEATTACHMENT	attr="" autoattached="1" comment="Bozzola" date="1153768165" name="Bozzola.jpg" path="Bozzola.jpg" size="22307" user="Main.DavidStokes" version=""
META FILEATTACHMENT	attr="" autoattached="1" comment="Frank" date="1153768121" name="frank.jpg" path="frank.jpg" size="23652" user="Main.DavidStokes" version=""

Added:

>
>

META FILEATTACHMENT	attr="" autoattached="1" comment="Williams & Carter" date="1153768186" name="WilliamsCarter.jpg" path="WilliamsCarter.jpg" size="45410" user="Main.DavidStokes" version=""

META FILEATTACHMENT	attr="" autoattached="1" comment="Harris" date="1153768146" name="harris.jpg" path="harris.jpg" size="31673" user="Main.DavidStokes" version=""

Deleted:

<
<

META FILEATTACHMENT	attachment="WilliamsCarter.jpg" attr="" comment="Williams & Carter" date="1153768185" name="WilliamsCarter.jpg" path="WilliamsCarter.jpg" size="45410" stream="WilliamsCarter.jpg" user="Main.DavidStokes" version="0"

Revision 724 Jul 2006 - Main.DavidStokes

META TOPICPARENT	name="CemCourseGroup"

Cryoelectron Microscopy of Macromolecular Assemblies

NYU course G16.2617001 - Call #30137 - 3 credits

Contents

Instructors

David Stokes: stokes@saturn.med.nyu.edu
John Berriman: berriman@nysbc.org
Bill Rice: rice@nysbc.org
Iban Ubarretxena: iu@sci.ccny.cuny.edu
Hernando Sosa: hsosa@aecom.yu.edu
Joachim Frank: joachim@wadsworth.org
Carmen Mannella: carmen@wadsworth.org

Useful Textbooks

Reimer: "Transmission Electron Microscopy: Physics of Image Formation and Microanalysis"
Bozzola & Russell: "Electron Microscopy: Principles and Techniques for Biologists"
Frank: "Three Dimensional Electron Microscopy of Macromolecular Assemblies"
Harris: "Negative Staining and Cryoelectron Microscopy"
Williams & Carter: "Transmission Electron Microscopy: A Textbook for Materials Science"

Syllabus

Intro to EM and History of 3D Reconstruction - Sept 12 - David Stokes (NYSBC/NYU)

Basic EM techniques
- TEM
- SEM
- STEM
- Types of specimens
Electron sources
- tips (W, LaB6^?, FEG)
Physics of electrons
- Faraday's Law
- influence of a B field
- electrostatic and electromagnetic lens
Interaction of electrons with matter
- elastic scattering
- inelastic scattering
- secondary electrons
- backscattered electrons
- x-rays
- EELS
overview of 3D reconstruction strategies
- 2D crystallography
- helical reconstruction (Fourier-Bessel)
- single particle analysis
- tomography
negative stain of viruses
- model of negative stain
- matching of projection images
- quasiequivalence & icosahedral viruses
optical diffraction
- optical filtering
bacteriorhodopsin
acetylcholine receptor
ribosomes
insect flight muscle tomography

Sample preparation - Sept 19 - John Berriman (NYSBC)

Discussion leaders (Sept 26):

tissue -> sections
- positive stain
- immunolabeling
molecules -> negative stain
- single particles
- 2D crystals
cryo -> no stain
- frozen sections
- suspensions of molecules or 2D crystals

Diffraction and Fourier transforms - Sep 26 - Iban Ubarretxena (CCNY)

Discussion Leaders (Oct 3):

Diffraction of waves - Frauenhofer vs. Fresnel
Sum of cosines -> Fourier transform
Example functions (Gaussian, box, delta fcn, cosine)
Friedel's Law
Convolution fcn
Correlation fcn & Convolution Thm
Projection Thm

Single Particle Analysis I - Oct 3 - Joachim Frank (Wadsworth Ctr)

Discussion Leader (Oct 10):

philosophy of single-particle reconstruction
imaging considerations
- solid/perforated carbon
- automated data collection
how to get the initial model
- random conical tilt with defined orientations
- orientation determination using common lines
- 3D projection matching
model bias
correspondence analysis
classification and class-averages
refinement
defocus groups and CTF correction (Weiner filter)
weighted backprojection, ART and direct Fourier reconstruction
symmetry
resolution criteria (Fourier Shell Correlation)
overview of programs (Spider, Eman, Imagic)
applications

Single Particle Analysis II - Oct 10 - Joachim Frank (Wadsworth Ctr)

SPA practical (Oct 17):

Crystallography - Oct 17 - Iban Ubarretxena (CCNY)

Discussion Leaders (Oct 24):

Braggs law
real/reciprocal lattice
- unit cell
  - asymmetric unit
  - fractional coordinates
- symmetry
  - symmetry operators
  - plane groups & space groups
- Miller indices
- reciprocal lattice symmetry (ampl and phase)
- lattice lines
convolution fcn -> crystal
- convolution Thm -> reciprocal lattice
Projection Thm and radius of Ewald Sphere
strategy for 3D recontruction
- missing cone
imaging considerations
- electron diffraction
- spot-scan for images
electron diffraction for amplitudes
- radial background subtraction
- lattice refinement
- tilt angle/axis
- local background sub and spot integration
- merging
- refinement
- curve fitting
imaging for phases
- unbending
- defocus determination
- tilt angle/axis
- merging, weighting
- temperature factor compensation
resolution criteria (point-spread fcn)

Helical reconstruction - Oct 24 - Hernando Sosa (Einstein)

Discussion Leaders (Oct 31):

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
Hybrid methods - unbending
- separately refining small segments against average
- Egelman's spider implementation for helical structures
- real-space averaging of symmetry groups

Electron Optics - Oct 31 - David Stokes

Discussion Leaders (Nov 7):

Physics of electrons
- Faraday's Law
- influence of a B field
- electrostatic and electromagnetic lens
- deflectors
electron scattering
- scattering cross-section
- elastic scattering
- inelastic scattering
- secondary electrons
- backscattered electrons
- x-rays
- EELS
microscope column
- condensor, objective, intermediate, projector lenses
- gun, beam, image deflector coils
- condensor, objective, selected area apertures
optics
- focal length, magnification
- ray path diagram
- resolution
- aberrations
- coherency

Imaging strategies - Nov 7 - David Stokes

Discussion Leaders (Nov 14):

Radiation damage
- low dose imaging
Electron diffraction
Inelastic scattering
- energy filter and zero-loss imaging
Review of diffraction and Fourier transforms
- scattering - Fresnel and Frauenhofer
- sum of sines -> Fourier transform
- Friedel's Law
- Convolution Thm
- Correlation function
effect of sampling
- discrete Fourier transform
- box function and lattice function
- Nyquist sampling frequency
- boxing and floating
- aliasing
transfer functions and detectors (CCD and film)
- CTF: phase vs amplitude contrast (cryo vs neg stain)
- DQE, MTF, NTF

Tomography - Nov 14 - Carmen Mannella (Wadsworth Ctr)

Discussion Leader (Nov 28):

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

Hybrid Methods - Nov 28 - David Stokes (NYSBC/NYU)

Discussion Leader (Dec 5):

Unbending of 2D crystals
patch averaging of 2D crystals
Real-space averaging of helical reconstructions
SPA of helical assemblies
SPA of tomographic volumes
tomography of 2D crystals

Molecular fitting - Dec 5 - Hernando Sosa (Einstein)

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

Visit Cryo EM website at http://www.nysbc.org/facilities/CEM

Set ALLOWTOPICVIEW =

-- DavidStokes - 24 Jul 2006

META FILEATTACHMENT	attr="" autoattached="1" comment="Reimer" date="1153768095" name="Reimer.jpg" path="Reimer.jpg" size="23019" user="Main.DavidStokes" version=""

Added:

>
>

META FILEATTACHMENT	attr="" autoattached="1" comment="Bozzola" date="1153768165" name="Bozzola.jpg" path="Bozzola.jpg" size="22307" user="Main.DavidStokes" version=""

META FILEATTACHMENT	attr="" autoattached="1" comment="Frank" date="1153768121" name="frank.jpg" path="frank.jpg" size="23652" user="Main.DavidStokes" version=""
META FILEATTACHMENT	attr="" autoattached="1" comment="Harris" date="1153768146" name="harris.jpg" path="harris.jpg" size="31673" user="Main.DavidStokes" version=""

Changed:

<
<

META FILEATTACHMENT	attachment="Bozzola.jpg" attr="" comment="Bozzola" date="1153768164" name="Bozzola.jpg" path="Bozzola.jpg" size="22307" stream="Bozzola.jpg" user="Main.DavidStokes" version="0"

>
>

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Revision 624 Jul 2006 - Main.DavidStokes

META TOPICPARENT	name="CemCourseGroup"

Cryoelectron Microscopy of Macromolecular Assemblies

NYU course G16.2617001 - Call #30137 - 3 credits

Contents

Instructors

David Stokes: stokes@saturn.med.nyu.edu
John Berriman: berriman@nysbc.org
Bill Rice: rice@nysbc.org
Iban Ubarretxena: iu@sci.ccny.cuny.edu
Hernando Sosa: hsosa@aecom.yu.edu
Joachim Frank: joachim@wadsworth.org
Carmen Mannella: carmen@wadsworth.org

Useful Textbooks

Reimer: "Transmission Electron Microscopy: Physics of Image Formation and Microanalysis"
Bozzola & Russell: "Electron Microscopy: Principles and Techniques for Biologists"
Frank: "Three Dimensional Electron Microscopy of Macromolecular Assemblies"
Harris: "Negative Staining and Cryoelectron Microscopy"
Williams & Carter: "Transmission Electron Microscopy: A Textbook for Materials Science"

Syllabus

Intro to EM and History of 3D Reconstruction - Sept 12 - David Stokes (NYSBC/NYU)

Basic EM techniques
- TEM
- SEM
- STEM
- Types of specimens
Electron sources
- tips (W, LaB6^?, FEG)
Physics of electrons
- Faraday's Law
- influence of a B field
- electrostatic and electromagnetic lens
Interaction of electrons with matter
- elastic scattering
- inelastic scattering
- secondary electrons
- backscattered electrons
- x-rays
- EELS
overview of 3D reconstruction strategies
- 2D crystallography
- helical reconstruction (Fourier-Bessel)
- single particle analysis
- tomography
negative stain of viruses
- model of negative stain
- matching of projection images
- quasiequivalence & icosahedral viruses
optical diffraction
- optical filtering
bacteriorhodopsin
acetylcholine receptor
ribosomes
insect flight muscle tomography

Sample preparation - Sept 19 - John Berriman (NYSBC)

Discussion leaders (Sept 26):

tissue -> sections
- positive stain
- immunolabeling
molecules -> negative stain
- single particles
- 2D crystals
cryo -> no stain
- frozen sections
- suspensions of molecules or 2D crystals

Diffraction and Fourier transforms - Sep 26 - Iban Ubarretxena (CCNY)

Discussion Leaders (Oct 3):

Diffraction of waves - Frauenhofer vs. Fresnel
Sum of cosines -> Fourier transform
Example functions (Gaussian, box, delta fcn, cosine)
Friedel's Law
Convolution fcn
Correlation fcn & Convolution Thm
Projection Thm

Single Particle Analysis I - Oct 3 - Joachim Frank (Wadsworth Ctr)

Discussion Leader (Oct 10):

philosophy of single-particle reconstruction
imaging considerations
- solid/perforated carbon
- automated data collection
how to get the initial model
- random conical tilt with defined orientations
- orientation determination using common lines
- 3D projection matching
model bias
correspondence analysis
classification and class-averages
refinement
defocus groups and CTF correction (Weiner filter)
weighted backprojection, ART and direct Fourier reconstruction
symmetry
resolution criteria (Fourier Shell Correlation)
overview of programs (Spider, Eman, Imagic)
applications

Single Particle Analysis II - Oct 10 - Joachim Frank (Wadsworth Ctr)

SPA practical (Oct 17):

Crystallography - Oct 17 - Iban Ubarretxena (CCNY)

Discussion Leaders (Oct 24):

Braggs law
real/reciprocal lattice
- unit cell
  - asymmetric unit
  - fractional coordinates
- symmetry
  - symmetry operators
  - plane groups & space groups
- Miller indices
- reciprocal lattice symmetry (ampl and phase)
- lattice lines
convolution fcn -> crystal
- convolution Thm -> reciprocal lattice
Projection Thm and radius of Ewald Sphere
strategy for 3D recontruction
- missing cone
imaging considerations
- electron diffraction
- spot-scan for images
electron diffraction for amplitudes
- radial background subtraction
- lattice refinement
- tilt angle/axis
- local background sub and spot integration
- merging
- refinement
- curve fitting
imaging for phases
- unbending
- defocus determination
- tilt angle/axis
- merging, weighting
- temperature factor compensation
resolution criteria (point-spread fcn)

Helical reconstruction - Oct 24 - Hernando Sosa (Einstein)

Discussion Leaders (Oct 31):

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
Hybrid methods - unbending
- separately refining small segments against average
- Egelman's spider implementation for helical structures
- real-space averaging of symmetry groups

Electron Optics - Oct 31 - David Stokes

Discussion Leaders (Nov 7):

Physics of electrons
- Faraday's Law
- influence of a B field
- electrostatic and electromagnetic lens
- deflectors
electron scattering
- scattering cross-section
- elastic scattering
- inelastic scattering
- secondary electrons
- backscattered electrons
- x-rays
- EELS
microscope column
- condensor, objective, intermediate, projector lenses
- gun, beam, image deflector coils
- condensor, objective, selected area apertures
optics
- focal length, magnification
- ray path diagram
- resolution
- aberrations
- coherency

Imaging strategies - Nov 7 - David Stokes

Discussion Leaders (Nov 14):

Radiation damage
- low dose imaging
Electron diffraction
Inelastic scattering
- energy filter and zero-loss imaging
Review of diffraction and Fourier transforms
- scattering - Fresnel and Frauenhofer
- sum of sines -> Fourier transform
- Friedel's Law
- Convolution Thm
- Correlation function
effect of sampling
- discrete Fourier transform
- box function and lattice function
- Nyquist sampling frequency
- boxing and floating
- aliasing
transfer functions and detectors (CCD and film)
- CTF: phase vs amplitude contrast (cryo vs neg stain)
- DQE, MTF, NTF

Tomography - Nov 14 - Carmen Mannella (Wadsworth Ctr)

Discussion Leader (Nov 28):

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

Hybrid Methods - Nov 28 - David Stokes (NYSBC/NYU)

Discussion Leader (Dec 5):

Unbending of 2D crystals
patch averaging of 2D crystals
Real-space averaging of helical reconstructions
SPA of helical assemblies
SPA of tomographic volumes
tomography of 2D crystals

Molecular fitting - Dec 5 - Hernando Sosa (Einstein)

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

Visit Cryo EM website at http://www.nysbc.org/facilities/CEM

Set ALLOWTOPICVIEW =

-- DavidStokes - 24 Jul 2006

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Revision 524 Jul 2006 - Main.DavidStokes

META TOPICPARENT	name="CemCourseGroup"

Cryoelectron Microscopy of Macromolecular Assemblies

NYU course G16.2617001 - Call #30137 - 3 credits

Contents

Instructors

David Stokes: stokes@saturn.med.nyu.edu
John Berriman: berriman@nysbc.org
Bill Rice: rice@nysbc.org
Iban Ubarretxena: iu@sci.ccny.cuny.edu
Hernando Sosa: hsosa@aecom.yu.edu
Joachim Frank: joachim@wadsworth.org
Carmen Mannella: carmen@wadsworth.org

Useful Textbooks

Reimer: "Transmission Electron Microscopy: Physics of Image Formation and Microanalysis"
Bozzola & Russell: "Electron Microscopy: Principles and Techniques for Biologists"
Frank: "Three Dimensional Electron Microscopy of Macromolecular Assemblies"
Harris: "Negative Staining and Cryoelectron Microscopy"
Williams & Carter: "Transmission Electron Microscopy: A Textbook for Materials Science"

Syllabus

Intro to EM and History of 3D Reconstruction - Sept 12 - David Stokes (NYSBC/NYU)

Basic EM techniques
- TEM
- SEM
- STEM
- Types of specimens
Electron sources
- tips (W, LaB6^?, FEG)
Physics of electrons
- Faraday's Law
- influence of a B field
- electrostatic and electromagnetic lens
Interaction of electrons with matter
- elastic scattering
- inelastic scattering
- secondary electrons
- backscattered electrons
- x-rays
- EELS
overview of 3D reconstruction strategies
- 2D crystallography
- helical reconstruction (Fourier-Bessel)
- single particle analysis
- tomography
negative stain of viruses
- model of negative stain
- matching of projection images
- quasiequivalence & icosahedral viruses
optical diffraction
- optical filtering
bacteriorhodopsin
acetylcholine receptor
ribosomes
insect flight muscle tomography

Sample preparation - Sept 19 - John Berriman (NYSBC)

Discussion leaders (Sept 26):

tissue -> sections
- positive stain
- immunolabeling
molecules -> negative stain
- single particles
- 2D crystals
cryo -> no stain
- frozen sections
- suspensions of molecules or 2D crystals

Diffraction and Fourier transforms - Sep 26 - Iban Ubarretxena (CCNY)

Discussion Leaders (Oct 3):

Diffraction of waves - Frauenhofer vs. Fresnel
Sum of cosines -> Fourier transform
Example functions (Gaussian, box, delta fcn, cosine)
Friedel's Law
Convolution fcn
Correlation fcn & Convolution Thm
Projection Thm

Single Particle Analysis I - Oct 3 - Joachim Frank (Wadsworth Ctr)

Discussion Leader (Oct 10):

philosophy of single-particle reconstruction
imaging considerations
- solid/perforated carbon
- automated data collection
how to get the initial model
- random conical tilt with defined orientations
- orientation determination using common lines
- 3D projection matching
model bias
correspondence analysis
classification and class-averages
refinement
defocus groups and CTF correction (Weiner filter)
weighted backprojection, ART and direct Fourier reconstruction
symmetry
resolution criteria (Fourier Shell Correlation)
overview of programs (Spider, Eman, Imagic)
applications

Single Particle Analysis II - Oct 10 - Joachim Frank (Wadsworth Ctr)

SPA practical (Oct 17):

Crystallography - Oct 17 - Iban Ubarretxena (CCNY)

Discussion Leaders (Oct 24):

Braggs law
real/reciprocal lattice
- unit cell
  - asymmetric unit
  - fractional coordinates
- symmetry
  - symmetry operators
  - plane groups & space groups
- Miller indices
- reciprocal lattice symmetry (ampl and phase)
- lattice lines
convolution fcn -> crystal
- convolution Thm -> reciprocal lattice
Projection Thm and radius of Ewald Sphere
strategy for 3D recontruction
- missing cone
imaging considerations
- electron diffraction
- spot-scan for images
electron diffraction for amplitudes
- radial background subtraction
- lattice refinement
- tilt angle/axis
- local background sub and spot integration
- merging
- refinement
- curve fitting
imaging for phases
- unbending
- defocus determination
- tilt angle/axis
- merging, weighting
- temperature factor compensation
resolution criteria (point-spread fcn)

Helical reconstruction - Oct 24 - Hernando Sosa (Einstein)

Discussion Leaders (Oct 31):

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
Hybrid methods - unbending
- separately refining small segments against average
- Egelman's spider implementation for helical structures
- real-space averaging of symmetry groups

Electron Optics - Oct 31 - David Stokes

Discussion Leaders (Nov 7):

Physics of electrons
- Faraday's Law
- influence of a B field
- electrostatic and electromagnetic lens
- deflectors
electron scattering
- scattering cross-section
- elastic scattering
- inelastic scattering
- secondary electrons
- backscattered electrons
- x-rays
- EELS
microscope column
- condensor, objective, intermediate, projector lenses
- gun, beam, image deflector coils
- condensor, objective, selected area apertures
optics
- focal length, magnification
- ray path diagram
- resolution
- aberrations
- coherency

Imaging strategies - Nov 7 - David Stokes

Discussion Leaders (Nov 14):

Radiation damage
- low dose imaging
Electron diffraction
Inelastic scattering
- energy filter and zero-loss imaging
Review of diffraction and Fourier transforms
- scattering - Fresnel and Frauenhofer
- sum of sines -> Fourier transform
- Friedel's Law
- Convolution Thm
- Correlation function
effect of sampling
- discrete Fourier transform
- box function and lattice function
- Nyquist sampling frequency
- boxing and floating
- aliasing
transfer functions and detectors (CCD and film)
- CTF: phase vs amplitude contrast (cryo vs neg stain)
- DQE, MTF, NTF

Tomography - Nov 14 - Carmen Mannella (Wadsworth Ctr)

Discussion Leader (Nov 28):

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

Hybrid Methods - Nov 28 - David Stokes (NYSBC/NYU)

Discussion Leader (Dec 5):

Unbending of 2D crystals
patch averaging of 2D crystals
Real-space averaging of helical reconstructions
SPA of helical assemblies
SPA of tomographic volumes
tomography of 2D crystals

Molecular fitting - Dec 5 - Hernando Sosa (Einstein)

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

Visit Cryo EM website at http://www.nysbc.org/facilities/CEM

Set ALLOWTOPICVIEW =

-- DavidStokes - 24 Jul 2006

Changed:

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<

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Revision 424 Jul 2006 - Main.DavidStokes

META TOPICPARENT	name="CemCourseGroup"

Cryoelectron Microscopy of Macromolecular Assemblies

NYU course G16.2617001 - Call #30137 - 3 credits

Contents

Instructors

David Stokes: stokes@saturn.med.nyu.edu
John Berriman: berriman@nysbc.org
Bill Rice: rice@nysbc.org
Iban Ubarretxena: iu@sci.ccny.cuny.edu
Hernando Sosa: hsosa@aecom.yu.edu
Joachim Frank: joachim@wadsworth.org
Carmen Mannella: carmen@wadsworth.org

Useful Textbooks

Reimer: "Transmission Electron Microscopy: Physics of Image Formation and Microanalysis"
Bozzola & Russell: "Electron Microscopy: Principles and Techniques for Biologists"
Frank: "Three Dimensional Electron Microscopy of Macromolecular Assemblies"
Harris: "Negative Staining and Cryoelectron Microscopy"
Williams & Carter: "Transmission Electron Microscopy: A Textbook for Materials Science"

Syllabus

Intro to EM and History of 3D Reconstruction - Sept 12 - David Stokes (NYSBC/NYU)

Basic EM techniques
- TEM
- SEM
- STEM
- Types of specimens
Electron sources
- tips (W, LaB6^?, FEG)
Physics of electrons
- Faraday's Law
- influence of a B field
- electrostatic and electromagnetic lens
Interaction of electrons with matter
- elastic scattering
- inelastic scattering
- secondary electrons
- backscattered electrons
- x-rays
- EELS
overview of 3D reconstruction strategies
- 2D crystallography
- helical reconstruction (Fourier-Bessel)
- single particle analysis
- tomography
negative stain of viruses
- model of negative stain
- matching of projection images
- quasiequivalence & icosahedral viruses
optical diffraction
- optical filtering
bacteriorhodopsin
acetylcholine receptor
ribosomes
insect flight muscle tomography

Sample preparation - Sept 19 - John Berriman (NYSBC)

Discussion leaders (Sept 26):

tissue -> sections
- positive stain
- immunolabeling
molecules -> negative stain
- single particles
- 2D crystals
cryo -> no stain
- frozen sections
- suspensions of molecules or 2D crystals

Diffraction and Fourier transforms - Sep 26 - Iban Ubarretxena (CCNY)

Discussion Leaders (Oct 3):

Diffraction of waves - Frauenhofer vs. Fresnel
Sum of cosines -> Fourier transform
Example functions (Gaussian, box, delta fcn, cosine)
Friedel's Law
Convolution fcn
Correlation fcn & Convolution Thm
Projection Thm

Single Particle Analysis I - Oct 3 - Joachim Frank (Wadsworth Ctr)

Discussion Leader (Oct 10):

philosophy of single-particle reconstruction
imaging considerations
- solid/perforated carbon
- automated data collection
how to get the initial model
- random conical tilt with defined orientations
- orientation determination using common lines
- 3D projection matching
model bias
correspondence analysis
classification and class-averages
refinement
defocus groups and CTF correction (Weiner filter)
weighted backprojection, ART and direct Fourier reconstruction
symmetry
resolution criteria (Fourier Shell Correlation)
overview of programs (Spider, Eman, Imagic)
applications

Single Particle Analysis II - Oct 10 - Joachim Frank (Wadsworth Ctr)

SPA practical (Oct 17):

Crystallography - Oct 17 - Iban Ubarretxena (CCNY)

Discussion Leaders (Oct 24):

Braggs law
real/reciprocal lattice
- unit cell
  - asymmetric unit
  - fractional coordinates
- symmetry
  - symmetry operators
  - plane groups & space groups
- Miller indices
- reciprocal lattice symmetry (ampl and phase)
- lattice lines
convolution fcn -> crystal
- convolution Thm -> reciprocal lattice
Projection Thm and radius of Ewald Sphere
strategy for 3D recontruction
- missing cone
imaging considerations
- electron diffraction
- spot-scan for images
electron diffraction for amplitudes
- radial background subtraction
- lattice refinement
- tilt angle/axis
- local background sub and spot integration
- merging
- refinement
- curve fitting
imaging for phases
- unbending
- defocus determination
- tilt angle/axis
- merging, weighting
- temperature factor compensation
resolution criteria (point-spread fcn)

Helical reconstruction - Oct 24 - Hernando Sosa (Einstein)

Discussion Leaders (Oct 31):

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
Hybrid methods - unbending
- separately refining small segments against average
- Egelman's spider implementation for helical structures
- real-space averaging of symmetry groups

Electron Optics - Oct 31 - David Stokes

Discussion Leaders (Nov 7):

Physics of electrons
- Faraday's Law
- influence of a B field
- electrostatic and electromagnetic lens
- deflectors
electron scattering
- scattering cross-section
- elastic scattering
- inelastic scattering
- secondary electrons
- backscattered electrons
- x-rays
- EELS
microscope column
- condensor, objective, intermediate, projector lenses
- gun, beam, image deflector coils
- condensor, objective, selected area apertures
optics
- focal length, magnification
- ray path diagram
- resolution
- aberrations
- coherency

Imaging strategies - Nov 7 - David Stokes

Discussion Leaders (Nov 14):

Radiation damage
- low dose imaging
Electron diffraction
Inelastic scattering
- energy filter and zero-loss imaging
Review of diffraction and Fourier transforms
- scattering - Fresnel and Frauenhofer
- sum of sines -> Fourier transform
- Friedel's Law
- Convolution Thm
- Correlation function
effect of sampling
- discrete Fourier transform
- box function and lattice function
- Nyquist sampling frequency
- boxing and floating
- aliasing
transfer functions and detectors (CCD and film)
- CTF: phase vs amplitude contrast (cryo vs neg stain)
- DQE, MTF, NTF

Tomography - Nov 14 - Carmen Mannella (Wadsworth Ctr)

Discussion Leader (Nov 28):

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

Hybrid Methods - Nov 28 - David Stokes (NYSBC/NYU)

Discussion Leader (Dec 5):

Unbending of 2D crystals
patch averaging of 2D crystals
Real-space averaging of helical reconstructions
SPA of helical assemblies
SPA of tomographic volumes
tomography of 2D crystals

Molecular fitting - Dec 5 - Hernando Sosa (Einstein)

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

Visit Cryo EM website at http://www.nysbc.org/facilities/CEM

Set ALLOWTOPICVIEW =

-- DavidStokes - 24 Jul 2006

META FILEATTACHMENT	attachment="Reimer.jpg" attr="" comment="Reimer" date="1153768095" name="Reimer.jpg" path="Reimer.jpg" size="23019" stream="Reimer.jpg" user="Main.DavidStokes" version="0"

Added:

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>

META FILEATTACHMENT	attachment="frank.jpg" attr="" comment="Frank" date="1153768120" name="frank.jpg" path="frank.jpg" size="23652" stream="frank.jpg" user="Main.DavidStokes" version="0"

Revision 324 Jul 2006 - Main.DavidStokes

META TOPICPARENT	name="CemCourseGroup"

Cryoelectron Microscopy of Macromolecular Assemblies

NYU course G16.2617001 - Call #30137 - 3 credits

Contents

Instructors

David Stokes: stokes@saturn.med.nyu.edu
John Berriman: berriman@nysbc.org
Bill Rice: rice@nysbc.org
Iban Ubarretxena: iu@sci.ccny.cuny.edu
Hernando Sosa: hsosa@aecom.yu.edu
Joachim Frank: joachim@wadsworth.org
Carmen Mannella: carmen@wadsworth.org

Useful Textbooks

Reimer: "Transmission Electron Microscopy: Physics of Image Formation and Microanalysis"
Bozzola & Russell: "Electron Microscopy: Principles and Techniques for Biologists"
Frank: "Three Dimensional Electron Microscopy of Macromolecular Assemblies"
Harris: "Negative Staining and Cryoelectron Microscopy"
Williams & Carter: "Transmission Electron Microscopy: A Textbook for Materials Science"

Syllabus

Intro to EM and History of 3D Reconstruction - Sept 12 - David Stokes (NYSBC/NYU)

Basic EM techniques
- TEM
- SEM
- STEM
- Types of specimens
Electron sources
- tips (W, LaB6^?, FEG)
Physics of electrons
- Faraday's Law
- influence of a B field
- electrostatic and electromagnetic lens
Interaction of electrons with matter
- elastic scattering
- inelastic scattering
- secondary electrons
- backscattered electrons
- x-rays
- EELS
overview of 3D reconstruction strategies
- 2D crystallography
- helical reconstruction (Fourier-Bessel)
- single particle analysis
- tomography
negative stain of viruses
- model of negative stain
- matching of projection images
- quasiequivalence & icosahedral viruses
optical diffraction
- optical filtering
bacteriorhodopsin
acetylcholine receptor
ribosomes
insect flight muscle tomography

Sample preparation - Sept 19 - John Berriman (NYSBC)

Discussion leaders (Sept 26):

tissue -> sections
- positive stain
- immunolabeling
molecules -> negative stain
- single particles
- 2D crystals
cryo -> no stain
- frozen sections
- suspensions of molecules or 2D crystals

Diffraction and Fourier transforms - Sep 26 - Iban Ubarretxena (CCNY)

Discussion Leaders (Oct 3):

Diffraction of waves - Frauenhofer vs. Fresnel
Sum of cosines -> Fourier transform
Example functions (Gaussian, box, delta fcn, cosine)
Friedel's Law
Convolution fcn
Correlation fcn & Convolution Thm
Projection Thm

Single Particle Analysis I - Oct 3 - Joachim Frank (Wadsworth Ctr)

Discussion Leader (Oct 10):

philosophy of single-particle reconstruction
imaging considerations
- solid/perforated carbon
- automated data collection
how to get the initial model
- random conical tilt with defined orientations
- orientation determination using common lines
- 3D projection matching
model bias
correspondence analysis
classification and class-averages
refinement
defocus groups and CTF correction (Weiner filter)
weighted backprojection, ART and direct Fourier reconstruction
symmetry
resolution criteria (Fourier Shell Correlation)
overview of programs (Spider, Eman, Imagic)
applications

Single Particle Analysis II - Oct 10 - Joachim Frank (Wadsworth Ctr)

SPA practical (Oct 17):

Crystallography - Oct 17 - Iban Ubarretxena (CCNY)

Discussion Leaders (Oct 24):

Braggs law
real/reciprocal lattice
- unit cell
  - asymmetric unit
  - fractional coordinates
- symmetry
  - symmetry operators
  - plane groups & space groups
- Miller indices
- reciprocal lattice symmetry (ampl and phase)
- lattice lines
convolution fcn -> crystal
- convolution Thm -> reciprocal lattice
Projection Thm and radius of Ewald Sphere
strategy for 3D recontruction
- missing cone
imaging considerations
- electron diffraction
- spot-scan for images
electron diffraction for amplitudes
- radial background subtraction
- lattice refinement
- tilt angle/axis
- local background sub and spot integration
- merging
- refinement
- curve fitting
imaging for phases
- unbending
- defocus determination
- tilt angle/axis
- merging, weighting
- temperature factor compensation
resolution criteria (point-spread fcn)

Helical reconstruction - Oct 24 - Hernando Sosa (Einstein)

Discussion Leaders (Oct 31):

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
Hybrid methods - unbending
- separately refining small segments against average
- Egelman's spider implementation for helical structures
- real-space averaging of symmetry groups

Electron Optics - Oct 31 - David Stokes

Discussion Leaders (Nov 7):

Physics of electrons
- Faraday's Law
- influence of a B field
- electrostatic and electromagnetic lens
- deflectors
electron scattering
- scattering cross-section
- elastic scattering
- inelastic scattering
- secondary electrons
- backscattered electrons
- x-rays
- EELS
microscope column
- condensor, objective, intermediate, projector lenses
- gun, beam, image deflector coils
- condensor, objective, selected area apertures
optics
- focal length, magnification
- ray path diagram
- resolution
- aberrations
- coherency

Imaging strategies - Nov 7 - David Stokes

Discussion Leaders (Nov 14):

Radiation damage
- low dose imaging
Electron diffraction
Inelastic scattering
- energy filter and zero-loss imaging
Review of diffraction and Fourier transforms
- scattering - Fresnel and Frauenhofer
- sum of sines -> Fourier transform
- Friedel's Law
- Convolution Thm
- Correlation function
effect of sampling
- discrete Fourier transform
- box function and lattice function
- Nyquist sampling frequency
- boxing and floating
- aliasing
transfer functions and detectors (CCD and film)
- CTF: phase vs amplitude contrast (cryo vs neg stain)
- DQE, MTF, NTF

Tomography - Nov 14 - Carmen Mannella (Wadsworth Ctr)

Discussion Leader (Nov 28):

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

Hybrid Methods - Nov 28 - David Stokes (NYSBC/NYU)

Discussion Leader (Dec 5):

Unbending of 2D crystals
patch averaging of 2D crystals
Real-space averaging of helical reconstructions
SPA of helical assemblies
SPA of tomographic volumes
tomography of 2D crystals

Molecular fitting - Dec 5 - Hernando Sosa (Einstein)

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

Visit Cryo EM website at http://www.nysbc.org/facilities/CEM

Set ALLOWTOPICVIEW =

-- DavidStokes - 24 Jul 2006

Added:

>
>

META FILEATTACHMENT	attachment="Reimer.jpg" attr="" comment="Reimer" date="1153768095" name="Reimer.jpg" path="Reimer.jpg" size="23019" stream="Reimer.jpg" user="Main.DavidStokes" version="0"

Revision 224 Jul 2006 - Main.DavidStokes

META TOPICPARENT	name="CemCourseGroup"

Cryoelectron Microscopy of Macromolecular Assemblies

NYU course G16.2617001 - Call #30137 - 3 credits

Contents

Instructors

Instructors

David Stokes: stokes@saturn.med.nyu.edu
John Berriman: berriman@nysbc.org
Bill Rice: rice@nysbc.org
Iban Ubarretxena: iu@sci.ccny.cuny.edu
Hernando Sosa: hsosa@aecom.yu.edu
Joachim Frank: joachim@wadsworth.org
Carmen Mannella: carmen@wadsworth.org

Changed:

<
<

Potential Textbooks

>
>

Useful Textbooks

Reimer: "Transmission Electron Microscopy: Physics of Image Formation and Microanalysis"
Bozzola & Russell: "Electron Microscopy: Principles and Techniques for Biologists"
Frank: "Three Dimensional Electron Microscopy of Macromolecular Assemblies"
Harris: "Negative Staining and Cryoelectron Microscopy"
Williams & Carter: "Transmission Electron Microscopy: A Textbook for Materials Science"

Syllabus

Intro to EM and History of 3D Reconstruction - Sept 12 - David Stokes (NYSBC/NYU)

Basic EM techniques
- TEM
- SEM
- STEM
- Types of specimens
Electron sources
- tips (W, LaB6^?, FEG)
Physics of electrons
- Faraday's Law
- influence of a B field
- electrostatic and electromagnetic lens
Interaction of electrons with matter
- elastic scattering
- inelastic scattering
- secondary electrons
- backscattered electrons
- x-rays
- EELS
overview of 3D reconstruction strategies
- 2D crystallography
- helical reconstruction (Fourier-Bessel)
- single particle analysis
- tomography
negative stain of viruses
- model of negative stain
- matching of projection images
- quasiequivalence & icosahedral viruses
optical diffraction
- optical filtering
bacteriorhodopsin
acetylcholine receptor
ribosomes
insect flight muscle tomography

Sample preparation - Sept 19 - John Berriman (NYSBC)

Discussion leaders (Sept 26):

tissue -> sections
- positive stain
- immunolabeling
molecules -> negative stain
- single particles
- 2D crystals
cryo -> no stain
- frozen sections
- suspensions of molecules or 2D crystals

Diffraction and Fourier transforms - Sep 26 - Iban Ubarretxena (CCNY)

Discussion Leaders (Oct 3):

Diffraction of waves - Frauenhofer vs. Fresnel
Sum of cosines -> Fourier transform
Example functions (Gaussian, box, delta fcn, cosine)
Friedel's Law
Convolution fcn
Correlation fcn & Convolution Thm
Projection Thm

Single Particle Analysis I - Oct 3 - Joachim Frank (Wadsworth Ctr)

Discussion Leader (Oct 10):

philosophy of single-particle reconstruction
imaging considerations
- solid/perforated carbon
- automated data collection
how to get the initial model
- random conical tilt with defined orientations
- orientation determination using common lines
- 3D projection matching
model bias
correspondence analysis
classification and class-averages
refinement
defocus groups and CTF correction (Weiner filter)
weighted backprojection, ART and direct Fourier reconstruction
symmetry
resolution criteria (Fourier Shell Correlation)
overview of programs (Spider, Eman, Imagic)
applications

Single Particle Analysis II - Oct 10 - Joachim Frank (Wadsworth Ctr)

SPA practical (Oct 17):

Crystallography - Oct 17 - Iban Ubarretxena (CCNY)

Discussion Leaders (Oct 24):

Braggs law
real/reciprocal lattice
- unit cell
  - asymmetric unit
  - fractional coordinates
- symmetry
  - symmetry operators
  - plane groups & space groups
- Miller indices
- reciprocal lattice symmetry (ampl and phase)
- lattice lines
convolution fcn -> crystal
- convolution Thm -> reciprocal lattice
Projection Thm and radius of Ewald Sphere
strategy for 3D recontruction
- missing cone
imaging considerations
- electron diffraction
- spot-scan for images
electron diffraction for amplitudes
- radial background subtraction
- lattice refinement
- tilt angle/axis
- local background sub and spot integration
- merging
- refinement
- curve fitting
imaging for phases
- unbending
- defocus determination
- tilt angle/axis
- merging, weighting
- temperature factor compensation
resolution criteria (point-spread fcn)

Helical reconstruction - Oct 24 - Hernando Sosa (Einstein)

Discussion Leaders (Oct 31):

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
Hybrid methods - unbending
- separately refining small segments against average
- Egelman's spider implementation for helical structures
- real-space averaging of symmetry groups

Electron Optics - Oct 31 - David Stokes

Discussion Leaders (Nov 7):

Physics of electrons
- Faraday's Law
- influence of a B field
- electrostatic and electromagnetic lens
- deflectors
electron scattering
- scattering cross-section
- elastic scattering
- inelastic scattering
- secondary electrons
- backscattered electrons
- x-rays
- EELS
microscope column
- condensor, objective, intermediate, projector lenses
- gun, beam, image deflector coils
- condensor, objective, selected area apertures
optics
- focal length, magnification
- ray path diagram
- resolution
- aberrations
- coherency

Imaging strategies - Nov 7 - David Stokes

Discussion Leaders (Nov 14):

Radiation damage
- low dose imaging
Electron diffraction
Inelastic scattering
- energy filter and zero-loss imaging
Review of diffraction and Fourier transforms
- scattering - Fresnel and Frauenhofer
- sum of sines -> Fourier transform
- Friedel's Law
- Convolution Thm
- Correlation function
effect of sampling
- discrete Fourier transform
- box function and lattice function
- Nyquist sampling frequency
- boxing and floating
- aliasing
transfer functions and detectors (CCD and film)
- CTF: phase vs amplitude contrast (cryo vs neg stain)
- DQE, MTF, NTF

Tomography - Nov 14 - Carmen Mannella (Wadsworth Ctr)

Discussion Leader (Nov 28):

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

Hybrid Methods - Nov 28 - David Stokes (NYSBC/NYU)

Discussion Leader (Dec 5):

Unbending of 2D crystals
patch averaging of 2D crystals
Real-space averaging of helical reconstructions
SPA of helical assemblies
SPA of tomographic volumes
tomography of 2D crystals

Molecular fitting - Dec 5 - Hernando Sosa (Einstein)

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

Visit Cryo EM website at http://www.nysbc.org/facilities/CEM

Set ALLOWTOPICVIEW =

-- DavidStokes - 24 Jul 2006

Revision 124 Jul 2006 - Main.DavidStokes

META TOPICPARENT	name="CemCourseGroup"

Cryoelectron Microscopy of Macromolecular Assemblies

NYU course G16.2617001 - Call #30137 - 3 credits

Contents

Instructors

David Stokes: stokes@saturn.med.nyu.edu
John Berriman: berriman@nysbc.org
Bill Rice: rice@nysbc.org
Iban Ubarretxena: iu@sci.ccny.cuny.edu
Hernando Sosa: hsosa@aecom.yu.edu
Joachim Frank: joachim@wadsworth.org
Carmen Mannella: carmen@wadsworth.org

Potential Textbooks

Reimer: "Transmission Electron Microscopy: Physics of Image Formation and Microanalysis"
Bozzola & Russell: "Electron Microscopy: Principles and Techniques for Biologists"
Frank: "Three Dimensional Electron Microscopy of Macromolecular Assemblies"
Harris: "Negative Staining and Cryoelectron Microscopy"
Williams & Carter: "Transmission Electron Microscopy: A Textbook for Materials Science"

Syllabus

Intro to EM and History of 3D Reconstruction - Sept 12 - David Stokes (NYSBC/NYU)

Basic EM techniques
- TEM
- SEM
- STEM
- Types of specimens
Electron sources
- tips (W, LaB6^?, FEG)
Physics of electrons
- Faraday's Law
- influence of a B field
- electrostatic and electromagnetic lens
Interaction of electrons with matter
- elastic scattering
- inelastic scattering
- secondary electrons
- backscattered electrons
- x-rays
- EELS
overview of 3D reconstruction strategies
- 2D crystallography
- helical reconstruction (Fourier-Bessel)
- single particle analysis
- tomography
negative stain of viruses
- model of negative stain
- matching of projection images
- quasiequivalence & icosahedral viruses
optical diffraction
- optical filtering
bacteriorhodopsin
acetylcholine receptor
ribosomes
insect flight muscle tomography

Sample preparation - Sept 19 - John Berriman (NYSBC)

Discussion leaders (Sept 26):

tissue -> sections
- positive stain
- immunolabeling
molecules -> negative stain
- single particles
- 2D crystals
cryo -> no stain
- frozen sections
- suspensions of molecules or 2D crystals

Diffraction and Fourier transforms - Sep 26 - Iban Ubarretxena (CCNY)

Discussion Leaders (Oct 3):

Diffraction of waves - Frauenhofer vs. Fresnel
Sum of cosines -> Fourier transform
Example functions (Gaussian, box, delta fcn, cosine)
Friedel's Law
Convolution fcn
Correlation fcn & Convolution Thm
Projection Thm

Single Particle Analysis I - Oct 3 - Joachim Frank (Wadsworth Ctr)

Discussion Leader (Oct 10):

philosophy of single-particle reconstruction
imaging considerations
- solid/perforated carbon
- automated data collection
how to get the initial model
- random conical tilt with defined orientations
- orientation determination using common lines
- 3D projection matching
model bias
correspondence analysis
classification and class-averages
refinement
defocus groups and CTF correction (Weiner filter)
weighted backprojection, ART and direct Fourier reconstruction
symmetry
resolution criteria (Fourier Shell Correlation)
overview of programs (Spider, Eman, Imagic)
applications

Single Particle Analysis II - Oct 10 - Joachim Frank (Wadsworth Ctr)

SPA practical (Oct 17):

Crystallography - Oct 17 - Iban Ubarretxena (CCNY)

Discussion Leaders (Oct 24):

Braggs law
real/reciprocal lattice
- unit cell
  - asymmetric unit
  - fractional coordinates
- symmetry
  - symmetry operators
  - plane groups & space groups
- Miller indices
- reciprocal lattice symmetry (ampl and phase)
- lattice lines
convolution fcn -> crystal
- convolution Thm -> reciprocal lattice
Projection Thm and radius of Ewald Sphere
strategy for 3D recontruction
- missing cone
imaging considerations
- electron diffraction
- spot-scan for images
electron diffraction for amplitudes
- radial background subtraction
- lattice refinement
- tilt angle/axis
- local background sub and spot integration
- merging
- refinement
- curve fitting
imaging for phases
- unbending
- defocus determination
- tilt angle/axis
- merging, weighting
- temperature factor compensation
resolution criteria (point-spread fcn)

Helical reconstruction - Oct 24 - Hernando Sosa (Einstein)

Discussion Leaders (Oct 31):

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
Hybrid methods - unbending
- separately refining small segments against average
- Egelman's spider implementation for helical structures
- real-space averaging of symmetry groups

Electron Optics - Oct 31 - David Stokes

Discussion Leaders (Nov 7):

Physics of electrons
- Faraday's Law
- influence of a B field
- electrostatic and electromagnetic lens
- deflectors
electron scattering
- scattering cross-section
- elastic scattering
- inelastic scattering
- secondary electrons
- backscattered electrons
- x-rays
- EELS
microscope column
- condensor, objective, intermediate, projector lenses
- gun, beam, image deflector coils
- condensor, objective, selected area apertures
optics
- focal length, magnification
- ray path diagram
- resolution
- aberrations
- coherency

Imaging strategies - Nov 7 - David Stokes

Discussion Leaders (Nov 14):

Radiation damage
- low dose imaging
Electron diffraction
Inelastic scattering
- energy filter and zero-loss imaging
Review of diffraction and Fourier transforms
- scattering - Fresnel and Frauenhofer
- sum of sines -> Fourier transform
- Friedel's Law
- Convolution Thm
- Correlation function
effect of sampling
- discrete Fourier transform
- box function and lattice function
- Nyquist sampling frequency
- boxing and floating
- aliasing
transfer functions and detectors (CCD and film)
- CTF: phase vs amplitude contrast (cryo vs neg stain)
- DQE, MTF, NTF

Tomography - Nov 14 - Carmen Mannella (Wadsworth Ctr)

Discussion Leader (Nov 28):

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

Hybrid Methods - Nov 28 - David Stokes (NYSBC/NYU)

Discussion Leader (Dec 5):

Unbending of 2D crystals
patch averaging of 2D crystals
Real-space averaging of helical reconstructions
SPA of helical assemblies
SPA of tomographic volumes
tomography of 2D crystals

Molecular fitting - Dec 5 - Hernando Sosa (Einstein)

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

Visit Cryo EM website at http://www.nysbc.org/facilities/CEM

Set ALLOWTOPICVIEW =

-- DavidStokes - 24 Jul 2006

Difference: CemCourseSyllabus06 (1 vs. 16)

Revision 1613 Mar 2009 - Main.DavidCowburn

Instructors

Useful Textbooks

Syllabus

Intro to EM and History of 3D Reconstruction - Sept 12 - David Stokes (NYSBC/NYU)

Sample preparation - Sept 19 - John Berriman (NYSBC)

Discussion leaders (Sept 26):

Diffraction and Fourier transforms - Sep 26 - Iban Ubarretxena (CCNY)

Discussion Leaders (Oct 3): Jaime Llodra

Single Particle Analysis I - Oct 3 - Joachim Frank (Wadsworth Ctr)

Discussion Leader (Oct 10): Jaclyn Greimann & David Grandy

Single Particle Analysis II - Oct 10 - Joachim Frank (Wadsworth Ctr)

SPA practical (Oct 17):

Crystallography - Oct 17 - Iban Ubarretxena (CCNY)

Discussion Leaders (Oct 24): Allyson Bunbury

Helical reconstruction - Oct 24 - Hernando Sosa (Einstein)

Discussion Leaders (Oct 31): Vikas Jain

Electron Optics - Oct 31 - David Stokes

Discussion Leaders (Nov 7): Jinrang Kim

Imaging strategies and Media - Nov 7 - David Stokes

Discussion Leaders (Nov 14): Jorge Mansilla-Soto

Tomography - Nov 14 - Carmen Mannella (Wadsworth Ctr)

Discussion Leader (Nov 28): W. Nicholson Price

Hybrid Methods - Nov 28 - David Stokes (NYSBC/NYU)

Discussion Leader (Dec 5): Shyam Vaidya

Molecular fitting - Dec 5 - Hernando Sosa (Einstein)

Revision 1501 Sep 2008 - Main.DavidStokes

Instructors

Useful Textbooks

Syllabus

Intro to EM and History of 3D Reconstruction - Sept 12 - David Stokes (NYSBC/NYU)

Sample preparation - Sept 19 - John Berriman (NYSBC)

Discussion leaders (Sept 26):

Diffraction and Fourier transforms - Sep 26 - Iban Ubarretxena (CCNY)

Discussion Leaders (Oct 3): Jaime Llodra

Single Particle Analysis I - Oct 3 - Joachim Frank (Wadsworth Ctr)

Discussion Leader (Oct 10): Jaclyn Greimann & David Grandy

Single Particle Analysis II - Oct 10 - Joachim Frank (Wadsworth Ctr)

SPA practical (Oct 17):

Crystallography - Oct 17 - Iban Ubarretxena (CCNY)

Discussion Leaders (Oct 24): Allyson Bunbury

Helical reconstruction - Oct 24 - Hernando Sosa (Einstein)

Discussion Leaders (Oct 31): Vikas Jain

Electron Optics - Oct 31 - David Stokes

Discussion Leaders (Nov 7): Jinrang Kim

Imaging strategies and Media - Nov 7 - David Stokes

Discussion Leaders (Nov 14): Jorge Mansilla-Soto

Tomography - Nov 14 - Carmen Mannella (Wadsworth Ctr)

Discussion Leader (Nov 28): W. Nicholson Price

Hybrid Methods - Nov 28 - David Stokes (NYSBC/NYU)

Discussion Leader (Dec 5): Shyam Vaidya

Molecular fitting - Dec 5 - Hernando Sosa (Einstein)

Revision 1425 Sep 2006 - Main.DavidStokes

Instructors

Useful Textbooks

Syllabus

Intro to EM and History of 3D Reconstruction - Sept 12 - David Stokes (NYSBC/NYU)

Sample preparation - Sept 19 - John Berriman (NYSBC)

Discussion leaders (Sept 26):

Diffraction and Fourier transforms - Sep 26 - Iban Ubarretxena (CCNY)

Discussion Leaders (Oct 3):

Discussion Leaders (Oct 3): Jaime Llodra

Single Particle Analysis I - Oct 3 - Joachim Frank (Wadsworth Ctr)

Discussion Leader (Oct 10):

Discussion Leader (Oct 10): Jaclyn Greimann & David Grandy

Single Particle Analysis II - Oct 10 - Joachim Frank (Wadsworth Ctr)

SPA practical (Oct 17):

Crystallography - Oct 17 - Iban Ubarretxena (CCNY)

Discussion Leaders (Oct 24):

Discussion Leaders (Oct 24): Allyson Bunbury

Helical reconstruction - Oct 24 - Hernando Sosa (Einstein)

Discussion Leaders (Oct 31):

Discussion Leaders (Oct 31): Vikas Jain

Electron Optics - Oct 31 - David Stokes

Discussion Leaders (Nov 7):

Discussion Leaders (Nov 7): Jinrang Kim

Imaging strategies and Media - Nov 7 - David Stokes

Discussion Leaders (Nov 14):

Discussion Leaders (Nov 14): Jorge Mansilla-Soto