Difference: CemCourseAnnouncement05 (1 vs. 5)

Revision 524 Jul 2006 - Main.DavidStokes

Changed:
<
<
META TOPICPARENT name="CemCourseGroup"
Cryoelectron Microscopy of Macromolecular Assemblies Graduate Course offered at NYSBC Fall 2005

Description: A comprehensive course in the theory and practice of solving molecular structures by electron microscopy. We will start with optics, sample preparation and a basic mathematical description of diffraction before moving into a detailed exploration of the three main methods of structure determination: electron crystallography, single particle analysis, and electron tomography. We will end with a discussion of map interpretation and molecular fitting. This is predominantly a lecture course involving one 2-hour lecture per week accompanied by a discussion session and an occasional practical session using facilities at the New York Structural Biology Center. Lecturers will be given by expert electron microscopists from around NYC and students from various campuses will be encouraged to attend.
Course Director: David Stokes 212-263-1580 stokes@saturn.med.nyu.edu

CemCourseAnnounce.pdf: download the CEM course flier

PhD students and Postdoctoral fellows are welcome.

This course will be listed in the catalogue of the New York University School of Medicine (http://www.med.nyu.edu/sackler/courses). NYU has cooperative agreements that allow students at most other New York institutions to take courses for credit (2 or 3 credits).

Tentative schedule is to offer a 2-hour lecture on Tuesdays from 3:30-5:30. We hope to also offer a discussion session later in the week. Both will be simultaneously broadcast over the web.

Syllabus

Microscope types - Sept 13 or 15 - David Stokes (NYU/NYSBC)

  • TEM
  • SEM
  • STEM
  • contrast mechanisms (ampl vs. phase)
    • elastic vs inelastic scattering
  • x-ray analysis
  • EELS

Optics - Sept 20 or 22 - John Berriman (NYSBC)

  • Lenses, focal lengths, ray tracing,
  • Microscope design
    • light vs. electron microscope
    • objective lens
    • lens configuration for EM
  • aberrations (Cs and Cc)
  • electron source
  • resolution

Sample preparation - Sept 27 or 29 - John Berriman (with practical)

  • 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 - Oct 4 or 6 - Iban Ubarretxena (CCNY)

  • 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

Imaging strategies - Oct 11 or 13 - David Stokes (NYU/NYSBC)

  • radiation damage/section shrinkage
  • detectors (film, CCD, imaging plates)
    • transfer functions & DQE
  • contrast transfer function
    • phase contrast
    • amplitude contrast
  • beam tilt
  • sampling
    • discrete Fourier transform
    • Nyquist sampling frequency
    • aliasing
    • boxing and floating

History of 3D reconstruction - Oct 18 or 20 - David Stokes (NYU/NYSBC)

  • negative stain of viruses
    • model of negative stain
    • matching of projection images
    • quasiequivalence & icosahedral viruses
  • optical diffraction
    • optical filtering

Crystallography I - Oct 25 or 27 - Seth Darst (Rockefeller Univ.)

  • Braggs law
  • real/reciprocal lattice
    • symmetry
      • plane groups & space groups
    • Miller indices
    • lattice lines
  • convolution fcn -> crystal
    • convolution Thm -> reciprocal lattice
  • Projection Thm and radius of Ewald Sphere
  • strategy for 3D recontruction
    • missing cone

Crystallography II & Intro to Single Particle Analysis - Nov 1 or 3 - Iban Ubarretxena (CCNY)

  • 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)
  • Intro to Single Particle Analysis
    • sample considerations (size, homogeneity, internal symmetry
    • useful functions
      • cross correlation
      • radon transform
      • low pass/high pass filters
      • Weiner filter
    • particle picking
    • alignment
    • class averages
    • reconstruction strategies
      • random conical tilt
      • angular reconstitution
    • reconstruction packages (Spider, EMAN, IMAGIC)

Helical reconstruction - Nov 8 or 10 - Hernando Sosa (Albert Einstein College of Medicine)

  • 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
    • real-space averaging

Single Particle Analysis - Nov 15 or 17 - Joachim Frank (Wadsworth Ctr)

  • imaging considerations
    • solid/perforated carbon
    • automated data collection
  • initial model
    • random conical tilt with defined orientations (neg stain)
  • orientation of frozen-hydrated particles with common line analysis
    • projection matching
  • model bias
  • classification and class-averages
  • correspondance analysis
  • refinement
  • CTF correction (Weiner filter)
  • backprojection vs. Fourier synthesis
  • symmetry
  • resolution criteria (Fourier Shell Correlation)
  • programs (Spider, Emen, Imagic)
  • applications

Tomography - Nov 29 or Dec 1 - Bruce McEwen? (Wadsworth Ctr)

  • 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

Molecular fitting - Dec 6 or 8 - Hernando Sosa (Albert 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

-- DavidStokes - 14 Apr 2005

>
>
META TOPICPARENT name="CemCourse2005"
Cryoelectron Microscopy of Macromolecular Assemblies Graduate Course offered at NYSBC Fall 2005

Description: A comprehensive course in the theory and practice of solving molecular structures by electron microscopy. We will start with optics, sample preparation and a basic mathematical description of diffraction before moving into a detailed exploration of the three main methods of structure determination: electron crystallography, single particle analysis, and electron tomography. We will end with a discussion of map interpretation and molecular fitting. This is predominantly a lecture course involving one 2-hour lecture per week accompanied by a discussion session and an occasional practical session using facilities at the New York Structural Biology Center. Lecturers will be given by expert electron microscopists from around NYC and students from various campuses will be encouraged to attend.
Course Director: David Stokes 212-263-1580 stokes@saturn.med.nyu.edu

CemCourseAnnounce.pdf: download the CEM course flier

PhD students and Postdoctoral fellows are welcome.

This course will be listed in the catalogue of the New York University School of Medicine (http://www.med.nyu.edu/sackler/courses). NYU has cooperative agreements that allow students at most other New York institutions to take courses for credit (2 or 3 credits).

Tentative schedule is to offer a 2-hour lecture on Tuesdays from 3:30-5:30. We hope to also offer a discussion session later in the week. Both will be simultaneously broadcast over the web.

Syllabus

Microscope types - Sept 13 or 15 - David Stokes (NYU/NYSBC)

  • TEM
  • SEM
  • STEM
  • contrast mechanisms (ampl vs. phase)
    • elastic vs inelastic scattering
  • x-ray analysis
  • EELS

Optics - Sept 20 or 22 - John Berriman (NYSBC)

  • Lenses, focal lengths, ray tracing,
  • Microscope design
    • light vs. electron microscope
    • objective lens
    • lens configuration for EM
  • aberrations (Cs and Cc)
  • electron source
  • resolution

Sample preparation - Sept 27 or 29 - John Berriman (with practical)

  • 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 - Oct 4 or 6 - Iban Ubarretxena (CCNY)

  • 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

Imaging strategies - Oct 11 or 13 - David Stokes (NYU/NYSBC)

  • radiation damage/section shrinkage
  • detectors (film, CCD, imaging plates)
    • transfer functions & DQE
  • contrast transfer function
    • phase contrast
    • amplitude contrast
  • beam tilt
  • sampling
    • discrete Fourier transform
    • Nyquist sampling frequency
    • aliasing
    • boxing and floating

History of 3D reconstruction - Oct 18 or 20 - David Stokes (NYU/NYSBC)

  • negative stain of viruses
    • model of negative stain
    • matching of projection images
    • quasiequivalence & icosahedral viruses
  • optical diffraction
    • optical filtering

Crystallography I - Oct 25 or 27 - Seth Darst (Rockefeller Univ.)

  • Braggs law
  • real/reciprocal lattice
    • symmetry
      • plane groups & space groups
    • Miller indices
    • lattice lines
  • convolution fcn -> crystal
    • convolution Thm -> reciprocal lattice
  • Projection Thm and radius of Ewald Sphere
  • strategy for 3D recontruction
    • missing cone

Crystallography II & Intro to Single Particle Analysis - Nov 1 or 3 - Iban Ubarretxena (CCNY)

  • 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)
  • Intro to Single Particle Analysis
    • sample considerations (size, homogeneity, internal symmetry
    • useful functions
      • cross correlation
      • radon transform
      • low pass/high pass filters
      • Weiner filter
    • particle picking
    • alignment
    • class averages
    • reconstruction strategies
      • random conical tilt
      • angular reconstitution
    • reconstruction packages (Spider, EMAN, IMAGIC)

Helical reconstruction - Nov 8 or 10 - Hernando Sosa (Albert Einstein College of Medicine)

  • 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
    • real-space averaging

Single Particle Analysis - Nov 15 or 17 - Joachim Frank (Wadsworth Ctr)

  • imaging considerations
    • solid/perforated carbon
    • automated data collection
  • initial model
    • random conical tilt with defined orientations (neg stain)
  • orientation of frozen-hydrated particles with common line analysis
    • projection matching
  • model bias
  • classification and class-averages
  • correspondance analysis
  • refinement
  • CTF correction (Weiner filter)
  • backprojection vs. Fourier synthesis
  • symmetry
  • resolution criteria (Fourier Shell Correlation)
  • programs (Spider, Emen, Imagic)
  • applications

Tomography - Nov 29 or Dec 1 - Bruce McEwen? (Wadsworth Ctr)

  • 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

Molecular fitting - Dec 6 or 8 - Hernando Sosa (Albert 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

-- DavidStokes - 14 Apr 2005

 

META FILEATTACHMENT attr="" comment="CEM course flier" date="1140113010" name="CemCourseAnnounce.pdf" path="CemCourseAnnounce.pdf" size="481908" user="DavidStokes" version="1.1"
META TOPICMOVED by="DavidStokes" date="1153751851" from="Main.CemCourseAnnouncement" to="Main.CemCourseAnnouncement05"

Revision 424 Jul 2006 - Main.DavidStokes

 
META TOPICPARENT name="CemCourseGroup"
Cryoelectron Microscopy of Macromolecular Assemblies Graduate Course offered at NYSBC Fall 2005

Description: A comprehensive course in the theory and practice of solving molecular structures by electron microscopy. We will start with optics, sample preparation and a basic mathematical description of diffraction before moving into a detailed exploration of the three main methods of structure determination: electron crystallography, single particle analysis, and electron tomography. We will end with a discussion of map interpretation and molecular fitting. This is predominantly a lecture course involving one 2-hour lecture per week accompanied by a discussion session and an occasional practical session using facilities at the New York Structural Biology Center. Lecturers will be given by expert electron microscopists from around NYC and students from various campuses will be encouraged to attend.
Course Director: David Stokes 212-263-1580 stokes@saturn.med.nyu.edu

CemCourseAnnounce.pdf: download the CEM course flier

PhD students and Postdoctoral fellows are welcome.

This course will be listed in the catalogue of the New York University School of Medicine (http://www.med.nyu.edu/sackler/courses). NYU has cooperative agreements that allow students at most other New York institutions to take courses for credit (2 or 3 credits).

Tentative schedule is to offer a 2-hour lecture on Tuesdays from 3:30-5:30. We hope to also offer a discussion session later in the week. Both will be simultaneously broadcast over the web.

Syllabus

Microscope types - Sept 13 or 15 - David Stokes (NYU/NYSBC)

Changed:
<
<
  • TEM
  • SEM
  • STEM
  • contrast mechanisms (ampl vs. phase)
    • elastic vs inelastic scattering
  • x-ray analysis
  • EELS
>
>
  • TEM
  • SEM
  • STEM
  • contrast mechanisms (ampl vs. phase)
    • elastic vs inelastic scattering
  • x-ray analysis
  • EELS
 

Optics - Sept 20 or 22 - John Berriman (NYSBC)

Changed:
<
<
  • Lenses, focal lengths, ray tracing,
  • Microscope design
    • light vs. electron microscope
    • objective lens
    • lens configuration for EM
  • aberrations (Cs and Cc)
  • electron source
  • resolution
>
>
  • Lenses, focal lengths, ray tracing,
  • Microscope design
    • light vs. electron microscope
    • objective lens
    • lens configuration for EM
  • aberrations (Cs and Cc)
  • electron source
  • resolution
 

Sample preparation - Sept 27 or 29 - John Berriman (with practical)

Changed:
<
<
  • tissue -> sections
    • positive stain
    • immunolabeling
  • molecules -> negative stain
    • single particles
    • 2D crystals
  • cryo -> no stain
    • frozen sections
    • suspensions of molecules or 2D crystals
>
>
  • 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 - Oct 4 or 6 - Iban Ubarretxena (CCNY)

Changed:
<
<
  • 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
>
>
  • 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
 

Imaging strategies - Oct 11 or 13 - David Stokes (NYU/NYSBC)

Changed:
<
<
  • radiation damage/section shrinkage
  • detectors (film, CCD, imaging plates)
    • transfer functions & DQE
  • contrast transfer function
    • phase contrast
    • amplitude contrast
  • beam tilt
  • sampling
    • discrete Fourier transform
    • Nyquist sampling frequency
    • aliasing
    • boxing and floating
>
>
  • radiation damage/section shrinkage
  • detectors (film, CCD, imaging plates)
    • transfer functions & DQE
  • contrast transfer function
    • phase contrast
    • amplitude contrast
  • beam tilt
  • sampling
    • discrete Fourier transform
    • Nyquist sampling frequency
    • aliasing
    • boxing and floating
 

History of 3D reconstruction - Oct 18 or 20 - David Stokes (NYU/NYSBC)

Changed:
<
<
  • negative stain of viruses
    • model of negative stain
    • matching of projection images
    • quasiequivalence & icosahedral viruses
  • optical diffraction
    • optical filtering
>
>
  • negative stain of viruses
    • model of negative stain
    • matching of projection images
    • quasiequivalence & icosahedral viruses
  • optical diffraction
    • optical filtering
 

Crystallography I - Oct 25 or 27 - Seth Darst (Rockefeller Univ.)

Changed:
<
<
  • Braggs law
  • real/reciprocal lattice
    • symmetry
      • plane groups & space groups
    • Miller indices
    • lattice lines
  • convolution fcn -> crystal
    • convolution Thm -> reciprocal lattice
  • Projection Thm and radius of Ewald Sphere
  • strategy for 3D recontruction
    • missing cone
>
>
  • Braggs law
  • real/reciprocal lattice
    • symmetry
      • plane groups & space groups
    • Miller indices
    • lattice lines
  • convolution fcn -> crystal
    • convolution Thm -> reciprocal lattice
  • Projection Thm and radius of Ewald Sphere
  • strategy for 3D recontruction
    • missing cone
 

Crystallography II & Intro to Single Particle Analysis - Nov 1 or 3 - Iban Ubarretxena (CCNY)

Changed:
<
<
  • 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)
  • Intro to Single Particle Analysis
    • sample considerations (size, homogeneity, internal symmetry
    • useful functions
      • cross correlation
      • radon transform
      • low pass/high pass filters
      • Weiner filter
    • particle picking
    • alignment
    • class averages
    • reconstruction strategies
      • random conical tilt
      • angular reconstitution
    • reconstruction packages (Spider, EMAN, IMAGIC)
>
>
  • 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)
  • Intro to Single Particle Analysis
    • sample considerations (size, homogeneity, internal symmetry
    • useful functions
      • cross correlation
      • radon transform
      • low pass/high pass filters
      • Weiner filter
    • particle picking
    • alignment
    • class averages
    • reconstruction strategies
      • random conical tilt
      • angular reconstitution
    • reconstruction packages (Spider, EMAN, IMAGIC)
 

Helical reconstruction - Nov 8 or 10 - Hernando Sosa (Albert Einstein College of Medicine)

Changed:
<
<
  • 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
    • real-space averaging
>
>
  • 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
    • real-space averaging
 

Single Particle Analysis - Nov 15 or 17 - Joachim Frank (Wadsworth Ctr)

Changed:
<
<
  • imaging considerations
    • solid/perforated carbon
    • automated data collection
  • initial model
    • random conical tilt with defined orientations (neg stain)
  • orientation of frozen-hydrated particles with common line analysis
    • projection matching
  • model bias
  • classification and class-averages
  • correspondance analysis
  • refinement
  • CTF correction (Weiner filter)
  • backprojection vs. Fourier synthesis
  • symmetry
  • resolution criteria (Fourier Shell Correlation)
  • programs (Spider, Emen, Imagic)
  • applications
>
>
  • imaging considerations
    • solid/perforated carbon
    • automated data collection
  • initial model
    • random conical tilt with defined orientations (neg stain)
  • orientation of frozen-hydrated particles with common line analysis
    • projection matching
  • model bias
  • classification and class-averages
  • correspondance analysis
  • refinement
  • CTF correction (Weiner filter)
  • backprojection vs. Fourier synthesis
  • symmetry
  • resolution criteria (Fourier Shell Correlation)
  • programs (Spider, Emen, Imagic)
  • applications
 

Tomography - Nov 29 or Dec 1 - Bruce McEwen? (Wadsworth Ctr)

Changed:
<
<
  • 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
>
>
  • 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
 

Molecular fitting - Dec 6 or 8 - Hernando Sosa (Albert Einstein)

Changed:
<
<
  • Boundary determination
    • isodensity contour
    • segmentation
  • Automated strategies
    • Situs
    • helix hunter
  • Criteria for fit
>
>
  • Boundary determination
    • isodensity contour
    • segmentation
  • Automated strategies
    • Situs
    • helix hunter
  • Criteria for fit
 

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

-- DavidStokes - 14 Apr 2005

Changed:
<
<
>
>
 

META FILEATTACHMENT attr="" comment="CEM course flier" date="1140113010" name="CemCourseAnnounce.pdf" path="CemCourseAnnounce.pdf" size="481908" user="DavidStokes" version="1.1"
Added:
>
>
META TOPICMOVED by="DavidStokes" date="1153751851" from="Main.CemCourseAnnouncement" to="Main.CemCourseAnnouncement05"
 

Revision 316 Feb 2006 - Main.DavidStokes

Added:
>
>
META TOPICPARENT name="CemCourseGroup"
 Cryoelectron Microscopy of Macromolecular Assemblies Graduate Course offered at NYSBC Fall 2005

Description: A comprehensive course in the theory and practice of solving molecular structures by electron microscopy. We will start with optics, sample preparation and a basic mathematical description of diffraction before moving into a detailed exploration of the three main methods of structure determination: electron crystallography, single particle analysis, and electron tomography. We will end with a discussion of map interpretation and molecular fitting. This is predominantly a lecture course involving one 2-hour lecture per week accompanied by a discussion session and an occasional practical session using facilities at the New York Structural Biology Center. Lecturers will be given by expert electron microscopists from around NYC and students from various campuses will be encouraged to attend.
Course Director: David Stokes 212-263-1580 stokes@saturn.med.nyu.edu

Added:
>
>		CemCourseAnnounce.pdf: download the CEM course flier

 
Changed:
<
<		PhD students and Postdoctoral fellows are welcome.
>
>		PhD students and Postdoctoral fellows are welcome.
 This course will be listed in the catalogue of the New York University School of Medicine (http://www.med.nyu.edu/sackler/courses). NYU has cooperative agreements that allow students at most other New York institutions to take courses for credit (2 or 3 credits).

Tentative schedule is to offer a 2-hour lecture on Tuesdays from 3:30-5:30. We hope to also offer a discussion session later in the week. Both will be simultaneously broadcast over the web.

Syllabus

Microscope types - Sept 13 or 15 - David Stokes (NYU/NYSBC)

  • TEM
  • SEM
  • STEM
  • contrast mechanisms (ampl vs. phase)
    • elastic vs inelastic scattering
  • x-ray analysis
  • EELS

Optics - Sept 20 or 22 - John Berriman (NYSBC)

  • Lenses, focal lengths, ray tracing,
  • Microscope design
    • light vs. electron microscope
    • objective lens
    • lens configuration for EM
  • aberrations (Cs and Cc)
  • electron source
  • resolution

Sample preparation - Sept 27 or 29 - John Berriman (with practical)

  • 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 - Oct 4 or 6 - Iban Ubarretxena (CCNY)

  • 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

Imaging strategies - Oct 11 or 13 - David Stokes (NYU/NYSBC)

  • radiation damage/section shrinkage
  • detectors (film, CCD, imaging plates)
    • transfer functions & DQE
  • contrast transfer function
    • phase contrast
    • amplitude contrast
  • beam tilt
  • sampling
    • discrete Fourier transform
    • Nyquist sampling frequency
    • aliasing
    • boxing and floating

History of 3D reconstruction - Oct 18 or 20 - David Stokes (NYU/NYSBC)

  • negative stain of viruses
    • model of negative stain
    • matching of projection images
    • quasiequivalence & icosahedral viruses
  • optical diffraction
    • optical filtering

Crystallography I - Oct 25 or 27 - Seth Darst (Rockefeller Univ.)

  • Braggs law
  • real/reciprocal lattice
    • symmetry
      • plane groups & space groups
    • Miller indices
    • lattice lines
  • convolution fcn -> crystal
    • convolution Thm -> reciprocal lattice
  • Projection Thm and radius of Ewald Sphere
  • strategy for 3D recontruction
    • missing cone
Changed:
<
<

Crystallography II & Intro to Single Particle Analysis - Nov 1 or 3 - Iban

>
>

Crystallography II & Intro to Single Particle Analysis - Nov 1 or 3 - Iban Ubarretxena (CCNY)

 
  • 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)
  • Intro to Single Particle Analysis
    • sample considerations (size, homogeneity, internal symmetry
    • useful functions
      • cross correlation
      • radon transform
      • low pass/high pass filters
      • Weiner filter
    • particle picking
    • alignment
    • class averages
    • reconstruction strategies
      • random conical tilt
      • angular reconstitution
    • reconstruction packages (Spider, EMAN, IMAGIC)

Helical reconstruction - Nov 8 or 10 - Hernando Sosa (Albert Einstein College of Medicine)

  • 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
    • real-space averaging
Changed:
<
<

Single Particle Analysis - Nov 15 or 17 - Terry Wagenknecht/Joachim Frank/Rajendra Agrawal (Wadsworth Ctr)

>
>

Single Particle Analysis - Nov 15 or 17 - Joachim Frank (Wadsworth Ctr)

 
  • imaging considerations
    • solid/perforated carbon
    • automated data collection
  • initial model
    • random conical tilt with defined orientations (neg stain)
  • orientation of frozen-hydrated particles with common line analysis
    • projection matching
  • model bias
  • classification and class-averages
  • correspondance analysis
  • refinement
  • CTF correction (Weiner filter)
  • backprojection vs. Fourier synthesis
  • symmetry
  • resolution criteria (Fourier Shell Correlation)
  • programs (Spider, Emen, Imagic)
  • applications
Changed:
<
<

Tomography - Nov 29 or Dec 1 - Mike Marko/Bruce McEwen?/Carmen Mannella (Wadsworth Ctr)

>
>

Tomography - Nov 29 or Dec 1 - Bruce McEwen? (Wadsworth Ctr)

 
  • 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

Molecular fitting - Dec 6 or 8 - Hernando Sosa (Albert 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

-- DavidStokes - 14 Apr 2005

Added:
>
>

META FILEATTACHMENT attr="" comment="CEM course flier" date="1140113010" name="CemCourseAnnounce.pdf" path="CemCourseAnnounce.pdf" size="481908" user="DavidStokes" version="1.1"
 

Revision 227 May 2005 - Main.DavidStokes

 Cryoelectron Microscopy of Macromolecular Assemblies Graduate Course offered at NYSBC Fall 2005

Description: A comprehensive course in the theory and practice of solving molecular structures by electron microscopy. We will start with optics, sample preparation and a basic mathematical description of diffraction before moving into a detailed exploration of the three main methods of structure determination: electron crystallography, single particle analysis, and electron tomography. We will end with a discussion of map interpretation and molecular fitting. This is predominantly a lecture course involving one 2-hour lecture per week accompanied by a discussion session and an occasional practical session using facilities at the New York Structural Biology Center. Lecturers will be given by expert electron microscopists from around NYC and students from various campuses will be encouraged to attend.
Course Director: David Stokes 212-263-1580 stokes@saturn.med.nyu.edu

PhD students and Postdoctoral fellows are welcome.

This course will be listed in the catalogue of the New York University School of Medicine (http://www.med.nyu.edu/sackler/courses). NYU has cooperative agreements that allow students at most other New York institutions to take courses for credit (2 or 3 credits).

Tentative schedule is to offer a 2-hour lecture on Tuesdays from 3:30-5:30. We hope to also offer a discussion session later in the week. Both will be simultaneously broadcast over the web.

Syllabus

Microscope types - Sept 13 or 15 - David Stokes (NYU/NYSBC)

  • TEM
  • SEM
  • STEM
  • contrast mechanisms (ampl vs. phase)
    • elastic vs inelastic scattering
  • x-ray analysis
  • EELS

Optics - Sept 20 or 22 - John Berriman (NYSBC)

  • Lenses, focal lengths, ray tracing,
  • Microscope design
    • light vs. electron microscope
    • objective lens
    • lens configuration for EM
  • aberrations (Cs and Cc)
  • electron source
  • resolution

Sample preparation - Sept 27 or 29 - John Berriman (with practical)

  • 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 - Oct 4 or 6 - Iban Ubarretxena (CCNY)

  • 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

Imaging strategies - Oct 11 or 13 - David Stokes (NYU/NYSBC)

  • radiation damage/section shrinkage
  • detectors (film, CCD, imaging plates)
    • transfer functions & DQE
  • contrast transfer function
    • phase contrast
    • amplitude contrast
  • beam tilt
  • sampling
    • discrete Fourier transform
    • Nyquist sampling frequency
    • aliasing
    • boxing and floating

History of 3D reconstruction - Oct 18 or 20 - David Stokes (NYU/NYSBC)

  • negative stain of viruses
    • model of negative stain
    • matching of projection images
    • quasiequivalence & icosahedral viruses
  • optical diffraction
    • optical filtering

Crystallography I - Oct 25 or 27 - Seth Darst (Rockefeller Univ.)

  • Braggs law
  • real/reciprocal lattice
    • symmetry
      • plane groups & space groups
    • Miller indices
    • lattice lines
  • convolution fcn -> crystal
    • convolution Thm -> reciprocal lattice
  • Projection Thm and radius of Ewald Sphere
  • strategy for 3D recontruction
    • missing cone
Changed:
<
<

Crystallography II - Nov 1 or 3 - Iban Ubarretxena (CCNY)

>
>

Crystallography II & Intro to Single Particle Analysis - Nov 1 or 3 - Iban

 
  • 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)
Added:
>
>
  • Intro to Single Particle Analysis
    • sample considerations (size, homogeneity, internal symmetry
    • useful functions
      • cross correlation
      • radon transform
      • low pass/high pass filters
      • Weiner filter
    • particle picking
    • alignment
    • class averages
    • reconstruction strategies
      • random conical tilt
      • angular reconstitution
    • reconstruction packages (Spider, EMAN, IMAGIC)
 

Helical reconstruction - Nov 8 or 10 - Hernando Sosa (Albert Einstein College of Medicine)

  • 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
    • real-space averaging

Single Particle Analysis - Nov 15 or 17 - Terry Wagenknecht/Joachim Frank/Rajendra Agrawal (Wadsworth Ctr)

  • imaging considerations
    • solid/perforated carbon
    • automated data collection
  • initial model
    • random conical tilt with defined orientations (neg stain)
  • orientation of frozen-hydrated particles with common line analysis
    • projection matching
  • model bias
  • classification and class-averages
  • correspondance analysis
  • refinement
  • CTF correction (Weiner filter)
  • backprojection vs. Fourier synthesis
  • symmetry
  • resolution criteria (Fourier Shell Correlation)
  • programs (Spider, Emen, Imagic)
  • applications

Tomography - Nov 29 or Dec 1 - Mike Marko/Bruce McEwen?/Carmen Mannella (Wadsworth Ctr)

  • 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

Molecular fitting - Dec 6 or 8 - Hernando Sosa (Albert 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

-- DavidStokes - 14 Apr 2005

Revision 126 May 2005 - Main.DavidStokes

 Cryoelectron Microscopy of Macromolecular Assemblies Graduate Course offered at NYSBC Fall 2005

Description: A comprehensive course in the theory and practice of solving molecular structures by electron microscopy. We will start with optics, sample preparation and a basic mathematical description of diffraction before moving into a detailed exploration of the three main methods of structure determination: electron crystallography, single particle analysis, and electron tomography. We will end with a discussion of map interpretation and molecular fitting. This is predominantly a lecture course involving one 2-hour lecture per week accompanied by a discussion session and an occasional practical session using facilities at the New York Structural Biology Center. Lecturers will be given by expert electron microscopists from around NYC and students from various campuses will be encouraged to attend.
Course Director: David Stokes 212-263-1580 stokes@saturn.med.nyu.edu

PhD students and Postdoctoral fellows are welcome.

This course will be listed in the catalogue of the New York University School of Medicine (http://www.med.nyu.edu/sackler/courses). NYU has cooperative agreements that allow students at most other New York institutions to take courses for credit (2 or 3 credits).

Tentative schedule is to offer a 2-hour lecture on Tuesdays from 3:30-5:30. We hope to also offer a discussion session later in the week. Both will be simultaneously broadcast over the web.

Syllabus

Microscope types - Sept 13 or 15 - David Stokes (NYU/NYSBC)

  • TEM
  • SEM
  • STEM
  • contrast mechanisms (ampl vs. phase)
    • elastic vs inelastic scattering
  • x-ray analysis
  • EELS

Optics - Sept 20 or 22 - John Berriman (NYSBC)

  • Lenses, focal lengths, ray tracing,
  • Microscope design
    • light vs. electron microscope
    • objective lens
    • lens configuration for EM
  • aberrations (Cs and Cc)
  • electron source
  • resolution

Sample preparation - Sept 27 or 29 - John Berriman (with practical)

  • 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 - Oct 4 or 6 - Iban Ubarretxena (CCNY)

  • 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

Imaging strategies - Oct 11 or 13 - David Stokes (NYU/NYSBC)

  • radiation damage/section shrinkage
  • detectors (film, CCD, imaging plates)
    • transfer functions & DQE
  • contrast transfer function
    • phase contrast
    • amplitude contrast
  • beam tilt
  • sampling
    • discrete Fourier transform
    • Nyquist sampling frequency
    • aliasing
    • boxing and floating

History of 3D reconstruction - Oct 18 or 20 - David Stokes (NYU/NYSBC)

  • negative stain of viruses
    • model of negative stain
    • matching of projection images
    • quasiequivalence & icosahedral viruses
  • optical diffraction
    • optical filtering

Crystallography I - Oct 25 or 27 - Seth Darst (Rockefeller Univ.)

  • Braggs law
  • real/reciprocal lattice
    • symmetry
      • plane groups & space groups
    • Miller indices
    • lattice lines
  • convolution fcn -> crystal
    • convolution Thm -> reciprocal lattice
  • Projection Thm and radius of Ewald Sphere
  • strategy for 3D recontruction
    • missing cone

Crystallography II - Nov 1 or 3 - Iban Ubarretxena (CCNY)

  • 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 - Nov 8 or 10 - Hernando Sosa (Albert Einstein College of Medicine)

  • 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
    • real-space averaging

Single Particle Analysis - Nov 15 or 17 - Terry Wagenknecht/Joachim Frank/Rajendra Agrawal (Wadsworth Ctr)

  • imaging considerations
    • solid/perforated carbon
    • automated data collection
  • initial model
    • random conical tilt with defined orientations (neg stain)
  • orientation of frozen-hydrated particles with common line analysis
    • projection matching
  • model bias
  • classification and class-averages
  • correspondance analysis
  • refinement
  • CTF correction (Weiner filter)
  • backprojection vs. Fourier synthesis
  • symmetry
  • resolution criteria (Fourier Shell Correlation)
  • programs (Spider, Emen, Imagic)
  • applications

Tomography - Nov 29 or Dec 1 - Mike Marko/Bruce McEwen?/Carmen Mannella (Wadsworth Ctr)

  • 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

Molecular fitting - Dec 6 or 8 - Hernando Sosa (Albert 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

-- DavidStokes - 14 Apr 2005

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