Course Information

C9940 3-Dimensional Transmission Electron Microscopy (3DEM)

Extent and Intensity

2/0/2. 2 credit(s) (plus extra credits for completion). Type of Completion: zk (examination).
In-person direct teaching

Teacher(s)

Ing. Tibor Füzik, Ph.D. (lecturer)
Mgr. Jiří Nováček, Ph.D. (lecturer)
ing. Ondřej Sháněl, Ph.D. (lecturer), Mgr. Jiří Nováček, Ph.D. (deputy)

Guaranteed by

Mgr. Jiří Nováček, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science

Prerequisites

FB820

Course Enrolment Limitations

The course is offered to students of any study field.

Course objectives

The course will comprise lectures on advanced topics in the field of life-science (cryo-)electron microscopy (cryo-EM). The course will provide practical in-depth insight into advanced sample preparation approaches, provide detailed information about electron miscroscope construction, principles of image formation and data acquisition, and will focus on the advanced methods of cryo-EM and cryo-electron tomography data analysis.

Learning outcomes

Following the successful completion of the course, the students shall be capable: - select optimal strategy to solve different biological problems using electron microscopy - understand the principles of electron microscopy - understand the functionality of the electron microscope - analyze single particle cryo-EM data - analyze cryo-electron tomography data

Syllabus

• 1. Advanced sample preparation approaches
• 2. Propagation of electron wave through the microscope
• 3. Mechanisms of contrast formation in transmission and scanning electron microscopy
• 5. Image aberrations, image analysis in 2D
• 6. Scanning transmission electron microscopy, energy dispersive x-ray spectroscopy, zero-loss imaging, EELS
• 7. electron diffraction tomography, dark-field imaging, FIB/SEM microscopy
• 8. Practical aspects of single particle analysis
• 9. Practical aspects of cryo-electron tomography and sub-volume averaging

Teaching methods

Lectures, practicals

Assessment methods

Semester work, written examination

Language of instruction

English

Further Comments

The course is taught annually.
The course is taught: in blocks.

C9940 3-Dimensional Transmission Electron Microscopy (3DEM)

Extent and Intensity

2/0/2. 2 credit(s) (plus extra credits for completion). Type of Completion: zk (examination).

Teacher(s)

Ing. Tibor Füzik, Ph.D. (lecturer)
Mgr. Jiří Nováček, Ph.D. (lecturer)
ing. Ondřej Sháněl, Ph.D. (lecturer), Mgr. Jiří Nováček, Ph.D. (deputy)

Guaranteed by

Mgr. Jiří Nováček, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science

Prerequisites

FB820

Course Enrolment Limitations

The course is offered to students of any study field.

Course objectives

The course will comprise lectures on advanced topics in the field of life-science (cryo-)electron microscopy (cryo-EM). The course will provide practical in-depth insight into advanced sample preparation approaches, provide detailed information about electron miscroscope construction, principles of image formation and data acquisition, and will focus on the advanced methods of cryo-EM and cryo-electron tomography data analysis.

Learning outcomes

Following the successful completion of the course, the students shall be capable: - select optimal strategy to solve different biological problems using electron microscopy - understand the principles of electron microscopy - understand the functionality of the electron microscope - analyze single particle cryo-EM data - analyze cryo-electron tomography data

Syllabus

• 1. Advanced sample preparation approaches
• 2. Propagation of electron wave through the microscope
• 3. Mechanisms of contrast formation in transmission and scanning electron microscopy
• 5. Image aberrations, image analysis in 2D
• 6. Scanning transmission electron microscopy, energy dispersive x-ray spectroscopy, zero-loss imaging, EELS
• 7. electron diffraction tomography, dark-field imaging, FIB/SEM microscopy
• 8. Practical aspects of single particle analysis
• 9. Practical aspects of cryo-electron tomography and sub-volume averaging

Teaching methods

Lectures, practicals

Assessment methods

Semester work, written examination

Language of instruction

English

Further Comments

The course is taught annually.
The course is taught: in blocks.

C9940 3-Dimensional Transmission Electron Microscopy (3DEM)

Extent and Intensity

2/0/2. 2 credit(s) (plus extra credits for completion). Type of Completion: zk (examination).

Teacher(s)

Mgr. Jiří Nováček, Ph.D. (lecturer)
Dr. rer. nat. Jürgen Plitzko (lecturer)
Dr. Tanvir Shaikh (lecturer)

Guaranteed by

prof. RNDr. Vladimír Sklenář, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science

Course Enrolment Limitations

The course is offered to students of any study field.

Course objectives

Transmission electron microscopy (TEM) in its various flavours is nowadays an established characterization tool for structures in life as well as in material science. Especially in todays ‘nano-world’ it is, by and large the only technique for an in-depth visual investigations at the nanometer scale and even in the sub-nanometer regime. The study of complex materials and hybrid compounds, and their interfaces and defects by TEM was and is a major focus in material science. Moreover, three-dimensional (3D) electron microscopy (3DEM) has a particularly important role in the repertoire of techniques strcutural biologists use for probing the structure and functions of molecules and macromolecular complexes in their functional cellular context. 3DEM in life sciences comprises three major branches: cryo-electron crystallography, cryo-electron microscopy of purified single particles (where ‘particles’ stand for proteins and macromolecular complexes) and cryo-electron tomography (the three dimensional investigation of any non periodic - ‘pleiomorphic’ - object). This course will explain the basics of transmission electron microscopy, electron tomography and single particle cryo-EM. It will include the experimental setups and instrumental prerequisites for 3D work, and their actual implementation. Specimen preparation methods suited for biological applications will be described and explained in detail. Since all tomographic methods are based on different reconstruction algorithms, and elaborate image processing and visualization routines, they will be included in this tutorial as well. At the end of the course students should understand the principles of structural analysis by TEM and its application in chemistry, biochemistry, structural biology, biophysics and materials science.

Syllabus

• 1. Introduction: TEM history and contemporary trends - applications of TEM to structural studies. 2. Introduction to electron optics, image formation, diffraction and automation. 3. Specimen preparation, negative stain, thin-film vitrification, high-pressure freezing, cryo-sectioning and modern micromachining methods. 4. Radiation effects; Introduction to image analysis; Sources of noise. 5. Principle and background of Fourier analysis, contrast transfer function (CTF), convolution and cross-correlation. 6. Electron tomography. 7. Principles of image analysis and 3D reconstruction methods 8. Single Particle analysis and image processing 9. 3D Visualization methods 10. Hybrid Methods: Combining X-ray crystallography and cryo-EM, combining light-microscopy and cryo-EM

Teaching methods

Lectures, seminars and tutorials

Assessment methods

Oral examination

Language of instruction

English

Further Comments

Study Materials
The course is taught annually.
The course is taught: in blocks.

C9940 3-Dimensional Transmission Electron Microscopy (3DEM)

Extent and Intensity

2/0/2. 2 credit(s) (plus extra credits for completion). Type of Completion: zk (examination).

Teacher(s)

Mgr. Jiří Nováček, Ph.D. (lecturer)
Dr. rer. nat. Jürgen Plitzko (lecturer)
Dr. Tanvir Shaikh (lecturer)

Guaranteed by

prof. RNDr. Vladimír Sklenář, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science

Course Enrolment Limitations

The course is offered to students of any study field.

Course objectives

Transmission electron microscopy (TEM) in its various flavours is nowadays an established characterization tool for structures in life as well as in material science. Especially in todays ‘nano-world’ it is, by and large the only technique for an in-depth visual investigations at the nanometer scale and even in the sub-nanometer regime. The study of complex materials and hybrid compounds, and their interfaces and defects by TEM was and is a major focus in material science. Moreover, three-dimensional (3D) electron microscopy (3DEM) has a particularly important role in the repertoire of techniques strcutural biologists use for probing the structure and functions of molecules and macromolecular complexes in their functional cellular context. 3DEM in life sciences comprises three major branches: cryo-electron crystallography, cryo-electron microscopy of purified single particles (where ‘particles’ stand for proteins and macromolecular complexes) and cryo-electron tomography (the three dimensional investigation of any non periodic - ‘pleiomorphic’ - object). This course will explain the basics of transmission electron microscopy, electron tomography and single particle cryo-EM. It will include the experimental setups and instrumental prerequisites for 3D work, and their actual implementation. Specimen preparation methods suited for biological applications will be described and explained in detail. Since all tomographic methods are based on different reconstruction algorithms, and elaborate image processing and visualization routines, they will be included in this tutorial as well. At the end of the course students should understand the principles of structural analysis by TEM and its application in chemistry, biochemistry, structural biology, biophysics and materials science.

Syllabus

• 1. Introduction: TEM history and contemporary trends - applications of TEM to structural studies. 2. Introduction to electron optics, image formation, diffraction and automation. 3. Specimen preparation, negative stain, thin-film vitrification, high-pressure freezing, cryo-sectioning and modern micromachining methods. 4. Radiation effects; Introduction to image analysis; Sources of noise. 5. Principle and background of Fourier analysis, contrast transfer function (CTF), convolution and cross-correlation. 6. Electron tomography. 7. Principles of image analysis and 3D reconstruction methods 8. Single Particle analysis and image processing 9. 3D Visualization methods 10. Hybrid Methods: Combining X-ray crystallography and cryo-EM, combining light-microscopy and cryo-EM

Teaching methods

Lectures, seminars and tutorials

Assessment methods

Oral examination

Language of instruction

English

Further Comments

Study Materials
The course is taught annually.
The course is taught: in blocks.

C9940 3-Dimensional Transmission Electron Microscopy (3DEM)

Extent and Intensity

2/0/2. 2 credit(s) (plus extra credits for completion). Type of Completion: zk (examination).

Teacher(s)

Mgr. Jiří Nováček, Ph.D. (lecturer)
Dr. rer. nat. Jürgen Plitzko (lecturer)
Dr. Tanvir Shaikh (lecturer)

Guaranteed by

prof. RNDr. Vladimír Sklenář, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science

Course Enrolment Limitations

The course is offered to students of any study field.

Course objectives

Transmission electron microscopy (TEM) in its various flavours is nowadays an established characterization tool for structures in life as well as in material science. Especially in todays ‘nano-world’ it is, by and large the only technique for an in-depth visual investigations at the nanometer scale and even in the sub-nanometer regime. The study of complex materials and hybrid compounds, and their interfaces and defects by TEM was and is a major focus in material science. Moreover, three-dimensional (3D) electron microscopy (3DEM) has a particularly important role in the repertoire of techniques strcutural biologists use for probing the structure and functions of molecules and macromolecular complexes in their functional cellular context. 3DEM in life sciences comprises three major branches: cryo-electron crystallography, cryo-electron microscopy of purified single particles (where ‘particles’ stand for proteins and macromolecular complexes) and cryo-electron tomography (the three dimensional investigation of any non periodic - ‘pleiomorphic’ - object). This course will explain the basics of transmission electron microscopy, electron tomography and single particle cryo-EM. It will include the experimental setups and instrumental prerequisites for 3D work, and their actual implementation. Specimen preparation methods suited for biological applications will be described and explained in detail. Since all tomographic methods are based on different reconstruction algorithms, and elaborate image processing and visualization routines, they will be included in this tutorial as well. At the end of the course students should understand the principles of structural analysis by TEM and its application in chemistry, biochemistry, structural biology, biophysics and materials science.

Syllabus

• 1. Introduction: TEM history and contemporary trends - applications of TEM to structural studies. 2. Introduction to electron optics, image formation, diffraction and automation. 3. Specimen preparation, negative stain, thin-film vitrification, high-pressure freezing, cryo-sectioning and modern micromachining methods. 4. Radiation effects; Introduction to image analysis; Sources of noise. 5. Principle and background of Fourier analysis, contrast transfer function (CTF), convolution and cross-correlation. 6. Electron tomography. 7. Principles of image analysis and 3D reconstruction methods 8. Single Particle analysis and image processing 9. 3D Visualization methods 10. Hybrid Methods: Combining X-ray crystallography and cryo-EM, combining light-microscopy and cryo-EM

Teaching methods

Lectures, seminars and tutorials

Assessment methods

Oral examination

Language of instruction

English

Further Comments

Study Materials
The course is taught annually.
The course is taught: in blocks.

C9940 3-Dimensional Transmission Electron Microscopy (3DEM)

Extent and Intensity

2/0/2. 2 credit(s) (plus extra credits for completion). Type of Completion: zk (examination).

Teacher(s)

Mgr. Jiří Nováček, Ph.D. (lecturer)
Dr. rer. nat. Jürgen Plitzko (lecturer)
Dr. Tanvir Shaikh (lecturer)

Guaranteed by

prof. RNDr. Vladimír Sklenář, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science

Course Enrolment Limitations

The course is offered to students of any study field.

Course objectives

Transmission electron microscopy (TEM) in its various flavours is nowadays an established characterization tool for structures in life as well as in material science. Especially in todays ‘nano-world’ it is, by and large the only technique for an in-depth visual investigations at the nanometer scale and even in the sub-nanometer regime. The study of complex materials and hybrid compounds, and their interfaces and defects by TEM was and is a major focus in material science. Moreover, three-dimensional (3D) electron microscopy (3DEM) has a particularly important role in the repertoire of techniques strcutural biologists use for probing the structure and functions of molecules and macromolecular complexes in their functional cellular context. 3DEM in life sciences comprises three major branches: cryo-electron crystallography, cryo-electron microscopy of purified single particles (where ‘particles’ stand for proteins and macromolecular complexes) and cryo-electron tomography (the three dimensional investigation of any non periodic - ‘pleiomorphic’ - object). This course will explain the basics of transmission electron microscopy, electron tomography and single particle cryo-EM. It will include the experimental setups and instrumental prerequisites for 3D work, and their actual implementation. Specimen preparation methods suited for biological applications will be described and explained in detail. Since all tomographic methods are based on different reconstruction algorithms, and elaborate image processing and visualization routines, they will be included in this tutorial as well. At the end of the course students should understand the principles of structural analysis by TEM and its application in chemistry, biochemistry, structural biology, biophysics and materials science.

Syllabus

• 1. Introduction: TEM history and contemporary trends - applications of TEM to structural studies. 2. Introduction to electron optics, image formation, diffraction and automation. 3. Specimen preparation, negative stain, thin-film vitrification, high-pressure freezing, cryo-sectioning and modern micromachining methods. 4. Radiation effects; Introduction to image analysis; Sources of noise. 5. Principle and background of Fourier analysis, contrast transfer function (CTF), convolution and cross-correlation. 6. Electron tomography. 7. Principles of image analysis and 3D reconstruction methods 8. Single Particle analysis and image processing 9. 3D Visualization methods 10. Hybrid Methods: Combining X-ray crystallography and cryo-EM, combining light-microscopy and cryo-EM

Teaching methods

Lectures, seminars and tutorials

Assessment methods

Oral examination

Language of instruction

English

Further Comments

The course is taught annually.
The course is taught: in blocks.

C9940 3-Dimensional Transmission Electron Microscopy (3DEM)

Extent and Intensity

2/0/2. 2 credit(s) (plus extra credits for completion). Type of Completion: zk (examination).

Teacher(s)

Mgr. Jiří Nováček, Ph.D. (lecturer)
Dr. rer. nat. Jürgen Plitzko (lecturer)
Dr. Tanvir Shaikh (lecturer)

Guaranteed by

prof. RNDr. Vladimír Sklenář, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science

Course Enrolment Limitations

The course is offered to students of any study field.

Course objectives

Transmission electron microscopy (TEM) in its various flavours is nowadays an established characterization tool for structures in life as well as in material science. Especially in todays ‘nano-world’ it is, by and large the only technique for an in-depth visual investigations at the nanometer scale and even in the sub-nanometer regime. The study of complex materials and hybrid compounds, and their interfaces and defects by TEM was and is a major focus in material science. Moreover, three-dimensional (3D) electron microscopy (3DEM) has a particularly important role in the repertoire of techniques strcutural biologists use for probing the structure and functions of molecules and macromolecular complexes in their functional cellular context. 3DEM in life sciences comprises three major branches: cryo-electron crystallography, cryo-electron microscopy of purified single particles (where ‘particles’ stand for proteins and macromolecular complexes) and cryo-electron tomography (the three dimensional investigation of any non periodic - ‘pleiomorphic’ - object). This course will explain the basics of transmission electron microscopy, electron tomography and single particle cryo-EM. It will include the experimental setups and instrumental prerequisites for 3D work, and their actual implementation. Specimen preparation methods suited for biological applications will be described and explained in detail. Since all tomographic methods are based on different reconstruction algorithms, and elaborate image processing and visualization routines, they will be included in this tutorial as well. At the end of the course students should understand the principles of structural analysis by TEM and its application in chemistry, biochemistry, structural biology, biophysics and materials science.

Syllabus

• 1. Introduction: TEM history and contemporary trends - applications of TEM to structural studies. 2. Introduction to electron optics, image formation, diffraction and automation. 3. Specimen preparation, negative stain, thin-film vitrification, high-pressure freezing, cryo-sectioning and modern micromachining methods. 4. Radiation effects; Introduction to image analysis; Sources of noise. 5. Principle and background of Fourier analysis, contrast transfer function (CTF), convolution and cross-correlation. 6. Electron tomography. 7. Principles of image analysis and 3D reconstruction methods 8. Single Particle analysis and image processing 9. 3D Visualization methods 10. Hybrid Methods: Combining X-ray crystallography and cryo-EM, combining light-microscopy and cryo-EM

Teaching methods

Lectures, seminars and tutorials

Assessment methods

Oral examination

Language of instruction

English

Further Comments

Study Materials
The course is taught annually.
The course is taught: in blocks.

C9940 3-Dimensional Transmission Electron Microscopy (3DEM)

Extent and Intensity

2/0/2. 2 credit(s) (plus extra credits for completion). Type of Completion: zk (examination).

Teacher(s)

Mgr. Jiří Nováček, Ph.D. (lecturer)
Dr. rer. nat. Jürgen Plitzko (lecturer)
Dr. Tanvir Shaikh (lecturer)

Guaranteed by

prof. RNDr. Vladimír Sklenář, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science

Course Enrolment Limitations

The course is offered to students of any study field.

Course objectives

Transmission electron microscopy (TEM) in its various flavours is nowadays an established characterization tool for structures in life as well as in material science. Especially in todays ‘nano-world’ it is, by and large the only technique for an in-depth visual investigations at the nanometer scale and even in the sub-nanometer regime. The study of complex materials and hybrid compounds, and their interfaces and defects by TEM was and is a major focus in material science. Moreover, three-dimensional (3D) electron microscopy (3DEM) has a particularly important role in the repertoire of techniques strcutural biologists use for probing the structure and functions of molecules and macromolecular complexes in their functional cellular context. 3DEM in life sciences comprises three major branches: cryo-electron crystallography, cryo-electron microscopy of purified single particles (where ‘particles’ stand for proteins and macromolecular complexes) and cryo-electron tomography (the three dimensional investigation of any non periodic - ‘pleiomorphic’ - object). This course will explain the basics of transmission electron microscopy, electron tomography and single particle cryo-EM. It will include the experimental setups and instrumental prerequisites for 3D work, and their actual implementation. Specimen preparation methods suited for biological applications will be described and explained in detail. Since all tomographic methods are based on different reconstruction algorithms, and elaborate image processing and visualization routines, they will be included in this tutorial as well. At the end of the course students should understand the principles of structural analysis by TEM and its application in chemistry, biochemistry, structural biology, biophysics and materials science.

Syllabus

• 1. Introduction: TEM history and contemporary trends - applications of TEM to structural studies. 2. Introduction to electron optics, image formation, diffraction and automation. 3. Specimen preparation, negative stain, thin-film vitrification, high-pressure freezing, cryo-sectioning and modern micromachining methods. 4. Radiation effects; Introduction to image analysis; Sources of noise. 5. Principle and background of Fourier analysis, contrast transfer function (CTF), convolution and cross-correlation. 6. Electron tomography. 7. Principles of image analysis and 3D reconstruction methods 8. Single Particle analysis and image processing 9. 3D Visualization methods 10. Hybrid Methods: Combining X-ray crystallography and cryo-EM, combining light-microscopy and cryo-EM

Teaching methods

Lectures, seminars and tutorials

Assessment methods

Oral examination

Language of instruction

English

Further Comments

Study Materials
The course is taught annually.
The course is taught: in blocks.

C9940 3-Dimensional Transmission Electron Microscopy (3DEM)

Extent and Intensity

2/0/2. 2 credit(s) (plus extra credits for completion). Type of Completion: zk (examination).

Teacher(s)

Mgr. Jiří Nováček, Ph.D. (lecturer)
Dr. rer. nat. Jürgen Plitzko (lecturer)
Dr. Tanvir Shaikh (lecturer)

Guaranteed by

prof. RNDr. Vladimír Sklenář, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science

Timetable

Mon 20. 2. to Mon 22. 5. Mon 14:00–15:50 E35/211

Course Enrolment Limitations

The course is offered to students of any study field.

Course objectives

Transmission electron microscopy (TEM) in its various flavours is nowadays an established characterization tool for structures in life as well as in material science. Especially in todays ‘nano-world’ it is, by and large the only technique for an in-depth visual investigations at the nanometer scale and even in the sub-nanometer regime. The study of complex materials and hybrid compounds, and their interfaces and defects by TEM was and is a major focus in material science. Moreover, three-dimensional (3D) electron microscopy (3DEM) has a particularly important role in the repertoire of techniques strcutural biologists use for probing the structure and functions of molecules and macromolecular complexes in their functional cellular context. 3DEM in life sciences comprises three major branches: cryo-electron crystallography, cryo-electron microscopy of purified single particles (where ‘particles’ stand for proteins and macromolecular complexes) and cryo-electron tomography (the three dimensional investigation of any non periodic - ‘pleiomorphic’ - object). This course will explain the basics of transmission electron microscopy, electron tomography and single particle cryo-EM. It will include the experimental setups and instrumental prerequisites for 3D work, and their actual implementation. Specimen preparation methods suited for biological applications will be described and explained in detail. Since all tomographic methods are based on different reconstruction algorithms, and elaborate image processing and visualization routines, they will be included in this tutorial as well. At the end of the course students should understand the principles of structural analysis by TEM and its application in chemistry, biochemistry, structural biology, biophysics and materials science.

Syllabus

• 1. Introduction: TEM history and contemporary trends - applications of TEM to structural studies. 2. Introduction to electron optics, image formation, diffraction and automation. 3. Specimen preparation, negative stain, thin-film vitrification, high-pressure freezing, cryo-sectioning and modern micromachining methods. 4. Radiation effects; Introduction to image analysis; Sources of noise. 5. Principle and background of Fourier analysis, contrast transfer function (CTF), convolution and cross-correlation. 6. Electron tomography. 7. Principles of image analysis and 3D reconstruction methods 8. Single Particle analysis and image processing 9. 3D Visualization methods 10. Hybrid Methods: Combining X-ray crystallography and cryo-EM, combining light-microscopy and cryo-EM

Teaching methods

Lectures, seminars and tutorials

Assessment methods

Oral examination

Language of instruction

English

Further Comments

Study Materials
The course is taught annually.

C9940 3-Dimensional Transmission Electron Microscopy (3DEM)

Extent and Intensity

2/0/2. 2 credit(s) (plus extra credits for completion). Type of Completion: zk (examination).

Teacher(s)

Mgr. Jiří Nováček, Ph.D. (lecturer)
Dr. rer. nat. Jürgen Plitzko (lecturer)
Dr. Tanvir Shaikh (lecturer)

Guaranteed by

prof. RNDr. Vladimír Sklenář, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science

Timetable

Mon 14:30–16:30 E35/211

Course Enrolment Limitations

The course is offered to students of any study field.

Course objectives

Transmission electron microscopy (TEM) in its various flavours is nowadays an established characterization tool for structures in life as well as in material science. Especially in todays ‘nano-world’ it is, by and large the only technique for an in-depth visual investigations at the nanometer scale and even in the sub-nanometer regime. The study of complex materials and hybrid compounds, and their interfaces and defects by TEM was and is a major focus in material science. Moreover, three-dimensional (3D) electron microscopy (3DEM) has a particularly important role in the repertoire of techniques strcutural biologists use for probing the structure and functions of molecules and macromolecular complexes in their functional cellular context. 3DEM in life sciences comprises three major branches: cryo-electron crystallography, cryo-electron microscopy of purified single particles (where ‘particles’ stand for proteins and macromolecular complexes) and cryo-electron tomography (the three dimensional investigation of any non periodic - ‘pleiomorphic’ - object). This course will explain the basics of transmission electron microscopy, electron tomography and single particle cryo-EM. It will include the experimental setups and instrumental prerequisites for 3D work, and their actual implementation. Specimen preparation methods suited for biological applications will be described and explained in detail. Since all tomographic methods are based on different reconstruction algorithms, and elaborate image processing and visualization routines, they will be included in this tutorial as well. At the end of the course students should understand the principles of structural analysis by TEM and its application in chemistry, biochemistry, structural biology, biophysics and materials science.

Syllabus

• 1. Introduction: TEM history and contemporary trends - applications of TEM to structural studies. 2. Introduction to electron optics, image formation, diffraction and automation. 3. Specimen preparation, negative stain, thin-film vitrification, high-pressure freezing, cryo-sectioning and modern micromachining methods. 4. Radiation effects; Introduction to image analysis; Sources of noise. 5. Principle and background of Fourier analysis, contrast transfer function (CTF), convolution and cross-correlation. 6. Electron tomography. 7. Principles of image analysis and 3D reconstruction methods 8. Single Particle analysis and image processing 9. 3D Visualization methods 10. Hybrid Methods: Combining X-ray crystallography and cryo-EM, combining light-microscopy and cryo-EM

Teaching methods

Lectures, seminars and tutorials

Assessment methods

Oral examination

Language of instruction

English

Further Comments

Study Materials
The course is taught annually.

C9940 3-Dimensional Transmission Electron Microscopy (3DEM)

Extent and Intensity

2/0/2. 2 credit(s) (plus extra credits for completion). Type of Completion: zk (examination).

Teacher(s)

RNDr. Daniel Němeček, Ph.D. (lecturer)
Dr. Tanvir Shaikh (lecturer)
Dr. rer. nat. Jürgen Plitzko (lecturer)

Guaranteed by

prof. RNDr. Vladimír Sklenář, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science

Timetable

Mon 14:00–15:50 E35/211

Course Enrolment Limitations

The course is offered to students of any study field.

Course objectives

Transmission electron microscopy (TEM) in its various flavours is nowadays an established characterization tool for structures in life as well as in material science. Especially in todays ‘nano-world’ it is, by and large the only technique for an in-depth visual investigations at the nanometer scale and even in the sub-nanometer regime. The study of complex materials and hybrid compounds, and their interfaces and defects by TEM was and is a major focus in material science. Moreover, three-dimensional (3D) electron microscopy (3DEM) has a particularly important role in the repertoire of techniques strcutural biologists use for probing the structure and functions of molecules and macromolecular complexes in their functional cellular context. 3DEM in life sciences comprises three major branches: cryo-electron crystallography, cryo-electron microscopy of purified single particles (where ‘particles’ stand for proteins and macromolecular complexes) and cryo-electron tomography (the three dimensional investigation of any non periodic - ‘pleiomorphic’ - object). This course will explain the basics of transmission electron microscopy, electron tomography and single particle cryo-EM. It will include the experimental setups and instrumental prerequisites for 3D work, and their actual implementation. Specimen preparation methods suited for biological applications will be described and explained in detail. Since all tomographic methods are based on different reconstruction algorithms, and elaborate image processing and visualization routines, they will be included in this tutorial as well. At the end of the course students should understand the principles of structural analysis by TEM and its application in chemistry, biochemistry, structural biology, biophysics and materials science.

Syllabus

• 1. Introduction: TEM history and contemporary trends - applications of TEM to structural studies. 2. Introduction to electron optics, image formation, diffraction and automation. 3. Specimen preparation, negative stain, thin-film vitrification, high-pressure freezing, cryo-sectioning and modern micromachining methods. 4. Radiation effects; Introduction to image analysis; Sources of noise. 5. Principle and background of Fourier analysis, contrast transfer function (CTF), convolution and cross-correlation. 6. Electron tomography. 7. Principles of image analysis and 3D reconstruction methods 8. Single Particle analysis and image processing 9. 3D Visualization methods 10. Hybrid Methods: Combining X-ray crystallography and cryo-EM, combining light-microscopy and cryo-EM

Teaching methods

Lectures, seminars and tutorials

Assessment methods

Oral examination

Language of instruction

English

Further Comments

Study Materials
The course is taught annually.

C9940 3-Dimensional Transmission Electron Microscopy (3DEM)

Extent and Intensity

2/0/2. Type of Completion: zk (examination).

Teacher(s)

Dr. rer. nat. Jürgen Plitzko (lecturer)

Guaranteed by

prof. RNDr. Vladimír Sklenář, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science

Timetable

Tue 14:00–15:50 C04/211, Thu 14:00–15:50 C04/118

Course Enrolment Limitations

The course is offered to students of any study field.

Course objectives

Transmission electron microscopy (TEM) in its various flavours is nowadays an established characterization tool for structures in life as well as in material science. Especially in todays ‘nano-world’ it is, by and large the only technique for an in-depth visual investigations at the nanometer scale and even in the sub-nanometer regime. The study of complex materials and hybrid compounds, and their interfaces and defects by TEM was and is a major focus in material science. Moreover, three-dimensional (3D) electron microscopy (3DEM) has a particularly important role in the repertoire of techniques strcutural biologists use for probing the structure and functions of molecules and macromolecular complexes in their functional cellular context. 3DEM in life sciences comprises three major branches: cryo-electron crystallography, cryo-electron microscopy of purified single particles (where ‘particles’ stand for proteins and macromolecular complexes) and cryo-electron tomography (the three dimensional investigation of any non periodic - ‘pleiomorphic’ - object). This course will explain the basics of transmission electron microscopy, electron tomography and single particle cryo-EM. It will include the experimental setups and instrumental prerequisites for 3D work, and their actual implementation. Specimen preparation methods suited for biological applications will be described and explained in detail. Since all tomographic methods are based on different reconstruction algorithms, and elaborate image processing and visualization routines, they will be included in this tutorial as well. At the end of the course students should understand the principles of structural analysis by TEM and its application in chemistry, biochemistry, structural biology, biophysics and materials science.

Syllabus

• 1. Introduction: TEM history and contemporary trends - applications of TEM to structural studies. 2. Introduction to electron optics, image formation, diffraction and automation. 3. Specimen preparation, negative stain, thin-film vitrification, high-pressure freezing, cryo-sectioning and modern micromachining methods. 4. Radiation effects; Introduction to image analysis; Sources of noise. 5. Principle and background of Fourier analysis, contrast transfer function (CTF), convolution and cross-correlation. 6. Electron tomography. 7. Principles of image analysis and 3D reconstruction methods 8. Single Particle analysis and image processing 9. 3D Visualization methods 10. Hybrid Methods: Combining X-ray crystallography and cryo-EM, combining light-microscopy and cryo-EM

Teaching methods

Lectures, seminars and tutorials

Assessment methods

Oral examination

Language of instruction

English

Further Comments

The course is taught annually.

C9940 3-Dimensional Transmission Electron Microscopy (3DEM)

Extent and Intensity

2/0/2. Type of Completion: zk (examination).

Teacher(s)

Dr. rer. nat. Jürgen Plitzko (lecturer)

Guaranteed by

prof. RNDr. Vladimír Sklenář, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science

Course Enrolment Limitations

The course is offered to students of any study field.

Course objectives

Transmission electron microscopy (TEM) in its various flavours is nowadays an established characterization tool for structures in life as well as in material science. Especially in todays ‘nano-world’ it is, by and large the only technique for an in-depth visual investigations at the nanometer scale and even in the sub-nanometer regime. The study of complex materials and hybrid compounds, and their interfaces and defects by TEM was and is a major focus in material science. Moreover, three-dimensional (3D) electron microscopy (3DEM) has a particularly important role in the repertoire of techniques strcutural biologists use for probing the structure and functions of molecules and macromolecular complexes in their functional cellular context. 3DEM in life sciences comprises three major branches: cryo-electron crystallography, cryo-electron microscopy of purified single particles (where ‘particles’ stand for proteins and macromolecular complexes) and cryo-electron tomography (the three dimensional investigation of any non periodic - ‘pleiomorphic’ - object). This course will explain the basics of transmission electron microscopy, electron tomography and single particle cryo-EM. It will include the experimental setups and instrumental prerequisites for 3D work, and their actual implementation. Specimen preparation methods suited for biological applications will be described and explained in detail. Since all tomographic methods are based on different reconstruction algorithms, and elaborate image processing and visualization routines, they will be included in this tutorial as well. At the end of the course students should understand the principles of structural analysis by TEM and its application in chemistry, biochemistry, structural biology, biophysics and materials science.

Syllabus

• 1. Introduction: TEM history and contemporary trends - applications of TEM to structural studies. 2. Introduction to electron optics, image formation, diffraction and automation. 3. Specimen preparation, negative stain, thin-film vitrification, high-pressure freezing, cryo-sectioning and modern micromachining methods. 4. Radiation effects; Introduction to image analysis; Sources of noise. 5. Principle and background of Fourier analysis, contrast transfer function (CTF), convolution and cross-correlation. 6. Electron tomography. 7. Principles of image analysis and 3D reconstruction methods 8. Single Particle analysis and image processing 9. 3D Visualization methods 10. Hybrid Methods: Combining X-ray crystallography and cryo-EM, combining light-microscopy and cryo-EM

Teaching methods

Lectures, seminars and tutorials

Assessment methods

Oral examination

Language of instruction

English

Further Comments

The course is taught annually.
The course is taught: in blocks.

C9940 3-Dimensional Transmission Electron Microscopy (3DEM)

Extent and Intensity

2/0/2. Type of Completion: zk (examination).

Teacher(s)

Dr. rer. nat. Jürgen Plitzko (lecturer)

Guaranteed by

prof. RNDr. Vladimír Sklenář, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science

Course Enrolment Limitations

The course is offered to students of any study field.

Course objectives

Transmission electron microscopy (TEM) in its various flavours is nowadays an established characterization tool for structures in life as well as in material science. Especially in todays ‘nano-world’ it is, by and large the only technique for an in-depth visual investigations at the nanometer scale and even in the sub-nanometer regime. The study of complex materials and hybrid compounds, and their interfaces and defects by TEM was and is a major focus in material science. Moreover, three-dimensional (3D) electron microscopy (3DEM) has a particularly important role in the repertoire of techniques strcutural biologists use for probing the structure and functions of molecules and macromolecular complexes in their functional cellular context. 3DEM in life sciences comprises three major branches: cryo-electron crystallography, cryo-electron microscopy of purified single particles (where ‘particles’ stand for proteins and macromolecular complexes) and cryo-electron tomography (the three dimensional investigation of any non periodic - ‘pleiomorphic’ - object). This course will explain the basics of transmission electron microscopy, electron tomography and single particle cryo-EM. It will include the experimental setups and instrumental prerequisites for 3D work, and their actual implementation. Specimen preparation methods suited for biological applications will be described and explained in detail. Since all tomographic methods are based on different reconstruction algorithms, and elaborate image processing and visualization routines, they will be included in this tutorial as well. At the end of the course students should understand the principles of structural analysis by TEM and its application in chemistry, biochemistry, structural biology, biophysics and materials science.

Syllabus

• 1. Introduction: TEM history and contemporary trends - applications of TEM to structural studies. 2. Introduction to electron optics, image formation, diffraction and automation. 3. Specimen preparation, negative stain, thin-film vitrification, high-pressure freezing, cryo-sectioning and modern micromachining methods. 4. Radiation effects; Introduction to image analysis; Sources of noise. 5. Principle and background of Fourier analysis, contrast transfer function (CTF), convolution and cross-correlation. 6. Electron tomography. 7. Principles of image analysis and 3D reconstruction methods 8. Single Particle analysis and image processing 9. 3D Visualization methods 10. Hybrid Methods: Combining X-ray crystallography and cryo-EM, combining light-microscopy and cryo-EM

Teaching methods

Lectures, seminars and tutorials

Assessment methods

Oral examination

Language of instruction

English

Further Comments

The course is taught annually.
The course is taught: in blocks.

C9940 3-Dimensional Transmission Electron Microscopy (3DEM)

The information about the term spring 2012 - acreditation is not made public

Extent and Intensity

2/0/2. Type of Completion: zk (examination).

Teacher(s)

Dr. rer. nat. Jürgen Plitzko (lecturer)

Guaranteed by

prof. RNDr. Vladimír Sklenář, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science

Course Enrolment Limitations

The course is offered to students of any study field.

Course objectives

Transmission electron microscopy (TEM) in its various flavours is nowadays an established characterization tool for structures in life as well as in material science. Especially in todays ‘nano-world’ it is, by and large the only technique for an in-depth visual investigations at the nanometer scale and even in the sub-nanometer regime. The study of complex materials and hybrid compounds, and their interfaces and defects by TEM was and is a major focus in material science. Moreover, three-dimensional (3D) electron microscopy (3DEM) has a particularly important role in the repertoire of techniques strcutural biologists use for probing the structure and functions of molecules and macromolecular complexes in their functional cellular context. 3DEM in life sciences comprises three major branches: cryo-electron crystallography, cryo-electron microscopy of purified single particles (where ‘particles’ stand for proteins and macromolecular complexes) and cryo-electron tomography (the three dimensional investigation of any non periodic - ‘pleiomorphic’ - object). This course will explain the basics of transmission electron microscopy, electron tomography and single particle cryo-EM. It will include the experimental setups and instrumental prerequisites for 3D work, and their actual implementation. Specimen preparation methods suited for biological applications will be described and explained in detail. Since all tomographic methods are based on different reconstruction algorithms, and elaborate image processing and visualization routines, they will be included in this tutorial as well. At the end of the course students should understand the principles of structural analysis by TEM and its application in chemistry, biochemistry, structural biology, biophysics and materials science.

Syllabus

• 1. Introduction: TEM history and contemporary trends - applications of TEM to structural studies. 2. Introduction to electron optics, image formation, diffraction and automation. 3. Specimen preparation, negative stain, thin-film vitrification, high-pressure freezing, cryo-sectioning and modern micromachining methods. 4. Radiation effects; Introduction to image analysis; Sources of noise. 5. Principle and background of Fourier analysis, contrast transfer function (CTF), convolution and cross-correlation. 6. Electron tomography. 7. Principles of image analysis and 3D reconstruction methods 8. Single Particle analysis and image processing 9. 3D Visualization methods 10. Hybrid Methods: Combining X-ray crystallography and cryo-EM, combining light-microscopy and cryo-EM

Teaching methods

Lectures, seminars and tutorials

Assessment methods

Oral examination

Language of instruction

English

Further Comments

The course is taught annually.
The course is taught: in blocks.

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