Informace o předmětu

C9940 3-Dimensional Transmission Electron Microscopy (3DEM)

Rozsah

2/0/2. 2 kr. (plus ukončení). Ukončení: zk.
Vyučováno kontaktně

Vyučující

Ing. Tibor Füzik, Ph.D. (přednášející)
Mgr. Jiří Nováček, Ph.D. (přednášející)
ing. Ondřej Sháněl, Ph.D. (přednášející), Mgr. Jiří Nováček, Ph.D. (zástupce)

Garance

Mgr. Jiří Nováček, Ph.D.
Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta
Dodavatelské pracoviště: Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta

Předpoklady

FB820

Omezení zápisu do předmětu

Předmět je otevřen studentům libovolného oboru.

Cíle předmětu

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.

Výstupy z učení

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

Osnova

• 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

Výukové metody

Lectures, practicals

Metody hodnocení

Semester work, written examination

Vyučovací jazyk

Angličtina

Další komentáře

Předmět je vyučován každoročně.
Výuka probíhá blokově.

C9940 3-Dimensional Transmission Electron Microscopy (3DEM)

Rozsah

2/0/2. 2 kr. (plus ukončení). Ukončení: zk.

Vyučující

Ing. Tibor Füzik, Ph.D. (přednášející)
Mgr. Jiří Nováček, Ph.D. (přednášející)
ing. Ondřej Sháněl, Ph.D. (přednášející), Mgr. Jiří Nováček, Ph.D. (zástupce)

Garance

Mgr. Jiří Nováček, Ph.D.
Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta
Dodavatelské pracoviště: Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta

Předpoklady

FB820

Omezení zápisu do předmětu

Předmět je otevřen studentům libovolného oboru.

Cíle předmětu

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.

Výstupy z učení

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

Osnova

• 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

Výukové metody

Lectures, practicals

Metody hodnocení

Semester work, written examination

Vyučovací jazyk

Angličtina

Další komentáře

Předmět je vyučován každoročně.
Výuka probíhá blokově.

C9940 3-Dimensional Transmission Electron Microscopy (3DEM)

Rozsah

2/0/2. 2 kr. (plus ukončení). Ukončení: zk.

Vyučující

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

Garance

prof. RNDr. Vladimír Sklenář, DrSc.
Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta
Dodavatelské pracoviště: Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta

Omezení zápisu do předmětu

Předmět je otevřen studentům libovolného oboru.

Cíle předmětu

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.

Osnova

• 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

Výukové metody

Lectures, seminars and tutorials

Metody hodnocení

Oral examination

Vyučovací jazyk

Angličtina

Další komentáře

Studijní materiály
Předmět je vyučován každoročně.
Výuka probíhá blokově.

C9940 3-Dimensional Transmission Electron Microscopy (3DEM)

Rozsah

2/0/2. 2 kr. (plus ukončení). Ukončení: zk.

Vyučující

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

Garance

prof. RNDr. Vladimír Sklenář, DrSc.
Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta
Dodavatelské pracoviště: Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta

Omezení zápisu do předmětu

Předmět je otevřen studentům libovolného oboru.

Cíle předmětu

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.

Osnova

• 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

Výukové metody

Lectures, seminars and tutorials

Metody hodnocení

Oral examination

Vyučovací jazyk

Angličtina

Další komentáře

Studijní materiály
Předmět je vyučován každoročně.
Výuka probíhá blokově.

C9940 3-Dimensional Transmission Electron Microscopy (3DEM)

Rozsah

2/0/2. 2 kr. (plus ukončení). Ukončení: zk.

Vyučující

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

Garance

prof. RNDr. Vladimír Sklenář, DrSc.
Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta
Dodavatelské pracoviště: Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta

Omezení zápisu do předmětu

Předmět je otevřen studentům libovolného oboru.

Cíle předmětu

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.

Osnova

• 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

Výukové metody

Lectures, seminars and tutorials

Metody hodnocení

Oral examination

Vyučovací jazyk

Angličtina

Další komentáře

Studijní materiály
Předmět je vyučován každoročně.
Výuka probíhá blokově.

C9940 3-Dimensional Transmission Electron Microscopy (3DEM)

Rozsah

2/0/2. 2 kr. (plus ukončení). Ukončení: zk.

Vyučující

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

Garance

prof. RNDr. Vladimír Sklenář, DrSc.
Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta
Dodavatelské pracoviště: Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta

Omezení zápisu do předmětu

Předmět je otevřen studentům libovolného oboru.

Cíle předmětu

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.

Osnova

• 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

Výukové metody

Lectures, seminars and tutorials

Metody hodnocení

Oral examination

Vyučovací jazyk

Angličtina

Další komentáře

Předmět je vyučován každoročně.
Výuka probíhá blokově.

C9940 3-Dimensional Transmission Electron Microscopy (3DEM)

Rozsah

2/0/2. 2 kr. (plus ukončení). Ukončení: zk.

Vyučující

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

Garance

prof. RNDr. Vladimír Sklenář, DrSc.
Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta
Dodavatelské pracoviště: Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta

Omezení zápisu do předmětu

Předmět je otevřen studentům libovolného oboru.

Cíle předmětu

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.

Osnova

• 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

Výukové metody

Lectures, seminars and tutorials

Metody hodnocení

Oral examination

Vyučovací jazyk

Angličtina

Další komentáře

Studijní materiály
Předmět je vyučován každoročně.
Výuka probíhá blokově.

C9940 3-Dimensional Transmission Electron Microscopy (3DEM)

Rozsah

2/0/2. 2 kr. (plus ukončení). Ukončení: zk.

Vyučující

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

Garance

prof. RNDr. Vladimír Sklenář, DrSc.
Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta
Dodavatelské pracoviště: Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta

Omezení zápisu do předmětu

Předmět je otevřen studentům libovolného oboru.

Cíle předmětu

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.

Osnova

• 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

Výukové metody

Lectures, seminars and tutorials

Metody hodnocení

Oral examination

Vyučovací jazyk

Angličtina

Další komentáře

Studijní materiály
Předmět je vyučován každoročně.
Výuka probíhá blokově.

C9940 3-Dimensional Transmission Electron Microscopy (3DEM)

Rozsah

2/0/2. 2 kr. (plus ukončení). Ukončení: zk.

Vyučující

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

Garance

prof. RNDr. Vladimír Sklenář, DrSc.
Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta
Dodavatelské pracoviště: Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta

Rozvrh

Po 20. 2. až Po 22. 5. Po 14:00–15:50 E35/211

Omezení zápisu do předmětu

Předmět je otevřen studentům libovolného oboru.

Cíle předmětu

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.

Osnova

• 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

Výukové metody

Lectures, seminars and tutorials

Metody hodnocení

Oral examination

Vyučovací jazyk

Angličtina

Další komentáře

Studijní materiály
Předmět je vyučován každoročně.

C9940 3-Dimensional Transmission Electron Microscopy (3DEM)

Rozsah

2/0/2. 2 kr. (plus ukončení). Ukončení: zk.

Vyučující

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

Garance

prof. RNDr. Vladimír Sklenář, DrSc.
Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta
Dodavatelské pracoviště: Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta

Rozvrh

Po 14:30–16:30 E35/211

Omezení zápisu do předmětu

Předmět je otevřen studentům libovolného oboru.

Cíle předmětu

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.

Osnova

• 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

Výukové metody

Lectures, seminars and tutorials

Metody hodnocení

Oral examination

Vyučovací jazyk

Angličtina

Další komentáře

Studijní materiály
Předmět je vyučován každoročně.

C9940 3-Dimensional Transmission Electron Microscopy (3DEM)

Rozsah

2/0/2. 2 kr. (plus ukončení). Ukončení: zk.

Vyučující

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

Garance

prof. RNDr. Vladimír Sklenář, DrSc.
Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta
Dodavatelské pracoviště: Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta

Rozvrh

Po 14:00–15:50 E35/211

Omezení zápisu do předmětu

Předmět je otevřen studentům libovolného oboru.

Cíle předmětu

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.

Osnova

• 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

Výukové metody

Lectures, seminars and tutorials

Metody hodnocení

Oral examination

Vyučovací jazyk

Angličtina

Další komentáře

Studijní materiály
Předmět je vyučován každoročně.

C9940 3-Dimensional Transmission Electron Microscopy (3DEM)

Rozsah

2/0/2. Ukončení: zk.

Vyučující

Dr. rer. nat. Jürgen Plitzko (přednášející)

Garance

prof. RNDr. Vladimír Sklenář, DrSc.
Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta
Dodavatelské pracoviště: Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta

Rozvrh

Út 14:00–15:50 C04/211, Čt 14:00–15:50 C04/118

Omezení zápisu do předmětu

Předmět je otevřen studentům libovolného oboru.

Cíle předmětu

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.

Osnova

• 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

Výukové metody

Lectures, seminars and tutorials

Metody hodnocení

Oral examination

Vyučovací jazyk

Angličtina

Další komentáře

Předmět je vyučován každoročně.

C9940 3-Dimensional Transmission Electron Microscopy (3DEM)

Rozsah

2/0/2. Ukončení: zk.

Vyučující

Dr. rer. nat. Jürgen Plitzko (přednášející)

Garance

prof. RNDr. Vladimír Sklenář, DrSc.
Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta
Dodavatelské pracoviště: Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta

Omezení zápisu do předmětu

Předmět je otevřen studentům libovolného oboru.

Cíle předmětu

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.

Osnova

• 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

Výukové metody

Lectures, seminars and tutorials

Metody hodnocení

Oral examination

Vyučovací jazyk

Angličtina

Další komentáře

Předmět je vyučován každoročně.
Výuka probíhá blokově.

C9940 3-Dimensional Transmission Electron Microscopy (3DEM)

Rozsah

2/0/2. Ukončení: zk.

Vyučující

Dr. rer. nat. Jürgen Plitzko (přednášející)

Garance

prof. RNDr. Vladimír Sklenář, DrSc.
Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta
Dodavatelské pracoviště: Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta

Omezení zápisu do předmětu

Předmět je otevřen studentům libovolného oboru.

Cíle předmětu

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.

Osnova

• 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

Výukové metody

Lectures, seminars and tutorials

Metody hodnocení

Oral examination

Vyučovací jazyk

Angličtina

Další komentáře

Předmět je vyučován každoročně.
Výuka probíhá blokově.

C9940 3-Dimensional Transmission Electron Microscopy (3DEM)

Údaje z období jaro 2012 - akreditace se nezveřejňují

Rozsah

2/0/2. Ukončení: zk.

Vyučující

Dr. rer. nat. Jürgen Plitzko (přednášející)

Garance

prof. RNDr. Vladimír Sklenář, DrSc.
Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta
Dodavatelské pracoviště: Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta

Omezení zápisu do předmětu

Předmět je otevřen studentům libovolného oboru.

Cíle předmětu

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.

Osnova

• 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

Výukové metody

Lectures, seminars and tutorials

Metody hodnocení

Oral examination

Vyučovací jazyk

Angličtina

Další komentáře

Předmět je vyučován každoročně.
Výuka probíhá blokově.

• Statistika zápisu (nejnovější)