Leschziner public wiki - User contributions [en]

Negative Stain Grid Contamination

2010-08-02T20:38:46Z

Bpappas:

Images relating to the message about grid contamination with negative stain. You may click on the image to obtain the full resolution file.

----

Image #1:

[[File:6_9_10_5r_3.jpg|700px]]

Image #2:

[[File:C5_3.jpg|700px]]

Image #3:

[[File:C5_4.jpg|700px]]

Image #4:

[[File:I3_M6_scan_001.jpg|700px]]

Negative Stain Grid Contamination

2010-08-02T20:24:17Z

Bpappas:

Images relating to the message about grid contamination with negative stain. You may click on the image to obtain the full resolution file.

[[File:6_9_10_5r_3.jpg|700px]]

[[File:C5_3.jpg|700px]]

[[File:C5_4.jpg|700px]]

[[File:I3_M6_scan_001.jpg|700px]]

Negative Stain Grid Contamination

2010-08-02T20:23:31Z

Bpappas:

File:I3 M6 scan 001.jpg

2010-08-02T20:23:13Z

Bpappas:

Negative Stain Grid Contamination

2010-08-02T20:22:58Z

Bpappas:

File:C5 4.jpg

2010-08-02T20:22:34Z

Bpappas:

Negative Stain Grid Contamination

2010-08-02T20:21:23Z

Bpappas:

Images relating to the message about grid contamination with negative stain. You may click on the image to obtain the full resolution file.

[[File:6_9_10_5r_3.jpg|700px]]

[[File:C5_3.jpg|700px]]

Negative Stain Grid Contamination

2010-08-02T20:19:04Z

Bpappas:

Images relating to the message about grid contamination with negative stain.

[[File:6_9_10_5r_3.jpg]]

[[File:C5_3.jpg]]

Negative Stain Grid Contamination

2010-08-02T20:18:48Z

Bpappas:

Images relating to the message about grid contamination with negative stain.

[[File:6_9_10_5r_3.jpg|center]]

[[File:C5_3.jpg|center]]

File:C5 3.jpg

2010-08-02T20:18:01Z

Bpappas:

File:6 9 10 5r 3.jpg

2010-08-02T20:16:34Z

Bpappas:

Negative Stain Grid Contamination

2010-08-02T20:08:37Z

Bpappas: Created page with 'Images relating to the message about grid contamination with negative stain.'

Images relating to the message about grid contamination with negative stain.

Main Page

2010-05-07T18:13:31Z

Bpappas:

<center><big> '''Welcome to the Leschziner Lab's Tutorials Wiki''' </big></center>

In these pages you will find tutorials designed to explain, in an accessible way, some of the principles behind the techniques used in our lab. They range from the very general (How does a microscope work?) to very specific approaches used in Three-Dimensional Electron Microscopy (3D-EM). This wiki is, by definition, a "work in progress"; we will periodically add new material and update what's already here. Blue links are for tutorials already available while red ones are for those we are still developing.

In the Leschziner Lab, we use electron microscopy to study structures of macromolecules. In particular, we look at single particles and use the techniques described in the sections below to generate three-dimensional structures of the proteins or protein complexes of interest. In addition to the study of protein structure, our lab is interested in improving techniques for 3D-EM.

We hope you find the material useful and welcome feedback on how to improve it. To give us feedback, please see the [[Talk:Main_Page|discussion tab]] at the top of the page, or [mailto:leschziner.tutorials@gmail.com e-mail us].

==Introduction==

The compound optical microscope, first recognized in 1590, is perhaps the most familiar of all laboratory instruments. The much younger electron microscope, for many years simply an exotic rarity, has also become a standard tool in biological research. As the convenience and accessibility of each has grown over the years, however, the understanding of relevant theory or even how the microscope itself functions has been lost among many users. While a firm understanding of the fundamental principles of optics and imaging is not often necessary for general function, eventually this knowledge becomes necessary for the proper use, interpretation of images, and choices of specific application. This is especially relevant for those who wish to innovate, or even effectively trouble-shoot, in the field.

This wiki is intended to provide both a brief overview of the fundamental concepts, as well as a more in-depth theoretical view for those readers who would like to examine more of the mathematics and physics behind imaging (such as with image formation, contrast, resolution limits). In particular, Fourier imaging will be discussed as it applies to the interpretation of data.

Since our focus is not directed toward crystalline data sets but rather what can be referred to as asymmetric structures, the image processing and data interpretation sections will deal with techniques particular to the latter.

==General imaging principles==
These conventions and basic physics concepts are fundamental tools for understanding optical and electron imaging.

*[[Light optics]]
*[[Microscope Ray Tracing]]
*[[Phase Contrast]]
*[[Depth of Field]]

==Electron imaging==
There are many caveats to imaging with electrons as opposed to photons.

*[[What is an Electron Microscope?]]
*[[History of the Electron Microscope]]
*[[Types of Signals]]
*[[Electron optics]]
*[[The Weak-Phase Object Approximation]]
*[[Contrast]]
*[[Ewald Sphere]]
*[[Aberrations]]
*[[Special Imaging Techniques]]

==Electron Microscopy of Macromolecules==

(Pipeline Picture)

*[[Sample Preparation]]
*[[Special Considerations]]
*[[Image Collection Schemes]]

==Two-Dimensional Averaging==

Once the data from imaging the macromolecules of interest are collected, several steps are taken to sift through the images and create a three-dimensional model.

==Three-dimensional reconstruction by EM==

A "30 Second Overview" of three-dimensional EM reconstruction.

<qt>file=EM intro2.mov|width=768|height=576|autoplay=false|controller=true</qt>

===Basics===
*[[Central Section Theorem]]
*[[Back Projection]]

===Existing Reconstruction Methods===
*[[Angular Reconstitution]] (AR)
*[[Random Conical Tilt]] (RCT)
*[[Orthogonal Tilt Reconstruction]] (OTR)

===Software Available===
An overview of the currently available software, links, and general descriptions.

==Resolution==

The concept of resolution in electron microscopy has brought out several debates in the past.

==Hardware Innovations to the Electron Microscope==
Some new, some old, there are many aspects of the microscope that may be changed, ostensibly altering the physics of image formation for the better.

*[[CMOS]]
*[[Phase Plates]]

----

Back to [https://leschzinerlab.ucsd.edu/ Leschziner Lab Main Site]

Sample Preparation

2010-05-07T18:00:42Z

Bpappas:

Imaging biological samples in their native state in the electron microscope can see like an impossible task: how can one immobilize a protein instantly and place it into the extreme environment of a vacuum without any structural changes occurring? However, advances in sample preparation techniques over the years have made it possible to do practically that.

==Support Grids==

==Negative Stain==

===Artifacts===

==Vitreous Ice Embedment==

===Cryo-Negative Staining===

==Labeling with Gold Clusters==

Main Page

2010-05-07T18:00:29Z

Bpappas: /* Electron Microscopy of Macromolecules */

<center><big> '''Welcome to the Leschziner Lab's Tutorials Wiki''' </big></center>

In these pages you will find tutorials designed to explain, in an accessible way, some of the principles behind the techniques used in our lab. They range from the very general (How does a microscope work?) to very specific approaches used in Three-Dimensional Electron Microscopy (3D-EM). This wiki is, by definition, a "work in progress"; we will periodically add new material and update what's already here. Blue links are for tutorials already available while red ones are for those we are still developing.

We hope you find the material useful and welcome feedback on how to improve it. To give us feedback, please see the [[Talk:Main_Page|discussion tab]] at the top of the page, or [mailto:leschziner.tutorials@gmail.com e-mail us].

==Introduction==

The compound optical microscope, first recognized in 1590, is perhaps the most familiar of all laboratory instruments. The much younger electron microscope, for many years simply an exotic rarity, has also become a standard tool in biological research. As the convenience and accessibility of each has grown over the years, however, the understanding of relevant theory or even how the microscope itself functions has been lost among many users. While a firm understanding of the fundamental principles of optics and imaging is not often necessary for general function, eventually this knowledge becomes necessary for the proper use, interpretation of images, and choices of specific application. This is especially relevant for those who wish to innovate, or even effectively trouble-shoot, in the field.

This wiki is intended to provide both a brief overview of the fundamental concepts, as well as a more in-depth theoretical view for those readers who would like to examine more of the mathematics and physics behind imaging (such as with image formation, contrast, resolution limits). In particular, Fourier imaging will be discussed as it applies to the interpretation of data.

Since our focus is not directed toward crystalline data sets but rather what can be referred to as asymmetric structures, the image processing and data interpretation sections will deal with techniques particular to the latter.

==General imaging principles==
These conventions and basic physics concepts are fundamental tools for understanding optical and electron imaging.

*[[Light optics]]
*[[Microscope Ray Tracing]]
*[[Phase Contrast]]
*[[Depth of Field]]

==Electron imaging==
There are many caveats to imaging with electrons as opposed to photons.

*[[What is an Electron Microscope?]]
*[[History of the Electron Microscope]]
*[[Types of Signals]]
*[[Electron optics]]
*[[The Weak-Phase Object Approximation]]
*[[Contrast]]
*[[Ewald Sphere]]
*[[Aberrations]]
*[[Special Imaging Techniques]]

==Electron Microscopy of Macromolecules==

(Pipeline Picture)

*[[Sample Preparation]]
*[[Special Considerations]]
*[[Image Collection Schemes]]

==Two-Dimensional Averaging==

Once the data from imaging the macromolecules of interest are collected, several steps are taken to sift through the images and create a three-dimensional model.

==Three-dimensional reconstruction by EM==

A "30 Second Overview" of three-dimensional EM reconstruction.

<qt>file=EM intro2.mov|width=768|height=576|autoplay=false|controller=true</qt>

===Basics===
*[[Central Section Theorem]]
*[[Back Projection]]

===Existing Reconstruction Methods===
*[[Angular Reconstitution]] (AR)
*[[Random Conical Tilt]] (RCT)
*[[Orthogonal Tilt Reconstruction]] (OTR)

===Software Available===
An overview of the currently available software, links, and general descriptions.

==Resolution==

The concept of resolution in electron microscopy has brought out several debates in the past.

==Hardware Innovations to the Electron Microscope==
Some new, some old, there are many aspects of the microscope that may be changed, ostensibly altering the physics of image formation for the better.

*[[CMOS]]
*[[Phase Plates]]

----

Back to [https://leschzinerlab.ucsd.edu/ Leschziner Lab Main Site]

Main Page

2010-05-07T17:59:35Z

Bpappas: /* Two-Dimensional Averaging */

<center><big> '''Welcome to the Leschziner Lab's Tutorials Wiki''' </big></center>

In these pages you will find tutorials designed to explain, in an accessible way, some of the principles behind the techniques used in our lab. They range from the very general (How does a microscope work?) to very specific approaches used in Three-Dimensional Electron Microscopy (3D-EM). This wiki is, by definition, a "work in progress"; we will periodically add new material and update what's already here. Blue links are for tutorials already available while red ones are for those we are still developing.

We hope you find the material useful and welcome feedback on how to improve it. To give us feedback, please see the [[Talk:Main_Page|discussion tab]] at the top of the page, or [mailto:leschziner.tutorials@gmail.com e-mail us].

==Introduction==

The compound optical microscope, first recognized in 1590, is perhaps the most familiar of all laboratory instruments. The much younger electron microscope, for many years simply an exotic rarity, has also become a standard tool in biological research. As the convenience and accessibility of each has grown over the years, however, the understanding of relevant theory or even how the microscope itself functions has been lost among many users. While a firm understanding of the fundamental principles of optics and imaging is not often necessary for general function, eventually this knowledge becomes necessary for the proper use, interpretation of images, and choices of specific application. This is especially relevant for those who wish to innovate, or even effectively trouble-shoot, in the field.

This wiki is intended to provide both a brief overview of the fundamental concepts, as well as a more in-depth theoretical view for those readers who would like to examine more of the mathematics and physics behind imaging (such as with image formation, contrast, resolution limits). In particular, Fourier imaging will be discussed as it applies to the interpretation of data.

Since our focus is not directed toward crystalline data sets but rather what can be referred to as asymmetric structures, the image processing and data interpretation sections will deal with techniques particular to the latter.

==General imaging principles==
These conventions and basic physics concepts are fundamental tools for understanding optical and electron imaging.

*[[Light optics]]
*[[Microscope Ray Tracing]]
*[[Phase Contrast]]
*[[Depth of Field]]

==Electron imaging==
There are many caveats to imaging with electrons as opposed to photons.

*[[What is an Electron Microscope?]]
*[[History of the Electron Microscope]]
*[[Types of Signals]]
*[[Electron optics]]
*[[The Weak-Phase Object Approximation]]
*[[Contrast]]
*[[Ewald Sphere]]
*[[Aberrations]]
*[[Special Imaging Techniques]]

==Electron Microscopy of Macromolecules==

Imaging biological samples in the electron microscope can see like an impossible task: how can one immobilize a protein instantly and place it into the extreme environment of a vacuum without any structural changes occurring? However, advances in sample preparation techniques over the years have made it possible to do practically that.

*[[Sample Preparation]]
*[[Special Considerations]]
*[[Image Collection Schemes]]

==Two-Dimensional Averaging==

Once the data from imaging the macromolecules of interest are collected, several steps are taken to sift through the images and create a three-dimensional model.

==Three-dimensional reconstruction by EM==

A "30 Second Overview" of three-dimensional EM reconstruction.

<qt>file=EM intro2.mov|width=768|height=576|autoplay=false|controller=true</qt>

===Basics===
*[[Central Section Theorem]]
*[[Back Projection]]

===Existing Reconstruction Methods===
*[[Angular Reconstitution]] (AR)
*[[Random Conical Tilt]] (RCT)
*[[Orthogonal Tilt Reconstruction]] (OTR)

===Software Available===
An overview of the currently available software, links, and general descriptions.

==Resolution==

The concept of resolution in electron microscopy has brought out several debates in the past.

==Hardware Innovations to the Electron Microscope==
Some new, some old, there are many aspects of the microscope that may be changed, ostensibly altering the physics of image formation for the better.

*[[CMOS]]
*[[Phase Plates]]

----

Back to [https://leschzinerlab.ucsd.edu/ Leschziner Lab Main Site]

Main Page

2010-05-07T17:57:40Z

Bpappas: /* Electron Microscopy of Macromolecules */

<center><big> '''Welcome to the Leschziner Lab's Tutorials Wiki''' </big></center>

In these pages you will find tutorials designed to explain, in an accessible way, some of the principles behind the techniques used in our lab. They range from the very general (How does a microscope work?) to very specific approaches used in Three-Dimensional Electron Microscopy (3D-EM). This wiki is, by definition, a "work in progress"; we will periodically add new material and update what's already here. Blue links are for tutorials already available while red ones are for those we are still developing.

We hope you find the material useful and welcome feedback on how to improve it. To give us feedback, please see the [[Talk:Main_Page|discussion tab]] at the top of the page, or [mailto:leschziner.tutorials@gmail.com e-mail us].

==Introduction==

The compound optical microscope, first recognized in 1590, is perhaps the most familiar of all laboratory instruments. The much younger electron microscope, for many years simply an exotic rarity, has also become a standard tool in biological research. As the convenience and accessibility of each has grown over the years, however, the understanding of relevant theory or even how the microscope itself functions has been lost among many users. While a firm understanding of the fundamental principles of optics and imaging is not often necessary for general function, eventually this knowledge becomes necessary for the proper use, interpretation of images, and choices of specific application. This is especially relevant for those who wish to innovate, or even effectively trouble-shoot, in the field.

This wiki is intended to provide both a brief overview of the fundamental concepts, as well as a more in-depth theoretical view for those readers who would like to examine more of the mathematics and physics behind imaging (such as with image formation, contrast, resolution limits). In particular, Fourier imaging will be discussed as it applies to the interpretation of data.

Since our focus is not directed toward crystalline data sets but rather what can be referred to as asymmetric structures, the image processing and data interpretation sections will deal with techniques particular to the latter.

==General imaging principles==
These conventions and basic physics concepts are fundamental tools for understanding optical and electron imaging.

*[[Light optics]]
*[[Microscope Ray Tracing]]
*[[Phase Contrast]]
*[[Depth of Field]]

==Electron imaging==
There are many caveats to imaging with electrons as opposed to photons.

*[[What is an Electron Microscope?]]
*[[History of the Electron Microscope]]
*[[Types of Signals]]
*[[Electron optics]]
*[[The Weak-Phase Object Approximation]]
*[[Contrast]]
*[[Ewald Sphere]]
*[[Aberrations]]
*[[Special Imaging Techniques]]

==Electron Microscopy of Macromolecules==

Imaging biological samples in the electron microscope can see like an impossible task: how can one immobilize a protein instantly and place it into the extreme environment of a vacuum without any structural changes occurring? However, advances in sample preparation techniques over the years have made it possible to do practically that.

*[[Sample Preparation]]
*[[Special Considerations]]
*[[Image Collection Schemes]]

==Two-Dimensional Averaging==

==Three-dimensional reconstruction by EM==

A "30 Second Overview" of three-dimensional EM reconstruction.

<qt>file=EM intro2.mov|width=768|height=576|autoplay=false|controller=true</qt>

===Basics===
*[[Central Section Theorem]]
*[[Back Projection]]

===Existing Reconstruction Methods===
*[[Angular Reconstitution]] (AR)
*[[Random Conical Tilt]] (RCT)
*[[Orthogonal Tilt Reconstruction]] (OTR)

===Software Available===
An overview of the currently available software, links, and general descriptions.

==Resolution==

The concept of resolution in electron microscopy has brought out several debates in the past.

==Hardware Innovations to the Electron Microscope==
Some new, some old, there are many aspects of the microscope that may be changed, ostensibly altering the physics of image formation for the better.

*[[CMOS]]
*[[Phase Plates]]

----

Back to [https://leschzinerlab.ucsd.edu/ Leschziner Lab Main Site]

Main Page

2010-05-07T17:56:49Z

Bpappas: /* Electron Microscopy of Macromolecules */

<center><big> '''Welcome to the Leschziner Lab's Tutorials Wiki''' </big></center>

In these pages you will find tutorials designed to explain, in an accessible way, some of the principles behind the techniques used in our lab. They range from the very general (How does a microscope work?) to very specific approaches used in Three-Dimensional Electron Microscopy (3D-EM). This wiki is, by definition, a "work in progress"; we will periodically add new material and update what's already here. Blue links are for tutorials already available while red ones are for those we are still developing.

We hope you find the material useful and welcome feedback on how to improve it. To give us feedback, please see the [[Talk:Main_Page|discussion tab]] at the top of the page, or [mailto:leschziner.tutorials@gmail.com e-mail us].

==Introduction==

The compound optical microscope, first recognized in 1590, is perhaps the most familiar of all laboratory instruments. The much younger electron microscope, for many years simply an exotic rarity, has also become a standard tool in biological research. As the convenience and accessibility of each has grown over the years, however, the understanding of relevant theory or even how the microscope itself functions has been lost among many users. While a firm understanding of the fundamental principles of optics and imaging is not often necessary for general function, eventually this knowledge becomes necessary for the proper use, interpretation of images, and choices of specific application. This is especially relevant for those who wish to innovate, or even effectively trouble-shoot, in the field.

This wiki is intended to provide both a brief overview of the fundamental concepts, as well as a more in-depth theoretical view for those readers who would like to examine more of the mathematics and physics behind imaging (such as with image formation, contrast, resolution limits). In particular, Fourier imaging will be discussed as it applies to the interpretation of data.

Since our focus is not directed toward crystalline data sets but rather what can be referred to as asymmetric structures, the image processing and data interpretation sections will deal with techniques particular to the latter.

==General imaging principles==
These conventions and basic physics concepts are fundamental tools for understanding optical and electron imaging.

*[[Light optics]]
*[[Microscope Ray Tracing]]
*[[Phase Contrast]]
*[[Depth of Field]]

==Electron imaging==
There are many caveats to imaging with electrons as opposed to photons.

*[[What is an Electron Microscope?]]
*[[History of the Electron Microscope]]
*[[Types of Signals]]
*[[Electron optics]]
*[[The Weak-Phase Object Approximation]]
*[[Contrast]]
*[[Ewald Sphere]]
*[[Aberrations]]
*[[Special Imaging Techniques]]

==Electron Microscopy of Macromolecules==

Imaging biological samples in the electron microscope can see like an impossible task: how can one immobilize a protein instantly and place it into the extreme environment of a vacuum without any structural changes occurring? However, advances in sample preparation techniques over the years have made it possible to do practically that.

*[[Sample Preparation]]
*[[Special Considerations]]

==Two-Dimensional Averaging==

==Three-dimensional reconstruction by EM==

A "30 Second Overview" of three-dimensional EM reconstruction.

<qt>file=EM intro2.mov|width=768|height=576|autoplay=false|controller=true</qt>

===Basics===
*[[Central Section Theorem]]
*[[Back Projection]]

===Existing Reconstruction Methods===
*[[Angular Reconstitution]] (AR)
*[[Random Conical Tilt]] (RCT)
*[[Orthogonal Tilt Reconstruction]] (OTR)

===Software Available===
An overview of the currently available software, links, and general descriptions.

==Resolution==

The concept of resolution in electron microscopy has brought out several debates in the past.

==Hardware Innovations to the Electron Microscope==
Some new, some old, there are many aspects of the microscope that may be changed, ostensibly altering the physics of image formation for the better.

*[[CMOS]]
*[[Phase Plates]]

----

Back to [https://leschzinerlab.ucsd.edu/ Leschziner Lab Main Site]

Main Page

2010-05-07T17:48:38Z

Bpappas: /* General imaging principles */

<center><big> '''Welcome to the Leschziner Lab's Tutorials Wiki''' </big></center>

In these pages you will find tutorials designed to explain, in an accessible way, some of the principles behind the techniques used in our lab. They range from the very general (How does a microscope work?) to very specific approaches used in Three-Dimensional Electron Microscopy (3D-EM). This wiki is, by definition, a "work in progress"; we will periodically add new material and update what's already here. Blue links are for tutorials already available while red ones are for those we are still developing.

We hope you find the material useful and welcome feedback on how to improve it. To give us feedback, please see the [[Talk:Main_Page|discussion tab]] at the top of the page, or [mailto:leschziner.tutorials@gmail.com e-mail us].

==Introduction==

The compound optical microscope, first recognized in 1590, is perhaps the most familiar of all laboratory instruments. The much younger electron microscope, for many years simply an exotic rarity, has also become a standard tool in biological research. As the convenience and accessibility of each has grown over the years, however, the understanding of relevant theory or even how the microscope itself functions has been lost among many users. While a firm understanding of the fundamental principles of optics and imaging is not often necessary for general function, eventually this knowledge becomes necessary for the proper use, interpretation of images, and choices of specific application. This is especially relevant for those who wish to innovate, or even effectively trouble-shoot, in the field.

This wiki is intended to provide both a brief overview of the fundamental concepts, as well as a more in-depth theoretical view for those readers who would like to examine more of the mathematics and physics behind imaging (such as with image formation, contrast, resolution limits). In particular, Fourier imaging will be discussed as it applies to the interpretation of data.

Since our focus is not directed toward crystalline data sets but rather what can be referred to as asymmetric structures, the image processing and data interpretation sections will deal with techniques particular to the latter.

==General imaging principles==
These conventions and basic physics concepts are fundamental tools for understanding optical and electron imaging.

*[[Light optics]]
*[[Microscope Ray Tracing]]
*[[Phase Contrast]]
*[[Depth of Field]]

==Electron imaging==
There are many caveats to imaging with electrons as opposed to photons.

*[[What is an Electron Microscope?]]
*[[History of the Electron Microscope]]
*[[Types of Signals]]
*[[Electron optics]]
*[[The Weak-Phase Object Approximation]]
*[[Contrast]]
*[[Ewald Sphere]]
*[[Aberrations]]
*[[Special Imaging Techniques]]

==Electron Microscopy of Macromolecules==

*[[Sample Preparation]]
*[[Special Considerations]]

==Two-Dimensional Averaging==

==Three-dimensional reconstruction by EM==

A "30 Second Overview" of three-dimensional EM reconstruction.

<qt>file=EM intro2.mov|width=768|height=576|autoplay=false|controller=true</qt>

===Basics===
*[[Central Section Theorem]]
*[[Back Projection]]

===Existing Reconstruction Methods===
*[[Angular Reconstitution]] (AR)
*[[Random Conical Tilt]] (RCT)
*[[Orthogonal Tilt Reconstruction]] (OTR)

===Software Available===
An overview of the currently available software, links, and general descriptions.

==Resolution==

The concept of resolution in electron microscopy has brought out several debates in the past.

==Hardware Innovations to the Electron Microscope==
Some new, some old, there are many aspects of the microscope that may be changed, ostensibly altering the physics of image formation for the better.

*[[CMOS]]
*[[Phase Plates]]

----

Back to [https://leschzinerlab.ucsd.edu/ Leschziner Lab Main Site]

Main Page

2010-05-07T17:47:43Z

Bpappas: /* Introduction */

<center><big> '''Welcome to the Leschziner Lab's Tutorials Wiki''' </big></center>

In these pages you will find tutorials designed to explain, in an accessible way, some of the principles behind the techniques used in our lab. They range from the very general (How does a microscope work?) to very specific approaches used in Three-Dimensional Electron Microscopy (3D-EM). This wiki is, by definition, a "work in progress"; we will periodically add new material and update what's already here. Blue links are for tutorials already available while red ones are for those we are still developing.

We hope you find the material useful and welcome feedback on how to improve it. To give us feedback, please see the [[Talk:Main_Page|discussion tab]] at the top of the page, or [mailto:leschziner.tutorials@gmail.com e-mail us].

==Introduction==

The compound optical microscope, first recognized in 1590, is perhaps the most familiar of all laboratory instruments. The much younger electron microscope, for many years simply an exotic rarity, has also become a standard tool in biological research. As the convenience and accessibility of each has grown over the years, however, the understanding of relevant theory or even how the microscope itself functions has been lost among many users. While a firm understanding of the fundamental principles of optics and imaging is not often necessary for general function, eventually this knowledge becomes necessary for the proper use, interpretation of images, and choices of specific application. This is especially relevant for those who wish to innovate, or even effectively trouble-shoot, in the field.

This wiki is intended to provide both a brief overview of the fundamental concepts, as well as a more in-depth theoretical view for those readers who would like to examine more of the mathematics and physics behind imaging (such as with image formation, contrast, resolution limits). In particular, Fourier imaging will be discussed as it applies to the interpretation of data.

Since our focus is not directed toward crystalline data sets but rather what can be referred to as asymmetric structures, the image processing and data interpretation sections will deal with techniques particular to the latter.

==General imaging principles==
These conventions and basic physics concepts are fundamental tools for understanding electron imaging.

*[[Light optics]]
*[[Microscope Ray Tracing]]
*[[Phase Contrast]]
*[[Depth of Field]]

==Electron imaging==
There are many caveats to imaging with electrons as opposed to photons.

*[[What is an Electron Microscope?]]
*[[History of the Electron Microscope]]
*[[Types of Signals]]
*[[Electron optics]]
*[[The Weak-Phase Object Approximation]]
*[[Contrast]]
*[[Ewald Sphere]]
*[[Aberrations]]
*[[Special Imaging Techniques]]

==Electron Microscopy of Macromolecules==

*[[Sample Preparation]]
*[[Special Considerations]]

==Two-Dimensional Averaging==

==Three-dimensional reconstruction by EM==

A "30 Second Overview" of three-dimensional EM reconstruction.

<qt>file=EM intro2.mov|width=768|height=576|autoplay=false|controller=true</qt>

===Basics===
*[[Central Section Theorem]]
*[[Back Projection]]

===Existing Reconstruction Methods===
*[[Angular Reconstitution]] (AR)
*[[Random Conical Tilt]] (RCT)
*[[Orthogonal Tilt Reconstruction]] (OTR)

===Software Available===
An overview of the currently available software, links, and general descriptions.

==Resolution==

The concept of resolution in electron microscopy has brought out several debates in the past.

==Hardware Innovations to the Electron Microscope==
Some new, some old, there are many aspects of the microscope that may be changed, ostensibly altering the physics of image formation for the better.

*[[CMOS]]
*[[Phase Plates]]

----

Back to [https://leschzinerlab.ucsd.edu/ Leschziner Lab Main Site]

Main Page

2010-05-07T17:33:05Z

Bpappas: /* Introduction */

<center><big> '''Welcome to the Leschziner Lab's Tutorials Wiki''' </big></center>

In these pages you will find tutorials designed to explain, in an accessible way, some of the principles behind the techniques used in our lab. They range from the very general (How does a microscope work?) to very specific approaches used in Three-Dimensional Electron Microscopy (3D-EM). This wiki is, by definition, a "work in progress"; we will periodically add new material and update what's already here. Blue links are for tutorials already available while red ones are for those we are still developing.

We hope you find the material useful and welcome feedback on how to improve it. To give us feedback, please see the [[Talk:Main_Page|discussion tab]] at the top of the page, or [mailto:leschziner.tutorials@gmail.com e-mail us].

==Introduction==

The compound optical microscope, first recognized in 1590, is probably the most familiar of all laboratory instruments, especially for biologists. The electron microscope, for many years simply an exotic rarity, has also become a standard tool in biological research. Both instruments are often used quite effectively with little knowledge of the relevant theory, or even how the particular microscope functions. Eventually, however, proper use, interpretation of images, and choices of specific application demand an understanding of fundamental principles.

This wiki is intended to provide both a brief overview of such concepts, as well as a more in-depth theoretical view for those readers who would like to examine more of the mathematics and physics behind imaging (such as with image formation, contrast, resolution limits). In particular, Fourier imaging will be discussed as it applies to the interpretation of data.

Since our focus is not directed toward crystalline data sets but rather what can be referred to as asymmetric structures, the image processing and data interpretation sections will deal with techniques particular to the latter.

==General imaging principles==
These conventions and basic physics concepts are fundamental tools for understanding electron imaging.

*[[Light optics]]
*[[Microscope Ray Tracing]]
*[[Phase Contrast]]
*[[Depth of Field]]

==Electron imaging==
There are many caveats to imaging with electrons as opposed to photons.

*[[What is an Electron Microscope?]]
*[[History of the Electron Microscope]]
*[[Types of Signals]]
*[[Electron optics]]
*[[The Weak-Phase Object Approximation]]
*[[Contrast]]
*[[Ewald Sphere]]
*[[Aberrations]]
*[[Special Imaging Techniques]]

==Electron Microscopy of Macromolecules==

*[[Sample Preparation]]
*[[Special Considerations]]

==Two-Dimensional Averaging==

==Three-dimensional reconstruction by EM==

A "30 Second Overview" of three-dimensional EM reconstruction.

<qt>file=EM intro2.mov|width=768|height=576|autoplay=false|controller=true</qt>

===Basics===
*[[Central Section Theorem]]
*[[Back Projection]]

===Existing Reconstruction Methods===
*[[Angular Reconstitution]] (AR)
*[[Random Conical Tilt]] (RCT)
*[[Orthogonal Tilt Reconstruction]] (OTR)

===Software Available===
An overview of the currently available software, links, and general descriptions.

==Resolution==

The concept of resolution in electron microscopy has brought out several debates in the past.

==Hardware Innovations to the Electron Microscope==
Some new, some old, there are many aspects of the microscope that may be changed, ostensibly altering the physics of image formation for the better.

*[[CMOS]]
*[[Phase Plates]]

----

Back to [https://leschzinerlab.ucsd.edu/ Leschziner Lab Main Site]

Main Page

2010-05-07T16:48:13Z

Bpappas: /* Introduction */

Main Page

2010-05-07T16:42:14Z

Bpappas:

<center><big> '''Welcome to the Leschziner Lab's Tutorials Wiki''' </big></center>

In these pages you will find tutorials designed to explain, in an accessible way, some of the principles behind the techniques used in our lab. They range from the very general (How does a microscope work?) to very specific approaches used in Three-Dimensional Electron Microscopy (3D-EM). This wiki is, by definition, a "work in progress"; we will periodically add new material and update what's already here. Blue links are for tutorials already available while red ones are for those we are still developing.

We hope you find the material useful and welcome feedback on how to improve it. To give us feedback, please see the [[Talk:Main_Page|discussion tab]] at the top of the page, or [mailto:leschziner.tutorials@gmail.com e-mail us].

==Introduction==

In the Leschziner Lab, we use electron microscopy to study structures of macromolecules. In particular, we look at single particles and use the techniques described in the sections below to generate three-dimensional structures of the proteins or protein complexes of interest.

In addition to the study of protein structure, our lab is interested in improving techniques for 3D-EM. There exists a bottleneck in structure determination using 3D-EM in the generation of initial models upon which to refine structures. It is a goal of the lab to remove the bottleneck in generating initial models of macromolecules, helping to make the entire reconstruction process faster and more robust.

==General imaging principles==
These conventions and basic physics concepts are fundamental tools for understanding electron imaging.

*[[Light optics]]
*[[Microscope Ray Tracing]]
*[[Phase Contrast]]
*[[Depth of Field]]

==Electron imaging==
There are many caveats to imaging with electrons as opposed to photons.

*[[What is an Electron Microscope?]]
*[[History of the Electron Microscope]]
*[[Types of Signals]]
*[[Electron optics]]
*[[The Weak-Phase Object Approximation]]
*[[Contrast]]
*[[Ewald Sphere]]
*[[Aberrations]]
*[[Special Imaging Techniques]]

==Electron Microscopy of Macromolecules==

*[[Sample Preparation]]
*[[Special Considerations]]

==Two-Dimensional Averaging==

==Three-dimensional reconstruction by EM==

A "30 Second Overview" of three-dimensional EM reconstruction.

<qt>file=EM intro2.mov|width=768|height=576|autoplay=false|controller=true</qt>

===Basics===
*[[Central Section Theorem]]
*[[Back Projection]]

===Existing Reconstruction Methods===
*[[Angular Reconstitution]] (AR)
*[[Random Conical Tilt]] (RCT)
*[[Orthogonal Tilt Reconstruction]] (OTR)

===Software Available===
An overview of the currently available software, links, and general descriptions.

==Resolution==

The concept of resolution in electron microscopy has brought out several debates in the past.

==Hardware Innovations to the Electron Microscope==
Some new, some old, there are many aspects of the microscope that may be changed, ostensibly altering the physics of image formation for the better.

*[[CMOS]]
*[[Phase Plates]]

----

Back to [https://leschzinerlab.ucsd.edu/ Leschziner Lab Main Site]

Aberrations

2010-05-04T19:21:20Z

Bpappas:

Considering merely the de Broglie wavelength of electrons accelerated at 100kV (a common accelerating voltage for biological-EM), the electron microscope performs dismally compared to how it theoretically could. The wavelength for such and electron is 0.037Å. The theoretical minimum separation, ''d'', that could be resolved with this wavelength is thus (from Bragg's law):

[[File:Bragg.jpg]]

Where ''n'' is the refractive index of the vacuum (which is equal to 1); ''sinθ'' is equal to 1, since the numerical aperture for an electron microscope is very narrow.

However, electromagnetic lens aberrations, particularly from the objective lens, ultimately limit the resolution of the microscope. The typical resolution limit reported for TEM is only about 1 angstrom (about 100 times worse than the theoretical limit).

==Spherical Aberration==

The electromagnetic lenses in the EM have a stronger magnetic field toward the outside of the lens. This means that the further off axis an electron is traveling, the more strongly it is bent back to the axis. This causes what begins as a point in the object to become a disc in the image.

[[File:NoCs.jpg|500px]]
[[File:Cs.jpg|500px]]
[[File:CsExp.jpg|500px]]

==Chromatic Aberration==

==Axial Astigmatism==

==Coma Aberration==

==Effects on the Resolution limit of the TEM==

Aberrations

2010-05-04T19:19:01Z

Bpappas:

Considering merely the de Broglie wavelength of electrons accelerated at 100kV (a common accelerating voltage for biological-EM), the electron microscope performs dismally compared to how it theoretically could. The wavelength for such and electron is 0.037Å. The theoretical minimum separation, ''d'', that could be resolved with this wavelength is thus (from Bragg's law):

[[File:Bragg.jpg]]

Where ''n'' is the refractive index of the vacuum (which is equal to 1); ''sinθ'' is equal to 1, since the numerical aperture for an electron microscope is very narrow.

However, electromagnetic lens aberrations, particularly from the objective lens, ultimately limit the resolution of the microscope. The typical resolution limit reported for TEM is only about 1 angstrom (about 100 times worse than the theoretical limit).

==Spherical Aberration==

The electromagnetic lenses in the EM have a stronger magnetic field toward the outside of the lens. This means that the further off axis an electron is traveling, the more strongly it is bent back to the axis. This causes what begins as a point in the object to become a disc in the image.

[[File:Example.jpg]]

[[File:NoCs.jpg]]

[[File:Cs.jpg]]

[[File:CsExp.jpg]]

==Chromatic Aberration==

==Axial Astigmatism==

==Coma Aberration==

==Effects on the Resolution limit of the TEM==

File:CsExp.jpg

2010-05-04T19:18:29Z

Bpappas:

File:Cs.jpg

2010-05-04T19:17:53Z

Bpappas:

File:NoCs.jpg

2010-05-04T19:17:31Z

Bpappas:

Aberrations

2010-05-04T19:16:41Z

Bpappas: /* Spherical Aberration */

Considering merely the de Broglie wavelength of electrons accelerated at 100kV (a common accelerating voltage for biological-EM), the electron microscope performs dismally compared to how it theoretically could. The wavelength for such and electron is 0.037Å. The theoretical minimum separation, ''d'', that could be resolved with this wavelength is thus (from Bragg's law):

[[File:Bragg.jpg]]

Where ''n'' is the refractive index of the vacuum (which is equal to 1); ''sinθ'' is equal to 1, since the numerical aperture for an electron microscope is very narrow.

However, electromagnetic lens aberrations, particularly from the objective lens, ultimately limit the resolution of the microscope. The typical resolution limit reported for TEM is only about 1 angstrom (about 100 times worse than the theoretical limit).

==Spherical Aberration==

The electromagnetic lenses in the EM have a stronger magnetic field toward the outside of the lens. This means that the further off axis an electron is traveling, the more strongly it is bent back to the axis. This causes what begins as a point in the object to become a disc in the image.

[[File:NoCs.jpg]]

[[File:Cs.jpg]]

[[File:CsExp.jpg]]

==Chromatic Aberration==

==Axial Astigmatism==

==Coma Aberration==

==Effects on the Resolution limit of the TEM==

Aberrations

2010-05-04T15:47:54Z

Bpappas:

Considering merely the de Broglie wavelength of electrons accelerated at 100kV (a common accelerating voltage for biological-EM), the electron microscope performs dismally compared to how it theoretically could. The wavelength for such and electron is 0.037Å. The theoretical minimum separation, ''d'', that could be resolved with this wavelength is thus (from Bragg's law):

[[File:Bragg.jpg]]

Where ''n'' is the refractive index of the vacuum (which is equal to 1); ''sinθ'' is equal to 1, since the numerical aperture for an electron microscope is very narrow.

However, electromagnetic lens aberrations, particularly from the objective lens, ultimately limit the resolution of the microscope. The typical resolution limit reported for TEM is only about 1 angstrom (about 100 times worse than the theoretical limit).

==Spherical Aberration==

==Chromatic Aberration==

==Axial Astigmatism==

==Coma Aberration==

==Effects on the Resolution limit of the TEM==

File:Bragg.jpg

2010-05-04T15:47:41Z

Bpappas: uploaded a new version of "File:Bragg.jpg"

File:Bragg.jpg

2010-05-04T15:46:49Z

Bpappas:

Aberrations

2010-05-04T15:46:38Z

Bpappas:

Considering merely the de Broglie wavelength of electrons accelerated at 100kV (a common accelerating voltage for biological-EM), the electron microscope performs dismally compared to how it theoretically could. The wavelength for such and electron is 0.037Å. The theoretical minimum separation, ''d'', that could be resolved with this wavelength is thus (from Bragg's law):

[[File:Bragg.jpg]]

Where ''n'' is the refractive index of the vacuum (which is equal to 1); ''sinθ'' is equal to 1, since the numerical aperture for an electron microscope is very narrow.

However, electromagnetic lens aberrations, particularly from the objective lens, ultimately limit the resolution of the microscope. The typical resolution limit reported for TEM is only about 1 angstrom (about 100 times worse than the theoretical limit).

==Spherical Aberration==

==Chromatic Aberration==

==Axial Astigmatism==

==Coma Aberration==

==Effects on the Resolution limit of the TEM==

Aberrations

2010-04-30T22:24:04Z

Bpappas:

Considering merely the de Broglie wavelength of electrons accelerated at 100kV (a common accelerating voltage for biological-EM), the electron microscope performs dismally compared to how it theoretically could. The wavelength for such and electron is 0.037 angstroms. The theoretical minimum separation that could be resolved with this wavelength is thus:

d=&lambda\over\2n\sin &theta

d=.037\over\2 &times 1 &times 1

d=0.0185 Å

Where n is the refractive index of the vacuum (which is equal to 1).sin &theta is equal to 1 as well, since the numerical aperture for an electron microscope is so narrow.

However, electromagnetic lens aberrations, particularly from the objective lens, ultimately limit the resolution of the microscope. The typical resolution limit reported for TEM is only about 1 angstrom (about 100 times worse than the theoretical limit).

==Spherical Aberration==

==Chromatic Aberration==

==Axial Astigmatism==

==Coma Aberration==

==Effects on the Resolution limit of the TEM==

Aberrations

2010-04-30T22:23:32Z

Bpappas:

Considering merely the de Broglie wavelength of electrons accelerated at 100kV (a common accelerating voltage for biological-EM), the electron microscope performs dismally compared to how it theoretically could. The wavelength for such and electron is 0.037 angstroms. The theoretical minimum separation that could be resolved with this wavelength is thus:

<math>x</math>

d{{=}}&lambda\over\2n\sin &theta

d{{=}}.037\over\2 &times 1 &times 1

d{{=}}0.0185 Å

Where n is the refractive index of the vacuum (which is equal to 1).sin &theta is equal to 1 as well, since the numerical aperture for an electron microscope is so narrow.

However, electromagnetic lens aberrations, particularly from the objective lens, ultimately limit the resolution of the microscope. The typical resolution limit reported for TEM is only about 1 angstrom (about 100 times worse than the theoretical limit).

==Spherical Aberration==

==Chromatic Aberration==

==Axial Astigmatism==

==Coma Aberration==

==Effects on the Resolution limit of the TEM==

What is an Electron Microscope?

2010-04-30T21:40:29Z

Bpappas: Created page with '==Introduction== ==Essential Pieces of the Microscope== Cathode Wehnelt Cylinder Condensor Lenses Objective Lens Intermediate lenses Projector Lens Fluorescent Screen Recording…'

==Introduction==

==Essential Pieces of the Microscope==

Cathode
Wehnelt Cylinder
Condensor Lenses
Objective Lens
Intermediate lenses
Projector Lens
Fluorescent Screen
Recording Device (CCD, Photograph)

==Types of Samples==

Aberrations

2010-04-30T21:30:35Z

Bpappas: Created page with ' However, in the EM, electromagnetic lens aberrations, particularly from the objective lens, ultimately limit the resolution of the microscope. ==Spherical Aberration== ==Chro…'

However, in the EM, electromagnetic lens aberrations, particularly from the objective lens, ultimately limit the resolution of the microscope.

==Spherical Aberration==

==Chromatic Aberration==

==Axial Astigmatism==

==Coma Aberration==

==Effects on the Resolution limit of the TEM==

Main Page

2010-04-30T21:01:50Z

Bpappas: /* Electron imaging */

Sample Preparation

2010-04-30T21:01:16Z

Bpappas: Created page with 'Intro ==Support Grids== ==Negative Stain== ===Artifacts=== ==Vitreous Ice Embedment== ===Cryo-Negative Staining=== ==Labeling with Gold Clusters=='

Intro

==Support Grids==

==Negative Stain==

===Artifacts===

==Vitreous Ice Embedment==

===Cryo-Negative Staining===

==Labeling with Gold Clusters==

Special Imaging Techniques

2010-04-30T20:47:49Z

Bpappas: Created page with '==Low-Dose Imaging== ==Spot-Scanning== ==Automated Data Collection== ==Energy Filtering=='

==Low-Dose Imaging==

==Spot-Scanning==

==Automated Data Collection==

==Energy Filtering==

Main Page

2010-04-30T20:46:44Z

Bpappas:

Main Page

2010-04-30T20:17:50Z

Bpappas:

Types of Signals

2010-04-30T20:16:14Z

Bpappas:

[[File:Signals.jpg]]

File:Signals.jpg

2010-04-30T20:15:41Z

Bpappas: From: Transmission Electron Microscopy: A Textbook for Materials Science (David B. Williams, C. Barry Carter)

From: Transmission Electron Microscopy: A Textbook for Materials Science
(David B. Williams, C. Barry Carter)

Types of Signals

2010-04-30T20:09:44Z

Bpappas: Created page with 'File:Signals.tiff'

[[File:Signals.tiff]]

Main Page

2010-04-30T20:09:22Z

Bpappas:

History of the Electron Microscope

2010-04-28T16:26:15Z

Bpappas: Created page with '==A Snapshot of the EM:== To quote Slayter and Slayter: ''“At first many physicists doubted that a practical [electron microscope] could be devised, because electron beams are …'

==A Snapshot of the EM:==
To quote Slayter and Slayter: ''“At first many physicists doubted that a practical [electron microscope] could be devised, because electron beams are destructive, and specimens (especially biological specimens) are fragile. Nevertheless, electron lenses were described in 1926, a prototype electron microscope was constructed by 1932, and the first commercial instrument was launched by 1939. By 1970, the resolving power was 0.6nm, and by 1990, 0.1-0.2nm.”'' (1)

==A Longer Exposure:==
In 1925, the wave nature of electron was first accredited to de Broglie during the modern physics movement.

===The Ruska/Knoll Early History:===
According to several accounts, devices developed to form electron images came about in the late twenties and early thirties by engineers, apparently independent of de Broglie’s description(2). Theory and practice met when the experimental improvements in resolving power were attributed to the short wavelengths of electrons. This is evidenced by Ernst Ruska’s claim that he had not heard of de Broglie’s theory until after his and Max Knoll’s paper in 1931 on electron lenses and the electron microscope (2). These two are credited with first coining the term electron microscope, and Ruska was awarded the Nobel Prize in 1986 for the discovery. In his Nobel lecture, the prototype electron microscope is described, using the short iron clad coils, on which he had written his thesis, as lenses:

''“Such an apparatus with two short coils was easily put together and in April 1931 I obtained the definite proof that it was possible. This apparatus is justifiably regarded today as the first electron microscope even though its total magnification of 3.6 x 4.8 = 14.4 was extremely modest.”''(3)

In this microscope, the first TEM images were taken: mesh grids place over the anode aperture(3).

===The Rüdenberg Early History:===
Interestingly, it seems that though Ruska and Knoll are honored with the title of inventors of the EM, that Reinhold Rüdenberg of the Siemens company and later Harvard University actually patented the microscope in 1931 under the Siemens name. In this case, Rüdenberg based the patent and experiments on the theory of his friend, Hans Busch, who theorized the electron lens in 1926, and de Broglie’s wave nature of the electron to solve the resolution limit described by Helmholtz and Abbé (4). Rüdenberg was driven to develop the instrument by a desire see the polio virus, a disease affecting his son(4). He was unable to claim right to his invention upon immigration to the US, as this was the policy of the German government at the time(4).

==Early Samples:==
In either case, by the mid thirties and forties, many other engineers and scientists joined the fray to produce electron microscopes. During this period, the first electron micrographs appeared of biological specimens:

*In Brussels in 1934, Ladislaus L. Marton made a horizontal electron microscope to study the photoelectric effect, and went on to study biological specimens at a magnification of 20-30,000x. Later in 1937, he published the first electron micrographs of bacteria.
**Ref: Marton, L. 1934. La microscopie electronique des onjectes biologiques. Bull. Acad. Belg. Cl. Sci. 20: 439-466
*Heinz Otto Mueller and Friedrich Krause, an electric engineer and a medical student respectively, worked to improve the instrument that Ruska built in 1933, taking micrographs of bacteria and other biological materials in the later thirties.
*In 1940, Helmuth Ruska, Ernst’s brother, used an electron microscope to obtain the first pictures of a virus.
**Ref: Ruska, H. 1940. Die Sichtbarmachung der BakteriophagenLyse im Ubermikroskop. Naturwissenschaaften. 28: 45-6.
*In 1942, Thomas Anderson and Salvador Luria photographed bacteriophages with the aid of an electron microscope, confirming earlier work by Ruska. They demonstrated that a T2 phage has a head and a tail.
**Ref: Luria, S. E. and T. F. Anderson. 1942. The identification and characterization of bacteriophages with the electron microscope. Proc. Natl. Acad. Sci. USA. 28: 127-13
*The first electron micrograph of an intact cell was published in The Journal of Experimental Medicine in March 1945, in "A Study of Tissue Culture Cells by Electron Microscopy," by K. R. Porter, A. Claude, and E. F. Fullam.

In the materials science world, far less was being accomplished early on due to limitations in specimen preparation. During the early forties, the main types of samples being studied were carbon black particles and those particles that colored cosmetics. It wasn’t until 1949 when Heidenreich thinned metal foils to electron transparency (2) that a lot of the early materials science work in EM took off.

==Building Better EMs:==
The first industrially (regularly) produced EM was by Siemens in 1939, starting with a series of events described by Ernst:

''"As first collaborators [Max Knoll and I] secured Heinz Otto Mueller for the practical development and Walter Glaser from Prag as theorist. We started in 1937, and in 1938 we had completed two prototypes with condenser and polepieces for objective and projective as well as airlocks for specimens and photoplates. The maximum magnification was 30,000x. One of these instruments was immediately used for first biological investigations by Helmut Ruska and several medical collaborators. […]By the end of 1939 the first serially produced Siemens instrument had been delivered to Hoechst. The instrument No. 26 was, by the way, delivered to Professor Arne Tiselius in Uppsala in autumn 1943. By Februrary 1945 more than 30 electron microscopes had been built in Berlin and delivered."''(3)

WWII, of course, disrupted a lot of this early push for EM, including the bombing of first visiting scientist laboratory that Siemens built in 1944, and Kruase and Mueller’s deaths during the early forties. Even so, by 1954 Siemens was again able to produce a scope with mass appeal: the Elmiskop. This was the first to have two condenser lenses, allowing for less heat irradiation of the sample(3).

According to Dykstra, the latter half of the 20th century was mainly focused on improving the auxiliary devices, and the overall operational systems. By 1946, the gross resolution improvements had essentially been done, after Hillier and Vance improved on their RCA TEM model to a 1.0nm resolution(5). The decade breakdown for improvements goes as follows from Dykstra’s chapter on the TEM(5):

*1950s and 1960s: Improvements in power supplies (smaller, solid-state circuit controlled supplies instead of vacuum tubes), lens manufacture (the Philips 75 had sliding objective lenses), vacuum systems (the addition of a LN2 cold trap improved pressure from 10^-4 to 10^-6 Torr), and mechanical controls (the Philips 200 now allowed for screw adjustments of the column elements, and the Hitachi HU-11E allowed for mechanical and electron alignments). For the user-friendly side of things, phosphorescent viewing screens were developed.

*1970s: Development of high voltage (1meV) TEMs, as well as an overall industry standard of a 0.344nm resolution on all TEMs sold in the latter half of the decade.

*1980s: Development of intermediate voltage EMs (300 to 400keV), and EMs with resolutions less than 2Å. Also, a boom in the development of better accessories occurred in this decade. Vacuum systems were made cleaner with better diffusion oil pumps, turbomolecular pumps, and ion getter pumps. New techniques including AFM, STM, and electron energy loss spectroscopy were invented, aiding in comparisons. Additionally, in the interest of increasing user-friendliness and precise control, the Philips CM and the Hitachi H-7000 were among the first to move to partial computer control in the 1980s.

*1990s: JEOL’s JEM-1210 was the first software driven TEM(5). Further improvements in user-friendliness and the reduction of noise and image defects seem to have been the main points of interest for the past decade or so.

==Main References:==
#Slayter, EM, Slayter, HS. Light and Electron Microscopy. Cambridge University Press, NY:1992.
#Williams and Carter. Transmission Electron Micrscopy: A Textbook for Materials Science. Springer, NY: 1996.
#Ruska, E. The development of the electron microscope and of early electron microscopy. Nobel Lecture: 8 December 1986.
#Rüdenberg, R. The Early History of the Electron Microscope. Journal of Applied Physics, 27 May 1943. p. 434-436.
#Dykstra, MJ. Biological Electron Microscopy: Theory, Techniques, and Troubleshooting. Plenum Press, NY: 1992.

Main Page

2010-04-27T20:56:32Z

Bpappas:

Depth of Field

2010-04-26T16:39:18Z

Bpappas:

<qt>file=Depth of field.mov|width=768|height=576|autoplay=false|controller=true</qt>

Phase Contrast

2010-04-26T16:39:00Z

Bpappas:

<qt>file=Phase contrast2.mov|width=768|height=576|autoplay=false|controller=true</qt>