[introduction to cryoelectron microscopy] Caltech open class course notes part 3:image formation

• Amplitude and phase contrast, scattering( scattering )
  • scattering ： What happens when electrons hit an object

Inelastic scattered electrons and elastic scattered electrons form images of different planes in the microscope . Therefore, energy filters are usually used to eliminate elastically scattered electrons .

Inelastic scattering has a wide range , And it will damage the sample .
actually , The basic resolution limitation in freeze electron microscopy is the radiation damage caused by inelastic scattering .

• Different electron microscope types
  Two different electron microscopes ：“scanning” vs “brightfield”
  Scanning mode and bright field mode . Scanning electron microscope means that we focus the incident electron beam on a very small point, maybe 1 Nanometer wide , Then give a sample , We use this dot to scan the image back and forth as a grating , The latter will illuminate the entire sample at once .

Three basic forms ：
1. Scanning electron microscope （SEM）
2. Scanning transmission electron microscope (STEM)
3. Transmission electron microscope (TEM)： Bright field mode

There are two kinds of contrast in transmission electron microscope , They are amplitude contrast and phase contrast .
two kinds of contrast: amplitude and phase

Want to understand phase contrast , The incident electrons must be treated as waves , It is scattered to all scattering directions at the same time .

Treat electrons as plane waves , Each pixel has an amplitude in phase . When the plane wave interacts with the sample , The sample will delay the phase and scatter , So you will have phase fluctuations . When the electron wave passes through the sample , They embed a series of fluctuations in them so that they cannot be drawn , All these waves together produce waves , In this direction or higher scattering angle . The lens bends the scattered rays and collects them . So there is a wave function , It exists on the back focal plane of the lens , This wave function has a strong amplitude at these positions of the Fourier component , It is the Fourier transform of sample density . As these rays continue to move along the electron microscope , All these Fourier components interfere with each other to form complex wave functions . Last , The wave function on the imaging plane is an enlarged version of the sample density , In this wave function, we finally record it on the detector .

Let's take an image as an example , For example, the sample is a complex image , Like this portrait of Professor Fourier .
Then the wave function existing in the focal plane behind the objective lens is the Fourier transform of the object density .
The wave function existing on the image plane behind the objective lens is the representation of the density of the original object after amplification . So this is the Fourier transform of the wave function of the back focal plane .
So in the microscope, the Fourier transform of the original image appears on the back focal plane , The representation of the original function appears on the acceptance plane .
But the above is the ideal situation . In reality, some scattered rays are transmitted to the image more strongly than others .

Under the electron microscope, not all components of the image appear equally strong , Some Fourier components are fully represented in the final image , Some show only half or complete absence .

• Wave propagation and phase shifts

  • How does the wave travel down through the mirror tube , And how the phase shift between these waves makes the waves invisible , And which are not , This will lead us to understand the contrast transfer function （CTF function）.

• The contrast transfer function

Understand why some Fourier components are strongly expressed in electron microscope images , And some components disappear .
When the electron wave strikes the sample, some will not scatter , Some will scatter , A single electron can experience all these phenomena , Its contribution to the final image depends on how all these processes interfere with each other .

• Defocus and its effects（ Defocus and its influence ）
• Envelopes
• CTF correction

（ It's not finished yet ）

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$$Author:Chier$$