Electron detection

Lecture 5

OutlineDetector characteristics & definitions

– Gain, noise, PSF, DQE, Nyquist Frequency Types of electron detectors and how they work

– Viewing screen – Semiconductor detectors – Photographic film – CCD cameras – Direct electron detectors

Detector characteristicsGain:

– Magnitude of signal amplification Shot noise:

– Random noise – Provides a natural limit

Resolution: – “Related to” the size of the pixel

Point Spread Function (PSF): – This is the real resolution: The PSF in many contexts can be thought of

as the extended blob in an image that represents an unresolved object. Dynamic range:

– Ratio of brightest pixel to dimmest pixel

Intensity

Point solid image

Point spread function

W&C: 7.1

Detector characteristicsDetection Quantum Efficiency (DQE)

– DQE measures the combined signal effects (related to image resolution and contrast) and noise performance of an imaging system that vary with spatial frequency

– It describes how effectively the camera can produce an image with a high signal-to-noise ratio (SNR)

– DQE is a good indicator for how much data is obtained per unit of electron dose to the sample

– Mathematically DQE is expressed as the relationship between the output and input of the SNR.

DQE =Sout

Nout

⎛

⎝⎜

⎞

⎠⎟

2Sin

Nin

⎛

⎝⎜

⎞

⎠⎟

2

http://www.gatan.com/improving-dqe-counting-and-super-resolution

Detector characteristicshttp://www.gatan.com/improving-dqe-counting-and-super-resolution

Low contrast picture of Siméon Poisson At 33% DQE - details of hair, eyes, etc. lost due to noise

Detector characteristicsNyquist-Shannon Theory:

– “a signal sampled at a rate F can be fully reconstructed if it contains only frequency components below half that sampling frequency: F/2”

– This frequency is known as the Nyquist frequency

http://www.gatan.com/nyquist-frequency

fNyquist ≥ 2fsignal

Detector characteristicsNyquist-Shannon Theory:

– “a signal sampled at a rate F can be fully reconstructed if it contains only frequency components below half that sampling frequency: F/2”

– This frequency is known as the Nyquist frequency

http://www.gatan.com/nyquist-frequency

When a component of the signal is above the Nyquist, a sampling error occurs that is called aliasing. Aliasing “names” a frequency above

Nyquist by an “alias” the same distance below Nyquist

Detector characteristics

Detector characteristics

https://www.youtube.com/watch?v=-wL1T4N9rRo&feature=youtu.be

Self assessment questionsWhat is the PSF?

What is DQE? What is the Nyquist frequency?

Some termsCathodoluminescence (CL)

• Production of visible light from the impact of high energy electrons

Scintillation • Light emission caused by

ionizing radiation

Fluorescence • “Rapid” emission (nanosecs)

Phosphorescence • “Slow” emission (secs)

W&C: 7.2

Viewing screen: a.k.a. “fluorescent screen”

ZnS or ZnS / CdS powder on a backing plate – Cathodoluminescence

– Dope to get to λ ≈ 550 nm, best eye sensitivity

– Grain sizes on the order of 100 to 50 µm, 10 µm on the focusing screen

Intensity is proportional to current density

Time constant on order of 10-5 to 10-3 secs Phosphoresces for a second or so afterwards

Very intense transmitted beam can damage the screen (over time) …

W&C: 7.2

Faraday cupFor quantitative work you may need to have a direct measure of the electron current A “Faraday cup” is used to capture all of the incident electrons and measure their current directly

W&C: 7.3d

Semiconductor detectorsEstablish a p-n junction in silicon Incident electrons excite valence electrons, which leads to electron-hole pairs and thus a detectable current Inherently high gain:

– 100keV electron produces 28,000 e-h pairs

– Even with losses, leads to gain of > 104

W&C: 7.3a

Semiconductor detectorsAdvantages:

– Easy to make, and in unusual (flat) shapes

– Inexpensive Disadvantages:

– Large “dark current” due to thermal activation

– Poor DQE unless signal is high

– Narrow bandwidth • Bad for rapidly

changing signal intensity

W&C: 7.3a

Scintillator/photomultiplier tubesUse a fast scintillator (short fluorescence time)

– Ce-doped Yttrium Aluminum Garnet (YAG)

– Decay times of order nanoseconds

Light amplified by photomultiplier tube Some loss from aluminum coating on YAG to reflect light photons

W&C: 7.3b

Scintillator/photomultiplier tubesAdvantages:

– Very high gain - of order 108

– High DQE (of order 0.9) Disadvantages:

– Susceptible to radiation damage

– Both expensive and bulky

– Low conversion of electrons to photons, which offsets gain advantage above

W&C: 7.3b

Charge-coupled devices (CCD’s)Based on accumulation of charge in a MOS capacitor

Apply a voltage pulse • Transient condition:

“deep depletion • ”Photo-injected

electrons” stored in this well

W&C: 7.3c

Charge-coupled devices (CCD’s)Clocking scheme used to transfer charge from one MOS capacitor to the next

t1

t2

t3

t4

V1 (+)

V1,V2 (+)

V1 < V2

V2 (+)

Must happen before thermal generation

Can have either serial or full frame readout

W&C: 7.3c

Charge-coupled devices (CCD’s)Need to convert e- to hν Thin aluminum to reflect any stray light (≈ 100 nm)

“Binning” • Average several pixels

YAG scintillator • Converts e- to hv • Must be relatively thick to

get sufficient conversion • Can result in a significant

“blooming” • Measured as “point spread

function”

W&C: 7.3c

CCD Camera useNeed to acquire a “dark reference” image

– Even with LN2 cooling, some shot noise is present

– Allows subtraction of an average ‘noise image’

Need to prepare “Gain Reference”

– This is a good low noise picture of the camera

– Used to subtract out the fiber optic honeycomb and any defects

– This is stored used with each subsequent image

Need to acquire “dark reference” image

• Even w. LN cooling, some shot noise present

• Allows subtraction of ‘noise’ image

This image was taken without ‘gain subtraction’. Note the honeycomb pattern from the fiber-optic coupling & dead pixels

CCD CamerasAdvantages:

–Good DQE, even at low input signal levels –High dynamic range

• Diffraction patterns –Linear –Convenient

Disadvantages: –Relatively low resolution, unless you spend a lot of money. Nowadays $60k - $80k gets 2k x 2k

–They are not cheap (see point #1) –Generally have slow readout speed

– But now, of order video rate

W&C: 7.3c

CCD CamerasIndividual pixels can handle only so many incident electrons

Creates too many e-/h+ pairs, which spill over into adjacent pixels

– Shows up as either a large intense region or a streak

In addition to being ugly, it makes quantitative diffraction difficult

W&C: 7.3c

Self assessment questionsHow do semiconductor detectors work?

What are the advantages and disadvantages of semiconductor detectors?

How does a scintillator-photomultiplier detector work?

What are the advantages and disadvantages of scintillator-photomultiplier detectors?

What are the advantages of CCD cameras?

What is a Faraday cup?

What is the difference between scintillation, fluorescence, and phosphorescence?

Why are ZnS-based viewing screens doped?

DQE limiting factors: • Electron scattering in low-Z Si sensor. • Electron back-scattering from fiber optic • Scattering of light in fiber optic • Distortions from fiber optic • Electronic read noise

Direct electron detectors

Scintillator electron to light conversion

Fiber optic light image transfer

CCD or CMOS sensor light to charge conversion

e-Electron to charge

conversione-

Traditional Fiber-Coupled Camera (CCD or CMOS)

Direct Detection Camera

Contarato, et al., Physica Proc., 37, 1504, 2012 Li, et al., Nat. Methods, 10, 584, 2013.

Following slides are courtesy of Cory Czarnik at Gatan

DQE limiting factors: • Electron scattering in low-Z Si sensor. • Electron back-scattering from fiber optic • Scattering of light in fiber optic • Distortions from fiber optic • Electronic read noise

DQE limiting factors: • Electron scattering in high-Z scintillator • Electron back-scattering from fiber optic • Scattering of light in fiber optic • Distortions from fiber optic • Electronic read noise

Direct electron detectors

Scintillator electron to light conversion

Fiber optic light image transfer

CCD or CMOS sensor light to charge conversion

e-Electron to charge

conversione-

Traditional Fiber-Coupled Camera (CCD or CMOS)

Direct Detection Camera

Contarato, et al., Physica Proc., 37, 1504, 2012 Li, et al., Nat. Methods, 10, 584, 2013.

Counting mode

https://www.youtube.com/watch?v=hGwf8w5KiCs&feature=youtu.be

1. Electron enters detector 2. Signal is scattered

3. Charge collects in each pixel

K2 Base: Charge Integration Improved DQE at high frequency

0.6

0.15 0.1

0.15

K2 Summit: Counting Improved DQE at low AND

high frequency

1

4. Events are reduced to the highest charge pixels

1. Electron enters detector 2. Signal is scattered

3. Charge collects in each pixel

K2 Base: Charge Integration Improved DQE at high frequency

0.6

0.15 0.1

0.15

K2 Summit: Counting Improved DQE at low AND

high frequency

4. Events are reduced to the highest charge pixels

1

“Super Resolution”

Dyn

amic

Qua

ntum

Effi

cien

cy

0

0.25

0.5

0.75

1

Fraction of physical Nyquist frequency

0 0.5 1 1.5 2

K2 Summit Super-ResolutionK2 Summit CountingK2 BaseUltrascan CCD Camera

>0.5 DQE at 0.5

Nyquist

Direct Detection

Counting Super-Resolution

300 kV

Advantage to counting mode

Single 2.5 ms frame using conventional

CCD-style charge read-out

Same frame after counting

Counting removes the variability from scattering, rejects the electronic read-noise, and restores the DQE

Counting require speed

It takes 400 fps to resolve electrons at a dose rate of 10 e-/pix/s

40 frames per second: events overlap & cannot be resolved

400 frames per second: events are resolved

Typical dose rate of 10 e-/pix/s

K2 Summit Super-Resolution mode boosts the signal even further

Nyquist Frequency Without Super-Resolution

Nyquist Frequency Without Super-Resolution

9.7 e-/Å2

K2 Summit Super-Resolution

Super resolution and aliasing

AdvantagesFeature Benefit

Frame RateK2-IS can capture subframes up to 1600 fps (0.000625 seconds / frame) for sub-ms time resolution

DQE Benefit High DQE across wide range of spatial frequencies

Thinned Direct Detection Sensor

Very little backscatter improves resolution with small pixels

No scintillator time lag (tau) issue – charge is collected quickly in small pixel so no time “point spread” issue

100% Fill FactorWith transmission scintillator, full area can be used to collect charge in each 5 µm pixel

100% Duty CycleSensor is continuously read-out so no electrons are missed (DQE is real time DQE, not “only when sensor is accumulating)

Long Continuous Recording TimeK2-IS can record every frame continuously written to disk up for > 15 minutes

Radiation Hard SensorLongest lifetime sensor required for usable lifetime at extreme doses

Disadvantages: Too much data!

Continuous imaging at 400 fps yields 4Tb of data on the SDD Drive 15 minutes of acquisition = 4Tb of data – It then must be moved off to take additional images

– This takes significant time to transfer to SAN Array Images are raw: scrambled raw data feeds Must be stitched back into images - also very time consuming

K2 Camera Digitizer

400 full fps

Summit processor

400 fps (bin x 2)

SSD High speed storage

Self assessment questionsHow does a direct electron detector work?

What are key advantages and disadvantages?

What is ‘super resolution’ in this context?