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Photodetection in Flow Cytometry
Slawomir Piatek
New Jersey Institute of Technology and
Hamamatsu Photonics, Bridgewater, NJ, USA
06.4. 2020
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■ Introduction to Flow Cytometry
■ Photodetection
■ How are Scattered Plots Affected?
Index
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Motivation
How does photodetection affect the science depicted in the scatter plots?
FSC-A 106
SS
C-A
106
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Introduction to Flow Cytometry
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Flow Cytometer Consists of Three Components:
Fluidics
Optics
Electronics
Photodetectors bridge these two components
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Fluidics
Interrogation or
analysis point
~100 μm~20 μm
1. Hydrodynamic focusing creates a narrow flow, known as the
core, where the cells arrange in a one-by-one file
2. The diameter of the core depends on the pressure difference
between the sheath fluid and the core fluid.
3. Only one cell at the time should be passing through the
interrogation point.
4. Sampling rate ~1,000 − 100,000 s-1
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Optics
FD
SCD
FSD
Laser 1
Laser
2Data collection
& analysis
Beam mixer
DM
DM
Flow
Legend:
FSD – forward-scatter detector
SCD – side-scatter detector
FD – fluorescence detector
DM – dichroic mirror
Fluorescence-tagged cell
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Interrogation Point
Beam profile (typically Gaussian)
before cylindrical lens (not to scale)
Beam profile at the interrogation
point (not to scale). The long
axis is perpendicular to the flow.
~100 μm
~20 μm
interrogation
point
cylindrical lens
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Light Sources
1. Solid-state lasers are the most common illuminators in modern flow cytometers
2. These lasers are compact, light weight, and can provide up to 150 mW of output power
3. Typical wavelengths [in nm]: 488, 505, 514, 532, 552, 561, 594
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Interaction of Light with the Cell: Signal Generation
reflection
refraction
diffraction/scattering
fluorescence
absorption
cell
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Spurious Light
𝑛1 𝑛2
Spurious light can be due to:
Impurities
Index of refraction differences
Flow turbulence
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Signal Formation
20 μm
100 μm
10-μm cell
Reference: “Practical Flow Cytometry” by Shapiro
1. Suppose we have 20-mW laser with 𝜆 = 488 nm
2. About 10% of the power (or 2 mW) will illuminate a 10-μm cell as it passes through the
interrogation point. The amount will be proportionally larger/smaller for a cell that is
larger/smaller
3. The implied illumination intensity is about 2.55×107 W/m2, which for 488-nm photons gives
6.27×1025 photons per m2 per s
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Signal Formation
20 μm
100 μm
10-μm cell
Reference: “Practical Flow Cytometry” by Shapiro
4. Thus the 10-μm cell is illuminated with 4.9×1015 photons per s.
5. If the interrogation rate is 1,000 cells per second, a cell will scatter a total of about 4.9×1012
photons
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Anatomy of a Pulse
𝜏
Pulse of lightlens
𝜏
Pow
er
time
Pulse duration
Peak power
Area of the pulse = total energy in the pulse
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Forward–Scatter Detection
Iris
Lens
Beam
blocker
Flow cell
Photodetector
typically a photodiode
Filter
λcenter = λlaser
1. The forward scatter signal is primarily determined by the size of the interrogated cell
2. The peak forward scatter power at 𝜆 = 488 nm using 2-μm microspheres and 20-mW laser is
about 4 μW
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Side-Scatter Optical Setup
APD/PMT/SiPM
Data processing
flow cell/interrogation point
collector and collimator
dic
hro
ic m
irro
rs
1. Light is a mixture of scattered laser light and
fluorescence
2. Light level is much lower than in the forward
scatter
3. Multiple fluorescence wavelengths can be
present
4. Need to use photodetectors with intrinsic gain
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The Role of the Photodetector
time
light le
vel
time
photodetector electronicsvo
ltag
e
A photodetector + electronics convert the input light signal (a pulse) into electrical pulse
(voltage as a function of time)
to A/D converter
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Current to Voltage Conversion
PD
i
Resistive termination
PD
i−
+
Transimpedance amplifier (pre-amplifier)
+ Simple circuit and inexpensive
+ Well-behaved frequency response
+ Well-understood noise (Johnson)
− Loads the PD, can lead to non-linearity
+ Virtual ground, no loading of the PD
− Complex noise and frequency response
− Needs biasing
𝑉𝑜𝑢𝑡 = 𝑖𝑅
𝑉𝑜𝑢𝑡 = −𝑖𝑅𝐹
virtual ground!
𝑅
𝑅𝐹
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What is Measured?
time
FWHM
Area
Peak
Outp
ut
voltage fro
m p
ream
plif
ier
The front-end electronics can be set up to measure the peak value of the pulse, its FWHM,
and/or area under the curve. These different measurements provide specific information
about the cell.
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Detection and Data Processing Chain
-
+
PD
Pre-amplifier
electronics to
measure peak,
area, or FWHMA/D
𝑅
𝑣𝑜
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Scatter Plots
Forward-scatter signal
Sid
e-s
catter
sig
nal
Fluorescence ch. 1
Flu
ore
scence c
h.
2
Scatter plots are ubiquitous to flow cytometry
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Histograms
No
. o
f ce
lls (
eve
nts
)
Signal, e.g. side scatter
Histograms of a given measured quantity are also common
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Photodetection
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Point Photodetectors used in Flow Cytometry
PMT PD APD SiPM
PMT – photomultiplier tube
PD – photodiode
APD – avalanche photodiode
SiPM – silicon photomultiplier
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Photomultiplier Tube
Light
𝐷1 𝐷2 𝐷3 𝐷4 𝐷5 𝐷6 𝑅𝑙
𝑣𝑜
𝑅1 𝑅2 𝑅3 𝑅4 𝑅5 𝑅6 𝑅7
𝑃𝐾𝑒−
𝑉~1000 V
𝐶1 𝐶2 𝐶3
𝐼𝑃
𝐼𝐾
𝑃 − anode𝐾 − cathode 𝐷1, …𝐷6 − Dynodes
There are two essential phenomena involved in the operation of a PMT: extrinsic
photoelectric effect and electron secondary emission.
Gain: 104 − 108
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Solid-State Photodetectors
Si PIN photodiode Si APD SiPM
p
i
n
hν
p
n
hν
Gain =1 Gain up to ~100
hν hν
Gain ~106
𝑣𝑜 𝑣𝑜𝑣𝑜𝑅 𝑅 𝑅
𝑉𝐵𝐼𝐴𝑆 𝑉𝐵𝐼𝐴𝑆 𝑉𝐵𝐼𝐴𝑆
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Detection Characteristics: Photosensitivity
Can we detect the “red” pulse?
PD E
A photodetector’s effective photosensitivity depends on its quantum efficiency (function of
wavelength) and intrinsic gain.
light
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Detection Characteristics: Gain Variations
PD E
1. Random gain variation of a photodetector increases noise, which translates into a larger scatter
of the measured quantity
2. All photodetectors with intrinsic gain exhibit gain variation. The contribution to noise is
expressed with excess noise factor 𝐹
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Gain and Excess Noise
PMT
APD
SiPM
105 − 107
105 − 106
1−100
𝐹𝜇
~1.2
~3 − 4
~1.1
𝐹 ≈𝛿
𝛿 − 1
𝐹 ≈ 𝜇0.3
𝐹 ≈ 1 + 𝑃𝑐𝑡
Legend
𝜇 − Intrinsic gain of a photodetector
𝐹 − Excess noise factor
𝛿 − Gain of the first dynode in a PMT (typically ~4)
𝑃𝑐𝑡 − Probability of crosstalk in a SiPM (typically less than 10%)
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Detection Characteristics: Dark Current
PD E
1. Photodetector’s dark current results in the output signal offset from zero
2. The variation around the mean is noise
3. The magnitude of dark current depends on the photodetector’s bias voltage and temperature
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Detection Characteristics: Bandwidth
Is there an output signal pileup?
PD E
1. Insufficient bandwidth degrades signal fidelity. At high counting rates this may lead to signal
pileup
2. Detection bandwidth is determined by the photodetector and front-end electronics
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Bandwidth and Noise
Too much bandwidth adds noise (indicated by the thicker line) but does not improve fidelity
PD E
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Bandwidth and Noise
100 kHz bandwidth 10 MHz bandwidth
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Detection Characteristics: Linearity and Dynamic Range
Is the output proportional to the input?
PD E
Linearity and dynamic range depend on the properties of the photodetector and
detection electronics
saturation
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Detection Characteristics: Stability
PD E
There are numerous factors that can affect stability (at different time scales):
gain variation, temperature drift, 1/f noise,…
Does the output vary for a constant input?
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Detection Characteristics: Temperature Drift
PD E
increasing temperature
1. If uncompensated, temperature drift will cause gain change of the photodetector. This effect is
very strong in APDs and SiPMs
2. Temperature drift also affects noise characteristics
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Signal-to-noise ratio
mean (Signal)
time
𝑆
𝑁𝑆
𝑁
1. Τ𝑆 𝑁 must be greater than 1 for detection to contain useful information
2. Τ𝑆 𝑁 depends on many factors such as incident light power, photodetector’s sensitivity, detection
bandwidth, type of frontend electronics, and more…
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Signal-to-Noise Ratio
𝑅 = 10 𝑘Ω
PMT
SiPM
APD
PD
𝜆 = 520 𝑛𝑚
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How are Scattered Plots Affected
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How are Scatter Plots Affected?
Forward-scatter signal
Sid
e-s
catter
sig
nal
Reference (Ideal)
Forward-scatter signalS
ide
-scatter
sig
nal
Power variation due to flow
![Page 41: Photodetection in Flow Cytometry · 2020-06-04 · Reference: “Practical Flow Cytometry” by Shapiro 4. Thus the 10-μm cell is illuminated with 4.9×1015 photons per s. 5. If](https://reader033.vdocuments.us/reader033/viewer/2022043004/5f88512e2b7f2d05ec233aa7/html5/thumbnails/41.jpg)
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How are Scatter Plots Affected?
Forward-scatter signal
Sid
e-s
catter
sig
nal
Reference (Ideal)
Forward-scatter signal
Sid
e-s
catter
sig
nal
Higher photosensitivity
![Page 42: Photodetection in Flow Cytometry · 2020-06-04 · Reference: “Practical Flow Cytometry” by Shapiro 4. Thus the 10-μm cell is illuminated with 4.9×1015 photons per s. 5. If](https://reader033.vdocuments.us/reader033/viewer/2022043004/5f88512e2b7f2d05ec233aa7/html5/thumbnails/42.jpg)
42🄫 Hamamatsu Photonics K.K. and its affiliates. All Rights Reserved.
How are Scatter Plots Affected?
Forward-scatter signal
Sid
e-s
catter
sig
nal
Reference (Ideal)
Forward-scatter signal
Sid
e-s
catter
sig
nal
Higher random noise
![Page 43: Photodetection in Flow Cytometry · 2020-06-04 · Reference: “Practical Flow Cytometry” by Shapiro 4. Thus the 10-μm cell is illuminated with 4.9×1015 photons per s. 5. If](https://reader033.vdocuments.us/reader033/viewer/2022043004/5f88512e2b7f2d05ec233aa7/html5/thumbnails/43.jpg)
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How are Scatter Plots Affected?
Forward-scatter signal
Sid
e-s
catt
er
sig
nal
Reference (with random noise)
Forward-scatter signal
Sid
e-s
ca
tte
r sig
na
l
(Detector without gain)
(Dete
cto
r w
ith g
ain
)
Gain drift
![Page 44: Photodetection in Flow Cytometry · 2020-06-04 · Reference: “Practical Flow Cytometry” by Shapiro 4. Thus the 10-μm cell is illuminated with 4.9×1015 photons per s. 5. If](https://reader033.vdocuments.us/reader033/viewer/2022043004/5f88512e2b7f2d05ec233aa7/html5/thumbnails/44.jpg)
44🄫 Hamamatsu Photonics K.K. and its affiliates. All Rights Reserved.
How are Scatter Plots Affected?
Forward-scatter signal
Sid
e-s
catter
sig
nal
Reference (with random noise)
Forward-scatter signal
Sid
e-s
catter
sig
nal
Limited dynamic range
![Page 45: Photodetection in Flow Cytometry · 2020-06-04 · Reference: “Practical Flow Cytometry” by Shapiro 4. Thus the 10-μm cell is illuminated with 4.9×1015 photons per s. 5. If](https://reader033.vdocuments.us/reader033/viewer/2022043004/5f88512e2b7f2d05ec233aa7/html5/thumbnails/45.jpg)
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How are Scatter Plots Affected?
![Page 46: Photodetection in Flow Cytometry · 2020-06-04 · Reference: “Practical Flow Cytometry” by Shapiro 4. Thus the 10-μm cell is illuminated with 4.9×1015 photons per s. 5. If](https://reader033.vdocuments.us/reader033/viewer/2022043004/5f88512e2b7f2d05ec233aa7/html5/thumbnails/46.jpg)
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Hamamatsu in flow cytometry
Manufactures all types of photodetectors used in flow cytometry
Designs and manufactures customized detection circuits and ASICs
Manufactures a variety of optical components for flow cytometry
Conducts R&D to quickly respond to the changing needs in flow cytometry technology
![Page 47: Photodetection in Flow Cytometry · 2020-06-04 · Reference: “Practical Flow Cytometry” by Shapiro 4. Thus the 10-μm cell is illuminated with 4.9×1015 photons per s. 5. If](https://reader033.vdocuments.us/reader033/viewer/2022043004/5f88512e2b7f2d05ec233aa7/html5/thumbnails/47.jpg)
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Hamamatsu in flow cytometry
Manufactures all types of photodetectors (APD, SiPM, SPAD, Cameras and PMT) used in flow
cytometry
Custom integrated optical assemblies from front-end electronics to complete ASICs
Manufactures a variety of optical components for flow cytometry
Work with customers on custom solutions to quickly respond to the changing needs in flow
cytometry technology
Because of our wide offering of optical components, Hamamatsu is unbiased
when recommending the correct detector depending on the specific customer’s
requirements.
![Page 48: Photodetection in Flow Cytometry · 2020-06-04 · Reference: “Practical Flow Cytometry” by Shapiro 4. Thus the 10-μm cell is illuminated with 4.9×1015 photons per s. 5. If](https://reader033.vdocuments.us/reader033/viewer/2022043004/5f88512e2b7f2d05ec233aa7/html5/thumbnails/48.jpg)
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Closing Remarks
1. Flow cytometry is a versatile technique to study cells and microparticles
2. Photodetector is an indispensable component of every flow cytometer
3. The choice of the photodetector should be based on the best 𝑆
𝑁performance of the detection
system
4. Limitations of the detection system will affect scatter plots and histograms masking or distorting
science
![Page 49: Photodetection in Flow Cytometry · 2020-06-04 · Reference: “Practical Flow Cytometry” by Shapiro 4. Thus the 10-μm cell is illuminated with 4.9×1015 photons per s. 5. If](https://reader033.vdocuments.us/reader033/viewer/2022043004/5f88512e2b7f2d05ec233aa7/html5/thumbnails/49.jpg)
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Thank you
Thank you for listening
Contact information:
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Join Us for 10 Weeks of FREE Photonics Webinars (17 Topics)
Week # Weekly Topics # of Talks Talk #1 Date Talk #2 Date
1 Introduction to Photodetectors 2 26-May-20 28-May-20
2 Emerging Applications - LiDAR & Flow Cytometry 2 2-Jun-20 4-Jun-20
3 Understanding Spectrometer 2 9-Jun-20 11-Jun-20
1 Weeks Break
4 Specialty Products – Introduction to Light Sources & X-Ray 2 23-Jun-20 25-Jun-20
5 Introduction to Image Sensors 2 30-Jun-20 02-Jul-20
1 Weeks Break
6 Specialty Products – Laser Driven Light Sources 2 14-Jul-20 16-Jul-20
7 Image Sensor Circuits and Scientific Camera 2 21-Jul-20 23-Jul-20
8 Mid-Infrared (MIR) Technologies & Applications 2 28-Jul-20 30-Jul-20
1 Weeks Break
9 Photon Counting Detectors – SiPM and SPAD 1 11-Aug-20
10 Using SNR Simulation to Select a Photodetector 1 18-Aug-20
To register and attend other webinar series, please visit link below:
https://www.hamamatsu.com/us/en/news/event/2020/20200526220000.html
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