J Estimator Validation — Fixed Bead Size, Variable Illumination#

This example demonstrates how to estimate the J parameter, which quantifies how the relative noise (robust coefficient of variation) scales with the signal strength under varying illumination power. We simulate a flow cytometry system with fixed bead diameter and varying illumination.

Setup and configuration#

import numpy as np
from TypedUnit import ureg

from FlowCyPy import FlowCytometer, SimulationSettings
from FlowCyPy.calibration import JEstimator
from FlowCyPy.fluidics import FlowCell, Fluidics, ScattererCollection
from FlowCyPy.opto_electronics import (
    Detector,
    OptoElectronics,
    TransimpedanceAmplifier,
    source,
)
from FlowCyPy.signal_processing import Digitizer, SignalProcessing

Configure simulation-level noise assumptions

SimulationSettings.include_noises = True
SimulationSettings.include_shot_noise = True
SimulationSettings.include_dark_current_noise = False
SimulationSettings.include_source_noise = False
SimulationSettings.include_amplifier_noise = False
SimulationSettings.assume_perfect_hydrodynamic_focusing = True
SimulationSettings.assume_amplifier_bandwidth_is_infinite = True
SimulationSettings.assume_perfect_digitizer = True
SimulationSettings.evenly_spaced_events = True


np.random.seed(3)  # Reproducibility

Construct simulation components#

flow_cell = FlowCell(
    sample_volume_flow=80 * ureg.microliter / ureg.minute,
    sheath_volume_flow=1 * ureg.milliliter / ureg.minute,
    width=400 * ureg.micrometer,
    height=400 * ureg.micrometer,
)

scatterer_collection = ScattererCollection(medium_refractive_index=1.33 * ureg.RIU)

fluidics = Fluidics(scatterer_collection=scatterer_collection, flow_cell=flow_cell)

source = source.GaussianBeam(
    numerical_aperture=0.2 * ureg.AU,
    wavelength=450 * ureg.nanometer,
    optical_power=0 * ureg.watt,
)

digitizer = Digitizer(
    bit_depth="16bit",
    saturation_levels=(0 * ureg.volt, 2 * ureg.volt),
    sampling_rate=60 * ureg.megahertz,
)

amplifier = TransimpedanceAmplifier(
    gain=10 * ureg.volt / ureg.ampere,
    bandwidth=60 * ureg.megahertz,
)

detector_0 = Detector(
    name="default",
    phi_angle=0 * ureg.degree,  # Forward scatter
    numerical_aperture=0.2 * ureg.AU,
    cache_numerical_aperture=0.0 * ureg.AU,
    responsivity=1 * ureg.ampere / ureg.watt,
)

opto_electronics = OptoElectronics(
    detectors=[detector_0], source=source, amplifier=amplifier
)

signal_processing = SignalProcessing(
    digitizer=digitizer,
    analog_processing=[],
)

flow_cytometer = FlowCytometer(
    opto_electronics=opto_electronics,
    fluidics=fluidics,
    signal_processing=signal_processing,
    background_power=source.optical_power * 0.001,
)

Run J Estimation Simulation#

j_estimator = JEstimator(debug_mode=False)

j_estimator.add_batch(
    illumination_powers=np.linspace(10, 380, 25) * ureg.milliwatt,
    bead_diameter=400 * ureg.nanometer,
    flow_cytometer=flow_cytometer,
    particle_count=50 * ureg.particle,
)
[INFO] Running simulation 1/25
Population  ScattererID
population  0               0.0
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Name: y, dtype: pint[meter][Float64] 716.1972439135291 nanometer
[INFO] Running simulation 2/25
Population  ScattererID
population  0              -0.0
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Name: y, dtype: pint[meter][Float64] 716.1972439135291 nanometer
[INFO] Running simulation 3/25
Population  ScattererID
population  0               0.0
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Name: y, dtype: pint[meter][Float64] 716.1972439135291 nanometer
[INFO] Running simulation 4/25
Population  ScattererID
population  0              -0.0
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                           ...
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Name: y, Length: 62, dtype: pint[meter][Float64] 716.1972439135291 nanometer
[INFO] Running simulation 5/25
Population  ScattererID
population  0              -0.0
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Name: y, dtype: pint[meter][Float64] 716.1972439135291 nanometer
[INFO] Running simulation 6/25
Population  ScattererID
population  0              -0.0
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Name: y, dtype: pint[meter][Float64] 716.1972439135291 nanometer
[INFO] Running simulation 7/25
Population  ScattererID
population  0               0.0
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Name: y, dtype: pint[meter][Float64] 716.1972439135291 nanometer
[INFO] Running simulation 8/25
Population  ScattererID
population  0               0.0
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Name: y, dtype: pint[meter][Float64] 716.1972439135291 nanometer
[INFO] Running simulation 9/25
Population  ScattererID
population  0              -0.0
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Name: y, dtype: pint[meter][Float64] 716.1972439135291 nanometer
[INFO] Running simulation 10/25
Population  ScattererID
population  0               0.0
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Name: y, dtype: pint[meter][Float64] 716.1972439135291 nanometer
[INFO] Running simulation 11/25
Population  ScattererID
population  0               0.0
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Name: y, dtype: pint[meter][Float64] 716.1972439135291 nanometer
[INFO] Running simulation 12/25
Population  ScattererID
population  0              -0.0
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Name: y, dtype: pint[meter][Float64] 716.1972439135291 nanometer
[INFO] Running simulation 13/25
Population  ScattererID
population  0              -0.0
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Name: y, dtype: pint[meter][Float64] 716.1972439135291 nanometer
[INFO] Running simulation 14/25
Population  ScattererID
population  0               0.0
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Name: y, dtype: pint[meter][Float64] 716.1972439135291 nanometer
[INFO] Running simulation 15/25
Population  ScattererID
population  0               0.0
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Name: y, dtype: pint[meter][Float64] 716.1972439135291 nanometer
[INFO] Running simulation 16/25
Population  ScattererID
population  0               0.0
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Name: y, dtype: pint[meter][Float64] 716.1972439135291 nanometer
[INFO] Running simulation 17/25
Population  ScattererID
population  0              -0.0
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            10             -0.0
            11              0.0
            12             -0.0
            13              0.0
            14             -0.0
            15             -0.0
            16              0.0
            17              0.0
            18             -0.0
            19             -0.0
            20              0.0
            21             -0.0
            22             -0.0
            23              0.0
            24              0.0
            25             -0.0
            26              0.0
            27              0.0
            28              0.0
            29             -0.0
            30             -0.0
            31              0.0
            32              0.0
            33              0.0
            34              0.0
            35             -0.0
            36             -0.0
            37             -0.0
            38              0.0
            39             -0.0
            40              0.0
            41              0.0
            42             -0.0
            43             -0.0
            44             -0.0
            45             -0.0
            46             -0.0
            47             -0.0
            48             -0.0
            49             -0.0
            50              0.0
            51             -0.0
            52             -0.0
            53             -0.0
            54             -0.0
            55             -0.0
            56              0.0
            57              0.0
            58             -0.0
Name: y, dtype: pint[meter][Float64] 716.1972439135291 nanometer
[INFO] Running simulation 18/25
Population  ScattererID
population  0               0.0
            1               0.0
            2              -0.0
            3              -0.0
            4               0.0
            5               0.0
            6              -0.0
            7               0.0
            8               0.0
            9              -0.0
            10              0.0
            11             -0.0
            12             -0.0
            13              0.0
            14             -0.0
            15              0.0
            16              0.0
            17             -0.0
            18             -0.0
            19              0.0
            20              0.0
            21              0.0
            22              0.0
            23             -0.0
            24              0.0
            25             -0.0
            26             -0.0
            27              0.0
            28             -0.0
            29             -0.0
            30              0.0
            31              0.0
            32              0.0
            33             -0.0
            34              0.0
            35              0.0
            36              0.0
            37              0.0
            38              0.0
            39              0.0
            40             -0.0
            41              0.0
            42             -0.0
            43             -0.0
            44             -0.0
            45             -0.0
            46             -0.0
            47             -0.0
            48              0.0
            49             -0.0
            50             -0.0
            51              0.0
Name: y, dtype: pint[meter][Float64] 716.1972439135291 nanometer
[INFO] Running simulation 19/25
Population  ScattererID
population  0              -0.0
            1              -0.0
            2              -0.0
            3               0.0
            4               0.0
            5              -0.0
            6              -0.0
            7              -0.0
            8               0.0
            9              -0.0
            10             -0.0
            11              0.0
            12             -0.0
            13              0.0
            14             -0.0
            15              0.0
            16              0.0
            17             -0.0
            18              0.0
            19             -0.0
            20             -0.0
            21              0.0
            22             -0.0
            23             -0.0
            24              0.0
            25             -0.0
            26              0.0
            27              0.0
            28             -0.0
            29              0.0
            30             -0.0
            31             -0.0
            32              0.0
            33             -0.0
            34             -0.0
            35             -0.0
            36              0.0
            37             -0.0
            38             -0.0
            39             -0.0
            40              0.0
            41             -0.0
            42             -0.0
            43              0.0
            44             -0.0
Name: y, dtype: pint[meter][Float64] 716.1972439135291 nanometer
[INFO] Running simulation 20/25
Population  ScattererID
population  0              -0.0
            1               0.0
            2              -0.0
            3               0.0
            4              -0.0
            5              -0.0
            6               0.0
            7               0.0
            8              -0.0
            9              -0.0
            10              0.0
            11             -0.0
            12              0.0
            13              0.0
            14              0.0
            15             -0.0
            16              0.0
            17             -0.0
            18             -0.0
            19              0.0
            20              0.0
            21              0.0
            22              0.0
            23              0.0
            24              0.0
            25              0.0
            26             -0.0
            27              0.0
            28              0.0
            29             -0.0
            30             -0.0
            31             -0.0
            32              0.0
            33              0.0
            34              0.0
            35              0.0
            36              0.0
            37              0.0
            38             -0.0
            39             -0.0
            40             -0.0
            41             -0.0
            42             -0.0
            43             -0.0
            44             -0.0
            45             -0.0
            46             -0.0
            47              0.0
Name: y, dtype: pint[meter][Float64] 716.1972439135291 nanometer
[INFO] Running simulation 21/25
Population  ScattererID
population  0               0.0
            1               0.0
            2               0.0
            3               0.0
            4              -0.0
                           ...
            56              0.0
            57              0.0
            58              0.0
            59             -0.0
            60              0.0
Name: y, Length: 61, dtype: pint[meter][Float64] 716.1972439135291 nanometer
[INFO] Running simulation 22/25
Population  ScattererID
population  0              -0.0
            1               0.0
            2              -0.0
            3              -0.0
            4               0.0
            5              -0.0
            6              -0.0
            7              -0.0
            8              -0.0
            9               0.0
            10              0.0
            11              0.0
            12              0.0
            13             -0.0
            14              0.0
            15              0.0
            16              0.0
            17             -0.0
            18             -0.0
            19              0.0
            20              0.0
            21              0.0
            22              0.0
            23             -0.0
            24              0.0
            25             -0.0
            26              0.0
            27              0.0
            28             -0.0
            29             -0.0
            30             -0.0
            31              0.0
            32             -0.0
            33             -0.0
            34             -0.0
            35              0.0
            36              0.0
            37              0.0
            38              0.0
            39             -0.0
            40              0.0
            41              0.0
            42             -0.0
            43             -0.0
            44              0.0
            45             -0.0
            46             -0.0
            47             -0.0
            48             -0.0
            49              0.0
            50              0.0
            51             -0.0
            52              0.0
            53              0.0
            54              0.0
Name: y, dtype: pint[meter][Float64] 716.1972439135291 nanometer
[INFO] Running simulation 23/25
Population  ScattererID
population  0              -0.0
            1               0.0
            2               0.0
            3              -0.0
            4               0.0
            5              -0.0
            6               0.0
            7               0.0
            8               0.0
            9               0.0
            10             -0.0
            11              0.0
            12              0.0
            13             -0.0
            14              0.0
            15              0.0
            16             -0.0
            17             -0.0
            18             -0.0
            19             -0.0
            20             -0.0
            21             -0.0
            22             -0.0
            23              0.0
            24             -0.0
            25              0.0
            26             -0.0
            27             -0.0
            28              0.0
            29             -0.0
            30             -0.0
            31              0.0
            32              0.0
            33             -0.0
            34              0.0
            35             -0.0
            36             -0.0
            37              0.0
            38              0.0
            39             -0.0
            40              0.0
            41             -0.0
            42              0.0
            43              0.0
            44              0.0
            45              0.0
            46             -0.0
            47             -0.0
            48              0.0
            49             -0.0
            50              0.0
            51              0.0
            52              0.0
Name: y, dtype: pint[meter][Float64] 716.1972439135291 nanometer
[INFO] Running simulation 24/25
Population  ScattererID
population  0              -0.0
            1               0.0
            2              -0.0
            3              -0.0
            4               0.0
            5              -0.0
            6               0.0
            7              -0.0
            8               0.0
            9               0.0
            10             -0.0
            11              0.0
            12              0.0
            13             -0.0
            14             -0.0
            15             -0.0
            16             -0.0
            17             -0.0
            18              0.0
            19             -0.0
            20              0.0
            21              0.0
            22              0.0
            23              0.0
            24              0.0
            25              0.0
            26              0.0
            27              0.0
            28              0.0
            29              0.0
            30              0.0
            31              0.0
            32              0.0
            33             -0.0
            34             -0.0
            35              0.0
            36              0.0
            37              0.0
            38             -0.0
            39             -0.0
Name: y, dtype: pint[meter][Float64] 716.1972439135291 nanometer
[INFO] Running simulation 25/25
Population  ScattererID
population  0              -0.0
            1              -0.0
            2               0.0
            3               0.0
            4              -0.0
            5              -0.0
            6              -0.0
            7              -0.0
            8              -0.0
            9              -0.0
            10             -0.0
            11              0.0
            12             -0.0
            13             -0.0
            14             -0.0
            15              0.0
            16              0.0
            17             -0.0
            18             -0.0
            19             -0.0
            20             -0.0
            21              0.0
            22             -0.0
            23              0.0
            24              0.0
            25             -0.0
            26              0.0
            27              0.0
            28             -0.0
            29              0.0
            30              0.0
            31             -0.0
            32             -0.0
            33              0.0
            34              0.0
            35              0.0
            36              0.0
            37              0.0
            38              0.0
            39             -0.0
            40             -0.0
            41             -0.0
            42             -0.0
            43              0.0
            44              0.0
            45              0.0
            46             -0.0
            47              0.0
            48              0.0
            49             -0.0
            50              0.0
            51             -0.0
Name: y, dtype: pint[meter][Float64] 716.1972439135291 nanometer

Plot estimation and diagnostics#

j_estimator.plot()
J Parameter Estimation

Plot relevant statistics#

j_estimator.plot_statistics()
Median Signal vs Illumination Power, STD vs Illumination Power

Total running time of the script: (0 minutes 48.850 seconds)

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