Flow Cytometry Simulation: FacsCanto System

This tutorial demonstrates how to set up and run a flow cytometry simulation using the FacsCanto instance from the FlowCyPy library. It includes defining a particle population, configuring the flow cytometer, running the simulation, and visualizing the results.

Step 0: Global Settings and Imports

from FlowCyPy.units import ureg
from FlowCyPy.presets.flow_cytometer import FacsCanto, SampleFlowRate, SheathFlowRate
from FlowCyPy.fluidics import populations, distributions


diameter = distributions.RosinRammler(
    scale=60 * ureg.nanometer,
    shape=150,
)

medium_refractive_index = 1.33

refractive_index = distributions.Normal(mean=1.44, standard_deviation=0.002)

population_0 = populations.SpherePopulation(
    name="Pop 0",
    concentration=5e9 * ureg.particle / ureg.milliliter,
    diameter=diameter,
    medium_refractive_index=medium_refractive_index,
    refractive_index=refractive_index,
)

facs_canto = FacsCanto(
    sample_volume_flow=SampleFlowRate.MEDIUM.value,
    sheath_volume_flow=SheathFlowRate.DEFAULT.value,
    optical_power=200 * ureg.milliwatt,
    threshold="3sigma",
    include_shot_noise=True,
    include_rin_noise=True,
    background_power=0.01 * ureg.nanowatt,
)

facs_canto.add_population(population_0)

facs_canto.dilute_sample(factor=100)

run_record = facs_canto.run(run_time=0.2 * ureg.millisecond)

run_record.plot_analog()

<Figure size 800x500 with 3 Axes>