FlowCytometry 0.0.3.post0

A package for flow-cytometry simulations.

Overview

The FlowCytometer Simulation Tool is a Python-based simulation framework designed to replicate the operation of a flow cytometer. It generates realistic raw signals for Forward Scatter (FSC) and Side Scatter (SSC) channels, incorporating noise, baseline shifts, signal saturation, and signal discretization into a specified number of bins. This tool is highly configurable, allowing users to simulate a wide range of scenarios and analyze the resulting signals.

Features

• Simulate Particle Events: Generate realistic FSC and SSC signals based on user-defined particle event parameters.

• Noise and Baseline Shift: Introduce Gaussian noise and sinusoidal baseline shifts to simulate real-world conditions.

• Signal Saturation: Apply saturation effects to replicate detector limits.

• Signal Discretization: Discretize the continuous signal into a specified number of bins for quantized signal analysis.

• Flexible Plotting: Visualize the simulated signals with customizable options for plotting specific channels or both together.

Installation

To install the FlowCytometer simulation tool, you can clone the repository and install the required dependencies:

git clone https://github.com/MartinPdeS/FlowCytometry.git
cd FlowCytometry
pip install .[testing]

Dependencies

• numpy: For numerical operations and signal generation.

• matplotlib: For plotting the simulated signals.

• scipy: A module to generate Gaussian pulses (part of this package or an external dependency).

Getting Started

Below is a quick guide on how to get started with the FlowCytometer simulation tool.

from FlowCytometry import FlowCytometer

cytometer = FlowCytometer(
    n_events=30,
    time_points=1000,
    noise_level=30,
    baseline_shift=0.01,
    saturation_level=10_000,
    n_bins=40,
)

# Simulate the flow cytometer signals
cytometer.simulate_pulse()

# Plot the generated signals
cytometer.plot()

This produce the following figure: