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Endocytosis Simulator

by Thibault Lagache

This plugin aims at simulating 2D time-lapse Total Internal Reflection Fluorescence (TIRF) microscope images of endocytosis.

Publication Id
ICY-A2E3A1
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Documentation

Endocytosis Simulator allows to generate synthetic 2D time-lapse sequences of endocytosis (such as observed experimentally with Total Internal Reflection Fluorescence (TIRF) microscope).

This plugin was initially designed to validate the tracking (eTrack plugin) and statistical classification of tracks durations developed in the article Bertot et al. "Quantitative and Statistical Study of the Dynamics of Clathrin-Dependent and -Independent Endocytosis Reveal a Differential Role of EndophilinA2" Cell Reports 6(22) 2018.

Plugin Parameters

Sequence Parameters 

  • Sequence width, height and length: Width, height (in pixels) and length (number of time frames) of generated synthetic sequences
  • Min. and Max. Spot Intensity: Minimum and Maximum Intensity (A.U.) of synthetic spots corresponding to the Point-Spread Function (PSF ~ 3 pixels wide) of each individual endocytosed particle.
  • Noise Parameters:  Two types of noise can be tuned in synthetic sequences: the Poisson shot noise (Poisson noise) and the (white) Gaussian noise (mean = 0, and the Standard variation of the Gaussian noise can be tuned). Signal to noise ratio (SNR)  is approximately equal to: SNR = Spot Intensity/[Poisson Noise +(Std Gaussian Noise)2].

Different populations of endocytosis track durations

First, each endocytosis track is confined in x-y spatial coordinates, and user can tune the x-y standard deviation of the (Brownian) confined motion of each spot.

Then, user can then choose the number of different populations (up to 6) of endocytosis tracks and tune their duration distribution. For each population, user can define the total number of tracks (=endocytosis events) and the type of probability distribution that determines the different track durations of the population.

There are two possible duration distributions: the Exponential and the Gaussian distribution. For an Exponential distribution with Time t0 the duration of each track of the population follows an exponential distribution with parameter t0, i.e. the probability that the duration of a given track is >t is equal to exp(-t/t0). For a Gaussian distribution with Mean m0 and Standard deviation s0 , the duration of each track of the population follows a Gaussian distribution with mean m0 and standard deviation s0.