README.md

In Ayan1/Cell-Trajectory-Analysis: Functions for biological trajectory analysis and video processing

Cell-Trajectory-Analysis

Synopsis

Cell-Trajectory-Analysis is a set of functions for cell tracking and biological trajectory analysis, to be used on video taken with fluorescence microscopy. This functions can be used to threshold video to detect cells marked with green fluorescence protein, generate trajectories for each cell, quantify each trajectory, and classify each trajectory using the k-nearest neighbors statistical learning model. This package is dependent on two other packages, namely flowcatchR and traj.

Documentation

fitModelKNN_CV

Description

Fits trajectory data into a K-nearest neighbors classifier using leave one out cross validation.

Usage

fitModelKNN_CV(trajDataFrame, labelVector, kVal)

Arguments

Argument | Description ---------|------------ trajDataFrame | A data frame with measures for each trajectory. This can be produced by function trajMeasures labelVector | A vector of labels for each trajectory. Its length must be equal to the number of rows in trajDataFrame kVal | The number of neighbors used for classification

Value

A vector of classified labels for each trajectory

Author

Ayan Bandyopadhyay, Bellarmine College Prep

Examples

data <- as.data.frame(matrix(1:4,nrow = 2,ncol = 2))
labels <- c("live","dead")
classifierKNN_CV<- fitModelKNN_CV(data,labels,3)

generateTraj

Description

Returns a TrajectorySet so that the y value is the distance from the bottom of the Frames object, not from the top.

Usage

generateTraj(particles, L = 26, R = 3, epsilon1 = 0, epsilon2 = 0, lambda1 = 1, lambda2 = 0, penaltyFunction = penaltyFunctionGenerator(), include.area = FALSE, frames)

Arguments

Argument | Description ---------|------------ particles | A ParticleSet object L | Maximum number of pixels an object can move in two consecutive frames R | Linkrange, i.e. the number of consecutive frames to search for potential candidate links epsilon1 | A numeric value, to be used in the formula. Jitter for allowing angular displacements epsilon2 | A numeric value, to be used in the formula. Jitter for allowing spatial displacements lambda1 | A numeric value. Multiplicative factor for the penalty function lambda2 | A numeric value. Multiplicative factor applied to the angular displacement penaltyFunction | A function structured in such a way to be applied as penalty function in the linking include.area | Logical, whether to include also area change of the particles in the cost function calculation frames | The Frames object that the ParticleSet object is derived from verboseOutput | Logical, whether the output should report additional intermediate steps. For debugging use mainly. prog | Logical, whether the a progress bar should be shown during the tracking phase include.intensity | Logical, whether to include also intensity change of the particles in the cost function calculation

Value

A TrajectorySet object

Author

Ayan Bandyopadhyay, Bellarmine College Prep

Examples

library(flowcatchR)
platelets <-particles(channel.Frames(MesenteriumSubset,"red"))
trajSet <- generateTraj(platelets,
                       L=26, R=3,
                       epsilon1=0, epsilon2=0,
                       lambda1=1, lambda2=0,
                       penaltyFunction=penaltyFunctionGenerator(),
                       include.area=FALSE, MesenteriumSubset)

greenThresh

Description

Green pixels, or pixels with H value between 61/360 and 140/360 and S value over 0.15 in the HSV color scheme, are treated as foreground. All other pixels are treated as background. This is useful in detecting the Green Flourescence Protein used to denote cell viability.

Usage

greenThresh(frames)

Arguments

Argument | Description ---------|------------ frames| A Frames object with all 3 color channels(R,G,B)

Value

a binary Frames object in the green color channel

Author

Ayan Bandyopadhyay, Bellarmine College Prep

Examples

library(flowcatchR)
threshedFrames <- greenThresh(MesenteriumSubset)

trajMeasures

Description

Removes trajectories with less than 4 data points. Generates 24 measures for each trajectory, including range, mean-over-time, standard deviation, coefficient of variation, change, and slope of the linear model. The full list of measures can be found in the vignette for package traj.

Usage

trajMeasures(trajSet, spf)

Arguments

Argument | Description ---------|------------ trajSet | This is a TrajectorySet object spf | Numeric. Seconds elapsed per frame.

Value

A matrix 24 columns wide. Each row corresponds to one trajectory.

Author

Ayan Bandyopadhyay, Bellarmine College Prep

Examples

library(flowcatchR)
trajPlatelets <- trajectories(particles(channel.Frames(MesenteriumSubset,"red")))
trajData <-trajMeasures(trajPlatelets, 1)

Ayan1/Cell-Trajectory-Analysis documentation built on May 5, 2019, 9:23 a.m.