##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)