extr_Meshes: Generic function to upload cell outlines from a .csv or .txt...

In vrrenske/shinyspots: Visualization and Analysis of Bacterial Cell Segmentation and Fluorescence Data

Generic function to upload cell outlines from a .csv or .txt file.

Description

Output needs to have at least the following columns:

X - The x-coordinate of one cell outline point.

Y - The y-coordinate of one cell outline point.

frame - The image frame number.

cell - The cell identifyer (numeric).

Optional:

max.length - The cell length (in pixels)

max.width - The cell diameter (in pixels)

Any other parameters will be saved in the output dataframe cellList.

Usage

extr_Meshes(dataloc, sep = ",", turn = TRUE, mag, cellList=FALSE)

Arguments

dataloc	The path to the .csv or .txt - file containing the mesh data.
sep	The separator of the columns in the .txt or .csv file, default = ","
turn	When turn==TRUE, the cells will be turned so that the mid-point is on coordinate [0,0] and the length axis parallel to the x axis.
mag	The magnification convertion factor (see addPixels2um). When given, the output will be also given in microns.
cellList	When TRUE, cellList will be part of the output of this function (see Value below).

Value

cellList	the original input as dataframe
mesh	the mesh data compatible with BactMAP

Author(s)

Renske van Raaphorst

See Also

pixel2um, mesh

Examples

## Not run: 
meshdata <- file.choose()

mesh_BM <- extr_Meshes(meshdata, sep=",", mag="100x_FRAP", turn=FALSE)

## End(Not run)

vrrenske/shinyspots documentation built on Oct. 28, 2023, 12:26 p.m.