extr_Meshes

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, the cellList (see Value below) will be part of the output.

Value

• cellList the original input as dataframe

• mesh the mesh data compatible with BactMAP

See Also

pixels2um

Mesh Dataframe Structure

Examples

meshdata <- file.choose()

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

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