extr_Morphometrics: Upload cell outlines segmented using Morphometrics

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

Upload cell outlines segmented using Morphometrics

Description

The 'CONTOURS'-output from Morphometrics is uploaded and converted to a *mesh*-dataframe compatible with bactMAPs plotting functions. Find more examples of usage of extr_Morphometrics on the BactMAP wiki.

Usage

extr_Morphometrics(morphpath, mag, turncells = TRUE, cellList=FALSE)

Arguments

morphpath	the path to the 'CONTOURS'- output of Morphometrics (for instance "mycells_01-01-2019_CONTOURS.mat").
mag	pixel conversion factor (see pixels2um). if added, the coordinates and cell length/width will be converted to micron
turncells	if set to TRUE (default), X and Y coordinates will be turned so that mid-cell is at [0,0], while the length axis of the cell's bounding box is parallel to the x axis.
cellList	when cellList==TRUE, the value cellList (see below) is part of the output.

Value

cellList	dataframe containing the original data extracted from Morphometrics.
mesh	dataframe containing the coordinates of the outlines of the cell, cell dimensions and if *turncells==TRUE*, the coordinates of each cell turned and repositioned to [0,0]
pixel2um	if *mag* was defined in the arguments, the conversion factor is saved in the output list.

Author(s)

Renske van Raaphorst

References

Ursell T, Lee TK, Shiomi D, et al. Rapid, precise quantification of bacterial cellular dimensions across a genomic-scale knockout library. BMC Biol. 2017;15(1):17. Published 2017 Feb 21. doi:10.1186/s12915-017-0348-8

Examples

## Not run: 
#Upload Morphometrics output from bactMAP example files

Example_MM <-  file.choose()
Example_output <- extr_Morphometrics(Example_MM)$mesh

#check output:
summary(Example_output)

#plot cells
plotRaw(Example_output, frameN=1)

## End(Not run)

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