extr_SuperSeggerCells: Convert SuperSegger cell outlines & genealogy to standard...

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

Convert SuperSegger cell outlines & genealogy to standard BactMAP format

Description

Part of the *extr_*-functions, extr_SuperSeggerCells takes the mask created by SuperSegger of each cell (and if available, timepoint) and saves this as a *mesh* dataframe.

extr_SuperSeggerClist() takes the clist (SuperSegger summarized output) and forms genealogy files which can be processed to network plots and trees.

Usage

extr_SuperSeggerCells(loc, frames, mag, timelapse=FALSE, startframe=0, cellList=FALSE)

extr_SuperSeggerClist(matfile, trim.orphans=TRUE, cellList=FALSE)

Arguments

For extr_SuperSeggercells:

loc	The file path where SuperSegger's output files are located
frames	The number of xy frames (so not timepoints, just different locations!) imaged
mag	magnification conversion factor name (which is part of Pixels2um)
timelapse	set timelapse to TRUE if you are analyzing a timelapse movie.
startframe	default = 0. set to 1 if the first of your xy-locations is 1.
cellList	Default=FALSE. When TRUE, the cellList (see below) will be part of the output of the function.

For extr_SuperSeggerClist:

matfile	Path to the Clist output of supersegger (save this manually from the SuperSegger Viewer after analysis).
trim.orphans	Default=TRUE. When TRUE, cells without offspring or parents will be removed from the dataset.

Details

Use *addPixels2um()* to add a new conversion factor.

Value

From extr_SuperSeggerCells():

cellList	dataframe with content similar to SuperSegger's "Clist"
mesh	dataframe containing cell coordinates and dimensions
pixel2um	the magnification conversion factor used

From extr_SuperSeggerClist():

cellList	copy of 2-dimensional cList output of SuperSegger
network	igraph network data of cell genealogy
generation_lists	phylo object describing cell genealogy
data_generation_dataframes	attribute data - dataframe with information on cell fluorescence, etc
cellList_trimmed	cellList without the "orphan" cells. in output when orphans==TRUE
orphans	the cells which are removed from the cellList when orphans==TRUE

Author(s)

Renske van Raaphorst

References

Stylianidou, Stella, et al. "SuperSegger: robust image segmentation, analysis and lineage tracking of bacterial cells." Molecular microbiology 102.4 (2016): 690-700.

Examples

## Not run: 
##pick supersegger output path. in this example there are 6 x/y frames.
out_supseg <- "path_to_supersegger_data"
##get cell outlines
cell_outlines <- extr_SuperSeggerCells( paste(out_supseg, "/clist.mat", sep=""),
                                        frames=6, startframe=0)
##get clist timelapse:
cell_clist <- extr_SuperSeggerClist(out_supseg)

## End(Not run)

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