The SuperSegger output is generally the Clist, a 2- or 3-dimensional matrix containing information about each cell. For now, BactMAP supports the extraction of two types of SuperSegger information: the cell masks and, when interested in plotting cell genealogy, the Clist containing parent-child information. To extract the cell masks, use extr_SuperSeggerCells, to extract the genealogy information, use extr_SuperSeggerClist.

Extr_SuperSeggerCells

Description

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

Usage

extr_SuperSeggerCells(loc, frames, mag)

Arguments

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 default is FALSE. set to TRUE if you are analyzing a timelapse movie

startframe default is 0. set to 1 if your xy-locations start with 1.

cellList When set to TRUE (default=FALSE), the cellList (see at 'Values' below) will be part of the output.

Value

cellList dataframe with content similar to SuperSegger's "Clist"

mesh dataframe containing cell coordinates and dimensions - for more information see the mesh dataframe.

pixel2um the magnification conversion factor used

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Extr_SuperSeggerClist

Description

extr_SuperSeggerClist converts the Clist from SuperSegger into a list of dataframes, most importantly containing information on cell genealogy.

Usage

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

Arguments

matfile "Clist" of timelapse analyzed with SuperSegger saved as .CSV file.

trim.Orphans When set to TRUE (default), cells without ancestor or children will be discarded from the analysis.

cellList When set to TRUE (default=FALSE), the cellList (see at 'Values' below) will be part of the output.

Values

cellList the original "Clist" in dataframe format

orphans when trim.Orphans = TRUE, the orphan cells are listed here

network the parent-child relation of the cells in network format, compatible with e.g. ggnetwork

phylos a list of phylo-objects (compatible with ggtree and ape)

data_attributes: the parent-daughter relationship of each phylo-object in data.frame format, containing all Clist information. Useful for adding information to ggtrees.

cellList_trimmed: the Clist, where the orphans are excluded.

References

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

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