View source: R/supersegger_meshes.R
extr_SuperSeggerCells | R Documentation |
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.
extr_SuperSeggerCells(loc, frames, mag, timelapse=FALSE, startframe=0, cellList=FALSE)
extr_SuperSeggerClist(matfile, trim.orphans=TRUE, cellList=FALSE)
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. |
Use *addPixels2um()* to add a new conversion factor.
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 |
Renske van Raaphorst
Stylianidou, Stella, et al. "SuperSegger: robust image segmentation, analysis and lineage tracking of bacterial cells." Molecular microbiology 102.4 (2016): 690-700.
## 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)
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