extr_Oufti - veeninglab/BactMAP GitHub Wiki

Function to upload Oufti meshes and spot localizations directly from .Mat, .TXT or .CSV files to R.

Usage

extr_Oufti(matfile, mag="No_PixelCorrection", phylo=FALSE, cellList=FALSE)

Arguments

matfile .MAT, .CSV or .TXT of oufti segmentation. Spot data, object data and fluorescence intensity will automatically be detected. Note: object data can only be extracted from .CSV or .TXT files for now!

mag The pixel-micron conversion factor. See bactMAP::getPixels2um() for more information. When not given, the factor will be 1.

phylo When TRUE, a list of child-parent nodes & phylo objects containing cell genealogy will be made. Default is set to FALSE

cellList When TRUE, the cellList (see below) will be part of the output list.

Value

A list containing:

$cellList (Optional) The complete cellList as it is displayed in oufti's output.

$mesh A dataframe containing the following columns: X, Y, cell, frame, num, max.width, length, steplength, max.length, area, Xmid, Ymid, X_rot, Y_rot, angle, Xrot_micron, Yrot_micron, max_um, maxwum. See standard mesh output for more information.

$pixel2um the pixel to micron conversion factor used

When spot data is included:

$spotframe A dataframe containing the following columns: l, d, x, y, position, adj_Rsquared, CI_xy, frame, cell. See www.oufti.org for more information on the spot data output.

$spots_relative A dataframe containing from the mesh data: max.width, max.length, area, cell, frame. from the spot data: l, d, x, y. Added: spot, totalspot, Lmid, Dum, max_um, maxwum, pole1, pole2.

When input is CSV or TXT file containing object data:

$objectframe A dataframe containing the coordinates of detected objects, cell ID, frame ID and object ID: ob_x, ob_y, obnum, obpath, frame, cell, obID

$object_relative A dataframe reminescent of spots_relative containing the following variables: "frame, cell, max.length, obnum, num, obpath, obID, max.width, Dum, Lmid, ob_out_x, ob_out_y, pole1, pole2

When "phylo" is set to TRUE:

$timelapsedata a list of:

  • generation_dataframes: a dataframe with cells with common ancestor,
  • generation_lists: phylo objects which can be used for tree plotting,
  • spot_relative_list: list of spot localization dataframes of cells with common ancestor, and
  • meshdata: a list of cell outline data of cells with common ancestor

References

www.oufti.org

Paintdakhi A, et al. (2016) Oufti: an integrated software package for high-accuracy, high-throughput quantitative microscopy analysis. Molecular Microbiology 99(4):767-777.

Examples


matfile <- file.choose()

##extract data using extr.Oufti()

output <- extr_Oufti(matfile)

##get spot dataframe

spots <- output$spotframe

##plot spots of frame no.1

ggplot2::ggplot(spots[spots$frame==1,], ggplot2::aes(x=x, y=y, color=as.factor(cell))) + ggplot2::geom_point() + ggplot2::theme_minimal()

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