import_basca: Import _BaSCA_ data

Description Usage Arguments Value References

Description

Imports a .mat file generated by BaSCA and converts it into a cell list and colony list containing all the cell instants and colony instants of the movie, respectively.

Usage

1
import_basca(file, pixelR, ringW = 10)

Arguments

file

A character string naming the .mat file generated by BaSCA (including the suffix ".mat") from which the data is to be imported. If it does not contain an absolute path, the file name is relative to the current working directory, getwd().

NOTE: The components should be separated by "/" on Windows.

pixelR

The pixel ratio in units of length, a non-zero positive numeric value.

ringW

The width of the ring (in pixels) which marks the boundary pixels of a colony, a non-zero positive integer value. This value is used to decide whether a cell is on the boundary of its colony or not. The default value is 10.

Value

A named list with the following components:

col_list

A list containing all the colony instants of the movie. Each element of the list is a named list with the following components:

  • colName is the name of the colony instant, a character string in the format "f<frame>_c<colony>", where "<frame>" and "<colony>" is the ID of the frame and colony (in the frame) of the colony instant, respectively.

  • prev_colName is a vector of character strings containing the colName of the corresponding colony instant(s) in the previous frame. For colony instants that do not have a corresponding colony instant in the previous frame, this is equal to "f0_c0".

  • next_colName is a character string containing the colName of the corresponding colony instant in the next frame. For colony instants that do not have a corresponding colony instant in the next frame, this is equal to "f00_c0".

  • colImage is the mask of the box surrounding the colony instant, a matrix of 0 and 1. 1s denote the pixels of cells and 0s the background pixels.

  • ULcorner is an 1x2 matrix of non-zero integer values denoting the upper-left pixel of the box surrounding the colony instant in global (frame) coordinates. The first integer represents the row and the second the column of the pixel.

  • colBoundaryPixels is a Nx2 matrix of non-zero integer values denoting the boundary pixels of the colony instant in colony coordinates (i.e. relative to the colImage). Each one of the N rows indicates a boundary pixel of the colony instant detected based on the ringW argument. The first column represents the row and the second the column of the boundary pixel.

  • colCentroid is an 1x2 matrix of non-zero numeric values denoting the centroid (geometric center) of the colony instant in colony coordinates (i.e. relative to the colImage).

cell_list

A list containing all the cell instants of the movie. Each element of the list is a named list with the following components:

  • cellName is the name of the cell, a character string in the format "x<------->_y<------->_f<frame>".

  • frame is the ID of the frame of the cell, a non-zero positive integer number.

  • colony is the ID of the colony of the cell in the frame, a non-zero positive integer number.

  • daughterIds is a vector of character strings containing the cellName of the linked cell(s) in the next frame, or NULL in case no such cells exist.

  • colId is a pointer to the corresponding colony instant of the cell in the col_list, a non-zero positive integer value.

    Colonies that entered the field of view at a time point and did not exist from the beginning of the movie (i.e. from the first frame) should not have tracked cells, until they merge (if this is the case) with another existing colony. This means that no element should point to such colony instants.

  • pixelList is a Nx2 matrix of non-zero integer values denoting the pixels of the cell in colony coordinates (i.e. relative to the colImage of the colIdth element in the col_list). Each one of the N rows indicates a pixel of the cell. The first column represents the row and the second the column of the pixel.

  • boundaryPixelList is a Nx2 matrix of non-zero integer values denoting the boundary pixels of the cell in colony coordinates (i.e. relative to the colImage of the colIdth element in the col_list). Each one of the N rows indicates a boundary pixel of the cell. The first column represents the row and the second the column of the boundary pixel.

  • centroid is an 1x2 matrix of non-zero numeric values denoting the centroid (geometric center) of the cell in colony coordinates (i.e. relative to the colImage of the colIdth element in the col_list). It is the mean of the pixelList by column.

  • length is the length of the cell in units of length, a non-zero positive numeric value.

  • width is the width of the cell in units of length, a non-zero positive numeric value.

  • LW is the length-to-width ratio, a non-zero positive numeric value.

  • area is the area of the cell in squared units of length, a non-zero positive numeric value.

  • perimeter is the perimeter of the cell in units of length, a non-zero positive numeric value.

  • minorAxis is the short axis of the ellipse surrounding the cell in units of length, a non-zero positive numeric value.

  • majorAxis is the long axis of the ellipse surrounding the cell in units of length, a non-zero positive numeric value.

  • eccentricity is a numeric value in the range [0, 1] defining the eccentricity of the cell.

  • orientation is a numeric value in the range [0, 360) defining the orientation of the cell in degrees.

  • solidity is a numeric value in the range [0, 1] defining the solidity of the cell.

  • distFromCentroid is the distance of the centroid of the cell from the centroid of its colony (i.e. the euclidean distance between the centroid and the colCentroid of the colIdth element in the col_list) in units of length, a non-zero positive numeric value.

  • isOnBoundary is a logical value (TRUE or FALSE) indicating whether the cell is on the boundary of its colony or not. It is TRUE in case there is more than 66 the colBoundaryPixels of the colIdth element in the col_list, FALSE otherwise.

  • fluorescenceInt<i> is a Nx1 matrix of positive numeric values indicating the cell fluorescence intensity of channel <i>. The values correspond to each one of the pixels in pixelList (1-1 correspondence).

  • fluorescenceInt<i>.mean is the mean cell fluorescence intensity of channel <i>, a positive numeric value.

  • fluorescenceInt<i>.std is the standard deviation of the cell fluorescence intensity of channel <i>, a positive numeric value.

  • fluorescenceInt<i>.coverage is the percentage of the cell area covered by fluorescence of channel <i>, a numeric value in the range [0, 1].

The fluorescenceInt<i>* components are included in case they were exctracted by BaSCA.

Nframes

Number of frames in the movie, a non-zero positive integer value. IDs of frames are in the range [1, Nframes].

Ncols

Number of colonies in the movie, a non-zero positive integer value. IDs of colonies are in the range [1, Ncols]. This value corresponds to the number of colonies at the start of the movie.

frameH

Frame image height in pixels, a non-zero positive integer value.

frameW

Frame image width in pixels, a non-zero positive integer value.

References

A. Balomenos, P. Tsakanikas, Z. Aspridou, A. Tampakaki, K. Koutsoumanis and E. Manolakos, “Image analysis driven single-cell analytics for systems microbiology”, BMC Systems Biology, vol. 11, no. 1, 2017.


vicstefanou/ViSCA documentation built on May 31, 2019, 10:50 p.m.