Description Usage Arguments Value References
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.
1 | import_basca(file, pixelR, ringW = 10)
|
file |
A character string naming the |
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 |
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:
|
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:
The |
Nframes |
Number of frames in the movie, a non-zero positive integer value.
IDs of frames are in the range |
Ncols |
Number of colonies in the movie, a non-zero positive integer value.
IDs of colonies are in the range |
frameH |
Frame image height in pixels, a non-zero positive integer value. |
frameW |
Frame image width in pixels, a non-zero positive integer value. |
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.
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