Description Usage Arguments Value Author(s)

Correct z-component of a 3D collagen invasion essay. The correction is achieved under the assumption that non-migrating cells of the essay approximately form a quadratic flow profile due to frictional effects, compare law of Hagen-Poiseuille for flow in a tube.

1 2 | ```
correctByConicalPlane(filename, nrfits = 1000, threshold = -30,
plot = FALSE, write_csv = TRUE)
``` |

`filename` |
Name of data file in csv format. It should contain columns "Pos_X", "Pos_Y" and "Pos_Z". |

`nrfits` |
Numeric, Number of randomly chosen starting points for the optimization. Choose lower values for speeding up computational time. Choose higher values for more reliable optimization results. |

`threshold` |
Numeric, A threshold for counting cells as being invaded or not. When cells move towards negative z-direction, threshold should be negative. |

`plot` |
Boole, if TRUE exemplary 3D plots before and after the correction are plotted |

`write_csv, ` |
if TRUE resulting corrected values are saved as a csv file |

Data.frame containing input positions, corrected z-positions as well as number and percentage of invaded cells.

Marcus Rosenblatt, marcus.rosenblatt@fdm.uni-freiburg.de

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