cells: Cell outlines simulated from CPM

In Almond-S/manifoldboost: Boosting Regression Models for Manifold Valued Data

Cell outlines simulated from CPM

Description

Irregularly (cells) and regularly sampled (cellr) 2D cell outlines extracted from cells simulated by the Cellular Potts Model (CPM) proposed by Thueroff et al. 2019, a stochastic biophysical model, for calibration to real-life cells (Schaffer 2021).

Usage

data(cells, package = "manifoldboost")

data(cellr, package = "manifoldboost")

Format

An object of class list of length 5.

An object of class list of length 5.

Details

The datasets contain the following covariate vectors:

• a substrate adhesion (CPM parameter, numeric)

• r signaling radius (CPM parameter, numeric)

• b bulk stiffness (CPM parameter, numeric)

• m membrane stiffness (CPM parameter, numeric)

For the irregular dataset cells:

• response A tibble with the cell outline data:

  • id cell ID (factor, ordered according to covariate vectors)

  • arg parameterization of the curves (numeric, between 0 and 1)

  • dim dimension indicator (two-leveled factor)

  • value x- and y-values of observed points of the outline (numeric)

For the regular dataset cellr:

• response A tbl_cube with the cell outline data:

  • Dimensions id,arg,dim: cell ID (factor, ordered according to covariate vectors), parameterization of the curves (integer, 1 to 70), dimension indicator (two-leveled factor)

  • Measures value x- and y-values of observed points of the outline (numeric)

Source

Thankfully provided by Sophia Schaffer.

References

Schaffer, S. A. (2021). Cytoskeletal dynamics in confined cell migration: experiment andmodelling. PhD thesis, LMU Munich. DOI: 10.5282/edoc.28480.

Thueroff, F., A. Goychuk, M. Reiter, and E. Frey (2019). Bridging the gap betweensingle-cell migration and collective dynamics. eLife 8, e46842.

Almond-S/manifoldboost documentation built on June 23, 2022, 11:06 a.m.