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config.yaml
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analysis_parameters:
sigma: 0.49
young: 49000 # young's modulus
pixelsize: 0.201 # pixel size of the image with beads in µm/pixel
window_size: 20 # window size for particle image velocimetry in µm
overlapp: 19 # overlap size for particle image velocimetry in µm. This should be at least window_size/2.
std_factor: 15 # additional filter for extreme values in deformation field
h: 300 # height of the substrate in µm
edge_padding: 0.1 # fraction of the image close to the borders that is ignored for any analyzed value
padding_cell_layer: 0.1 # additional region ignored for stress analysis in "cell layer" mode. Average stresses and line
# tension is only calculated on the area that is "edge_padding"+"padding_cell_layer" away from the image edge
TFM_mode: finite_thickness # mode of traction force microscopy ("finite_thickness" or "infinite_thcikness")
FEM_mode: colony # mode for FEM type. Either perform FEM on a single colony (mode: "colony") or on the whole
# filed of view (mode: "cell layer"). In "cell layer you select two areas and calculate stress and
# contractile energy on them. In "colony" you select the area of a colony and draw cell borders. These
# borders are used to analyze stresses along these borders.
min_obj_size: 1500 # all objects (cell patches/ isolated cells) below this size (in pixel) will be ignored
cv_pad: 0 # padding when calculating the coefficient of variation in µm// only necessary if the
# mask for the FEM area fits very closely to the mask for membranes
fig_parameters:
# list of which plots to generate depending on which analysis mode is chosen
# available plots are ["deformation","traction","FEM_borders","stress_map","energy_points"]
plots:
cell layer:
- deformation
- traction
- FEM_borders
- energy_points
- stress_map
colony:
- deformation
- traction
- FEM_borders
- stress_map
# dictionary specifying the name of the layer (in the cdb database) a lot is written to // you dont need to change this
plots_layers:
deformation: deformation
traction: traction
FEM_borders: FEM_borders
stress_map: stress_map
energy_points: energy_points
cbar_str: # label of the color bar
deformation: "deformation\n[pixel]"
traction: "traction\n[Pa]"
FEM_borders: "line tension\n[N/m]"
stress_map: "avg. normal stress\nin N/m"
energy_points: "contractile energy\nJ/pixel\n"
file_names:
deformation: deformation.png
traction: traction.png
FEM_borders: border_stress.png
stress_map: mean_normal_stress.png
energy_points: energy_distribution.png
cmap: rainbow # colormap for displaying magnitudes in deformation and traction fields
vmin: None # minimal value displayed in the colormap
vmax: None # maximal value displayed in the colormap
cbar_width: "2%" # width of the color bar in % of the main image. Must be string with % at the end.
cbar_height: "50%" # height of the color bar in % of the main image. Must be string with % at the end.
cbar_borderpad: 6 # distance between the edge of the image and the color bar (in pixels???)
scale_ratio: 0.2 # scale arrows so that the longest arrow is "maximum image dimension" * "scale ratio" long
cbar_title_pad: 10 # padding of the
headwidth: 3 # width of the arrow heads (in pixels?)
headlength: 3 # length of the arrow heads (in pixels?)
width: 0.002 # width of the arrow shaft (what unit?)
plot_t_vecs: False # plotting the stress vectors on the cell border stresses image
plot_n_arrows: False # plotting normal vectors on the cell border stresses image
linewidth: 4 # line width when plotting the cell border stresses
#"cm_cmap":{"FEM_borders":cm.rainbow}, # color map for plotting the cell border stresses. Needs a color maps object.
border_arrow_filter: 1 # plot only every n'th arrow for on the cell border stresses image
cbar_style: clickpoints # if "clickpoints" the color bar is plotted inside of the figure
plot_style: clickpoints
filter_factor: 1 # this factor defines how many arrows are shown in deformation and traction images.
# low number results in many arrows, high number results in few arrows
background_color: "#330033" # set a color for background values. "cmap_0" fill read the zero color of the colormap. "white" would make the background white..
# this doesn't effect images of deformation and traction
cbar_tick_label_size: 15 # size of the tick labels on the color bar
cbar_axes_fraction: 0.2 #fraction of the axes in horrizontal direction, that the colorbar takes up, when colorbar is plotted outside
# of the graph
boundary_resolution: 6 # resolution when plotting the line tension. Highest is 1. Increase for lower resolution,