tissue_mechanical_analysis: tissue_mechanical_analysis

In tbgitoo/textureAnalyzerGels: Reading and analyzing texture analyzer data

tissue_mechanical_analysis

Description

Analysis of biological tissue compression curves. Stress-strain curves from biological tissues are usually non-linearly increasing. This function evaluates the Young modulus as the slope in the stress strain curves for small strain segments: strain 0.05-0.15, strain 0.15 to 0.25, then 0.25 to 0.35 and so forth. This gives a quick, discrete overview over how the Young modulus increases with increasing strain.

Usage

tissue_mechanical_analysis(theData,start_height,approximate_touch_point=NULL,stress_column="pressure",stress_slope_column="pressureSlope")

Arguments

theData	Force-Distance data, typically from a "down"-"up" cycle of the chuck; the data needs to be smooth and contain already at the very least the columns Distance and direction, in addition to the colums described by the arguments stress_column and stress_slope_column. Such a variable is typically obtained by using read_texture_analyzer_tab and then smooth_texture_analyzer_data on the result. Care should be taken for the smoothing parameter sd in smooth_texture_analyzer_data, both the pressure and the pressureSlope should appear smooth in a diagram versus distance, while overall look of the curve with a flat part, a steeper elastic part, a less steep plateau and then again rising densitifcation in pressure vs. Distance should be conserved.
start_height	The texture Analyzer typically starts a file by Distance=0, so we loose the information on how high the chuck is above the substrate before starting compression. This needs to be noted separately and transmitted to this function in the start_height argument.
approximate_touch_point	Initial guess for the gel touch point (will be refined by a call to find_initial_touch_point)
stress_column	Name of the column in theData that contains the stress information. By default, this is the "pressure" column as produced by read_texture_analyzer_tab and smoothened by smooth_texture_analyzer_data. An alternative column can be used, for instance if chuck buoyancy is substracted with the creation of a new column (done manually).
stress_slope_column	Name of the column in theData that contains the slope of the stress. The units are the units of the stress column devided by the units of the Distance column. By default, this is the "pressureSlope" column as produced by read_texture_analyzer_tab and smoothened by smooth_texture_analyzer_data. An alternative column can be used, for instance if chuck buoyancy is substracted with the creation of a new column (done manually).

Details

The estimations of the Young modulus given in this function approximately corresponds to the local tangent modulus (ATSM E111); they are found by local linear regression (lm).

Value

A list with different geometric and mechanical measures:

touchpoint

A numeric vector describing the touchpoint coordinates found for the different directions (usually, "down" and "up").

sample_thickness

Estimation of the sample height

E

A matrix with rows for the directions ("down", "up" in general) and columns for the different strains at which the Young modulus is estimated (i.e. 9 colums for Young moduli at strains 0.1, 0.2, 0.3, ... , 0.9

hysteresis

An overall estimate of the hysteresis between compression ("down") and relaxation ("up"). This is the area between the "down" and "up" curve devided by the area under the "down" curve.

Author(s)

Thomas Braschler

References

ATSM standard E111: https://www.astm.org/Standards/E111.htm

See Also

find_initial_touch_point, used internally

Examples

# This is not necessarily the most appropriate use since with foam_mechanical_analysis, there is a more specific function for the foam-like cryogels. Here, one can see that the
# initial elastic Young modulus is high, followed by a plateau with lower Young moduli before a final increase

data(sampleGelSmooth)
results=tissue_mechanical_analysis(
	sampleGelSmooth,start_height=start_height_mm)
results

tbgitoo/textureAnalyzerGels documentation built on March 30, 2022, 4:53 a.m.