Hyperelastic Lookup Table for Real-Time Deformability Cytometry (RT-DC)
Hyperelastic Lookup Table for Real-Time Deformability Cytometry (RT-DC)
Background
In real-time deformability cytometry (RT-DC), the area and the deformation
of a sphere in a microfluidic channel at high flow rates can be translated
into Young's modulus [1] by employing a look-up-table (LUT). For the average
RT-DC user, these computations are usually performed by dclab [2].
Compared to the lookup table in [3, 4], the new dataset and lookup table is
based on a hyperelastic neo-Hookean material for the cells and considers
the full square channel geometry as well as the shear-thinning behavior
of the surrounding fluid.
Dataset
HDF5 Files:
- 20220826_HyperelasticLookup_2DAxis_nonNewtonian_All.hdf5
- 20220826_HyperelasticLookup_3D_nonNewtonian_All.hdf5
Contain the object shapes from the finite element simulations for the
LUT ('coords'), the shapes with the contour quantities like shear and
pressure stresses ('raw_contour') as well as surface quantities
and the Young's modulus, radius, deformation, etc. as attributes.
The HDF5-File contains for each Young's modulus a group which has for
each sphere radius a subgroup (numbered with i, j = 0, 1, 2, ...).
CSV Files:
Same as the HDF5-Files, but as comma-separated files without the object shapes
COMSOL 5.6 Model Files:
- CylindricalChannel_FSI_Model.mph
- CylindricalChannel_LargeDeformation_FSI_Model.mph
- SquareChannel_FSI_Model.mph
- SquareChannel_LargeDeformation_FSI_Model.mph
COMSOL 5.6 model files used to generate the object files in the HDF5 files.
Note: Due to changes in the continuum mechanics discretization in COMSOL 6.0
the model files do not work with COMSOL 6.0+!
ZIP File:
- rt_dc_measurements.zip
Exemplary RT-DC measurements of PAAm beads and HL60 cells.
Notes
- The cells are modeled as a hyperelastic neo-Hookean bulk material.
- In RT-DC, objects are flushed through a rectangular channel. The FEM
simulations are performed in cylindrical symmetry (axis-symmetric, 2DAxis)
as well as in a square channel geometry (3D).
- For generation of the LUTs, please refer to the data processing scripts in the
dclab repository [5].
References
[1] Alexander Mietke, Oliver Otto, Salvatore Girardo, Philipp Rosendahl,
Anna Taubenberger, Stefan Golfier, Elke Ulbricht, Sebastian Aland,
Jochen Guck, and Elisabeth Fischer-Friedrich. Extracting Cell Stiffness
from Real-Time Deformability Cytometry: Theory and Experiment.
Biophysical Journal, 109(10):2023–2036, nov 2015.
doi:10.1016/j.bpj.2015.09.006.
[2] https://dclab.readthedocs.io
[3] M. Mokbel, D. Mokbel, A. Mietke, N. Träber, S. Girardo, O. Otto,
J. Guck, and S. Aland. Numerical Simulation of Real-Time Deformability
Cytometry To Extract Cell Mechanical Properties.
ACS Biomaterials Science & Engineering, 3(11):2962–2973, jan 2017.
doi:10.1021/acsbiomaterials.6b00558.
[4] Wittwer, Lucas Daniel; Müller, Paul; Mokbel, Dominic; Mokbel, Marcel;
Guck, Jochen; Aland, Sebastian (2020): Finite element simulation data
for the computation of the Young's modulus in real-time deformability
cytometry. figshare. Dataset.
https://doi.org/10.6084/m9.figshare.12155064.v3
[5] https://github.com/ZELLMECHANIK-DRESDEN/dclab/tree/master/scripts
SHA256 sums
7b7cd67b1296a5261f2a256eeb367ecaca32f516bfb154a7476f31538a20d3ee 20220826_HyperelasticLookup_2DAxis_nonNewtonian_All.hdf5
2fa77ceb507f660f733e77291061dce2a436dcdb04d5e0bc4acf539736fb4ad6 20220826_HyperelasticLookup_3D_nonNewtonian_All.hdf5
712900bc65a7eb9309b1c3fa05d706a0db8cb9269a9801175d0de9edca0cbbc8 20220826_HyperelasticLookup_2DAxis_nonNewtonian_All.csv
c97a4696faed0640def78d705e3f4071029507732939e2998450fef0a461e7bc 20220826_HyperelasticLookup_3D_nonNewtonian_All.csv
645f6829fac65a504100cd43bc032d50de6ddf19595810d02d55ef2a1195feab CylindricalChannel_FSI_Model.mph
4964f2be10af404e6df020f37f373ea7c9a55b84f476f81925b0ed1d7f06986f CylindricalChannel_LargeDeformation_FSI_Model.mph
e8f684414e8d8a757ffd555444dec8b453b9c9ab0aa833f5459abb1014df61d1 SquareChannel_FSI_Model.mph
28d4894398aa985e344a83768a9b5432a10c9ca8d85f75501b8d9b049a903914 SquareChannel_LargeDeformation_FSI_Model.mph
ab056670b84c83c4691f678bb29b060a25a29b7ebea379222f0284aa7c31b051 rt_dc_measurements.zip
