Hyperelastic Lookup Table for Real-Time Deformability Cytometry (RT-DC)

Hyperelastic Lookup Table for Real-Time Deformability Cytometry (RT-DC) <br> 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]. <br> 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. <br> Dataset HDF5 Files: - 20220826_HyperelasticLookup_2DAxis_nonNewtonian_All.hdf5 - 20220826_HyperelasticLookup_3D_nonNewtonian_All.hdf5 <br> 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, ...). <br> CSV Files: Same as the HDF5-Files, but as comma-separated files without the object shapes <br> COMSOL 5.6 Model Files: - CylindricalChannel_FSI_Model.mph - CylindricalChannel_LargeDeformation_FSI_Model.mph - SquareChannel_FSI_Model.mph - SquareChannel_LargeDeformation_FSI_Model.mph <br> 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+! <br> ZIP File: - rt_dc_measurements.zip <br> Exemplary RT-DC measurements of PAAm beads and HL60 cells. <br> <br> <br> 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]. <br> <br> 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 &amp; 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 <br> <br> 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