DOI: 10.6084/m9.figshare.12155064.v2
title: Finite element simulation data for the computation of the Young's modulus in real-time deformability cytometry

description: <b>Finite element simulation data for the computation of the Young's modulus in real-time deformability cytometry<br></b><br><b>Background</b><br>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><br>The refurbished LUT introduced in dclab 0.24.0 was omputed from this dataset. The original LUT in dclab (version &lt;=0.23.0) was slightly smaller and it was not possible to derive volume-deformation isoelasticity lines (because those data were not available). Dominic Mokbel and Lucas Wittwer reran all the original simulations (in addition to a few new ones) to obtain this dataset.<br><br><br><b>Dataset<br></b>The dataset "20191113_ObjectShapes_RT-DC_2Daxis.hdf5" contains object shapes obtained with finite element method (FEM) simulations which were originally performed by Mokbel et al. [3]. The simulations were done for a linear elastic material. The HDF5 file contains the final object shapes and (via attributes) the corresponding values for Young's modulus, deformation, projected area, and volume. 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><br><br><b>Notes<br></b>- The sphere is modeled as a linear elastic material.<br>- In RT-DC, objects are flushed through a rectangular channel. The FEM simulations, however, are performed in cylindrical symmetry (axis-symmetric). The equivalent channel radius for a square channel was computed with a factor of 1.094 and employed in the simulations (see [1] supplemt S3).<br>- The fact that the simulations were performed with cylindrical symmetry is also important for objects with a large cross-sectional area. Here, the flow profile in the cylindrical channel does not anymore correctly approximate the corresponding profile in the square channel, leading to inaccurate object shapes. Furthermore, there have been numerical errors due to meshing if the area is above 290um^2. Therefore, simulations with cross-sectional areas above 290um^2 should not be considered reliable (they are excluded from the LUT in dclab).<br>- There are no simulations below an area of 200um^2 and a deformation below approximately 0.005. This is because those deformation values were not resolvable with FEM. In dclab, those missing values are filled in with values computed using the analytical solution [1]. For the sake of completeness, these missing values are included here in the file "LUT_analytical_linear-elastic_2Daxis.txt".<br>- Compared to the initial LUT in dclab&lt;=0.23.0, the values given here differ by a relative error below 0.001 (0.1%).<br>- For more information, please refer to the data processing scripts in the dclab repository [4].<br><br><br><b>References<br></b>[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.<br>[2] https://dclab.readthedocs.io<br>[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, (11):2962–2973, jan 2017. doi:10.1021/acsbiomaterials.6b00558.<br>[4] https://github.com/ZELLMECHANIK-DRESDEN/dclab/tree/master/scripts<br><br><br><b>SHA256 sums<br></b>c5f7d741ceec6dcddbe628bd40573b52666fe9b9e4dfe5888f9952932f003359 20191113_ObjectShapes_RT-DC_2Daxis.hdf5<br>908ded1a5bee8a39104eaef56d74ff692ab9a5c52777164af5ed4bf183a0cbe0 LUT_analytical_linear-elastic_2Daxis.txt<br><br>