Finite element simulation data for the computation of the Young's modulus in real-time deformability cytometry

<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<br>of a sphere in a microfluidic channel at high flow rates can be translated<br>into Young's modulus [1] by employing a look-up-table (LUT). For the average<br>RT-DC user, these computations are usually performed by dclab [2].<br><br>The refurbished LUT introduced in dclab 0.24.0 was computed from this dataset.<br>The original LUT in dclab (version &lt;=0.23.0) was slightly smaller and it was<br>not possible to derive volume-deformation isoelasticity lines (because those<br>data were not available). Lucas Wittwer reran all the original simulations<br>(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<br>obtained with finite element method (FEM) simulations which were originally<br>performed by Mokbel et al. [3]. The simulations were done for a linear elastic<br>material. The HDF5 file contains the final object shapes and (via attributes)<br>the corresponding values for Young's modulus, deformation, projected area, and<br>volume. The hdf5-File contains for each Young's modulus a group which has for<br>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<br> simulations, however, are performed in cylindrical symmetry (axis-symmetric).<br> The equivalent channel radius for a square channel was computed with a<br> 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<br> also important for objects with a large cross-sectional area. Here, the flow<br> profile in the cylindrical channel does not anymore correctly approximate<br> the corresponding profile in the square channel, leading to inaccurate<br> object shapes. Furthermore, there have been numerical errors due to meshing<br> if the area is above 290um^2. Therefore, simulations with cross-sectional<br> areas above 290um^2 should not be considered reliable (they are excluded<br> from the LUT in dclab).<br>- There are no simulations below an area of 200um^2 and a deformation below<br> approximately 0.005. This is because those deformation values were not<br> resolvable with FEM. In dclab, those missing values are filled in with<br> values computed using the analytical solution [1]. For the sake of<br> completeness, these missing values are included here in the file<br> "LUT_analytical_linear-elastic_2Daxis.txt".<br>- Compared to the initial LUT in dclab&lt;=0.23.0, the values given here<br> differ by a relative error below 0.001 (0.1%).<br>- For more information, please refer to the data processing scripts in the<br> dclab repository [4].<br><br><br><b>References<br></b>[1] Alexander Mietke, Oliver Otto, Salvatore Girardo, Philipp Rosendahl,<br> Anna Taubenberger, Stefan Golfier, Elke Ulbricht, Sebastian Aland,<br> Jochen Guck, and Elisabeth Fischer-Friedrich. Extracting Cell Stiffness<br> from Real-Time Deformability Cytometry: Theory and Experiment.<br> Biophysical Journal, 109(10):2023–2036, nov 2015.<br> 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,<br> J. Guck, and S. Aland. Numerical Simulation of Real-Time Deformability<br> Cytometry To Extract Cell Mechanical Properties.<br> ACS Biomaterials Science &amp; Engineering, 3(11):2962–2973, jan 2017.<br> 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>