3D cell tracking dataset of bacterial biofilm deformation and recovery under shear flow
DOI10.5281/zenodo.10091010Zenodo10091010MaRDI QIDQ6702015FDOQ6702015
Dataset published at Zenodo repository.
Konstantin Neuhaus, Jörn Dunkel, Dominic J. Skinner, Knut Drescher, Gary Choi, Takuya Ohmura
Publication date: 9 November 2023
Copyright license: Creative Commons Attribution 4.0 International
This MAT file includes dataset in the scientific article "In vivo microrheology reveals elastic and plastic responses inside three-dimensional bacterial biofilms" by the following authors: Takuya Ohmura, Dominic Skinner, Konstantin Neuhaus, Gary Choi, Jörn Dunkel, Knut Drescher. This MAT file can be conveniently opened with Matlab.When you open this file with Matlab, you will find 4 variables stored in the file "Data_v3_loop2_newRxy_bidx1_274.mat"Variable 1: name_parameterNames of 31 parameters for columns in 3 variables: 'deformation_all', 'recovery_all' , 'plasticity_all'. The parameters have cell displacements, orientations, coordinates, biofilm indexes and experimental conditions. When the parameters have units, they are shown in the names.'x_Frame1[um]y_Frame1[um]z_Frame1[um]Normalized_x_Frame1Normalized_y_Frame1Normalized_z_Frame1LocalDensity_Frame1(VolumeFractionAround30px)LocalCellNumberDensity_Frame1(VolumeFractionAround30px)NematicOrderParameter_Frame1AlignmentFlow_Frame1[rad]AlignmentRadial_Frame1[rad]AlignmentZaxis_Frame1[rad]d_x[um]d_y[um]d_z[um]Normalized_d_xNormalized_d_yNormalized_d_zd_LocalDensityd_LocalNumberDensity[um^-3]d_NematicOrderParameterd_AlignmentFlow[rad]d_AlignmentRadial[rad]d_AlignmentZaxis[rad]CrossProduct[um^2]BiofilmIndexNumberBiofilm_width[um]Biofilm_height[um]Biofilm_volume[um^3]FlowRate[ul/min]Duration[min]'Variable 2:deformation_allThe rows indicate 704198 single-cell trackings in deformations of 274 bacterial biofilms. Each of the 274 bacterial biofilms has a different 'BiofilmIndexNumber'. The columns indicate 31 parameters which names are shown in 'name_parameter'.Variable 3: recovery_allThe rows indicate 685991 single-cell trackings in recoveries of 274 bacterial biofilms. Each of the 274 bacterial biofilms has a different 'BiofilmIndexNumber'. The columns indicate 31 parameters which names are shown in 'name_parameter'.Variable 4: plasticity_allThe rows indicate 665749 single-cell trackings in plasticities of 274 bacterial biofilms. Each of the 274 bacterial biofilms has a different 'BiofilmIndexNumber'. The columns indicate 31 parameters which names are shown in 'name_parameter'.To plot the cell tracked data in the figures of the article, use our MATLAB code uploaded in our GitHub (https://github.com/knutdrescher/biofilm-rheology).
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