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_parameter Names 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_Frame1' 'Normalized_y_Frame1' 'Normalized_z_Frame1' 'LocalDensity_Frame1(VolumeFractionAround30px)' 'LocalCellNumberDensity_Frame1(VolumeFractionAround30px)' 'NematicOrderParameter_Frame1' 'AlignmentFlow_Frame1[rad]' 'AlignmentRadial_Frame1[rad]' 'AlignmentZaxis_Frame1[rad]' 'd_x[um]' 'd_y[um]' 'd_z[um]' 'Normalized_d_x' 'Normalized_d_y' 'Normalized_d_z' 'd_LocalDensity' 'd_LocalNumberDensity[um^-3]' 'd_NematicOrderParameter' 'd_AlignmentFlow[rad]' 'd_AlignmentRadial[rad]' 'd_AlignmentZaxis[rad]' 'CrossProduct[um^2]' 'BiofilmIndexNumber' 'Biofilm_width[um]' 'Biofilm_height[um]' 'Biofilm_volume[um^3]' 'FlowRate[ul/min]' 'Duration[min]' Variable 2: deformation_all The 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_all The 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_all The 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).