Supplementary Dataset: Multimodal imaging reveals hierarchical fibre mechanics

Data related to the publication “Multimodal imaging reveals hierarchical fibre mechanics”Full methodology described in the above publication, and all code available on GITHUB.CT Dataset167208_2560xy_2160z_pag100_us2p5.raw : Synchrotron CT image of IVD sample 1 at 1 N preload. Dimensions: x=2560, y=2560, z=2160. Format: 16-bit unsigned, big endian. Voxel size = 1.625 µm. Reconstructed using the filtered back projection algorithm with Paganin phase retrieval (δ/β value = 100). An unsharp mask (radius = 2.5 pixels and weight = 0.9) was applied using ImageJ. Used for fibre tracing and reference file for DVC analysis.167209_2560xy_2160z_pag100_us2p5.raw : Synchrotron CT image of IVD sample 1 after 50 µm compressive displacement. Dimensions: x=2560, y=2560, z=2160. Format: 16-bit, big endian. Voxel size = 1.625 µm. Reconstructed using the filtered back projection algorithm with Paganin phase retrieval (δ/β value = 100). An unsharp mask (radius = 2.5 pixels and weight = 0.9) was applied using ImageJ. Correlate file for DVC analysis.Orientation data for TomoSAXS reconstruction167208_fibreID_5x5.png : Dimensions of 167208_fibreID_5x5.tif.167208_fibreID_5x5.tif : 3D tif of fibreID for the preload image of IVD 1, voxel size = 5 CT voxels = 8.125 µm.167208_theta_5x5.png : Dimensions of 167208_theta_5x5.tif.167208_theta_5x5.tif : 3D tif of theta orientation (SAXS orientation alpha) for the preload image of IVD 1, voxel size = 5 CT voxels = 8.125 µm.167208_phi_5x5.png : Dimensions of 167208_phi_5x5.tif.167208_phi_5x5.tif : 3D tif of phi orientation (SAXS orientation beta) for the preload image of IVD 1, voxel size = 5 CT voxels = 8.125 µm.Inputs/ outputs of CT fibre tracing and DVC analysis167208_AFstrain_labels.tif : Smooth segmentation of the AF used for radial and circumferential strain calculations. Input for contourlines_strain.py167208_displacement.disp : Displacement measurements output from DVC analysis.167208_dvc_pointcloud.txt : Fibre based point cloud for input into iDVC.167208_fibre_means.csv : Per fibre mean values of Fibre Orientation Theta, Delta Theta, Delta Theta Magnitude, Fibre Orientation Phi, Delta Phi, Delta Phi Magnitude, Curvature, Delta Curvature, Delta Curvature Magnitude, Fibre Strain (no polynomial smoothing), Fibre Strain Magnitude, Fibre Strain Lsmooth (with polynomial smoothing), Fibre Strain Magnitude Lsmooth, 1st principal strain (ep1), 3rd principal strain (ep3), angle between 1st principal strain vector and fibre direction (ep1_alpha), angle between 3rd principal strain vector and fibre direction (ep3_alpha), Radial Strain, Radial Strain Magnitude, Circumferential Strain, Circumferential Strain Magnitude.167208_fibre_metrics.csv : 'x', 'y', 'z', 'theta', 'phi', 'delta theta', 'delta phi', 'k', 'delta k', 'm', 'L', 'Lsmooth', for each point in the DVC point cloud, data output from TomoSAXS_loaded_orientation.m.167208_fibres.xml : Fibre data exported from Avizo fibre tracing, for input into TomoSAXS_initial_orientation.m.167208_fibres.xlsx : 167208_fibres.xml converted to .xlsx, for input into TomoSAXS_initial_orientation.py.167208_fibres_spatialgraph.am : Avizo spatial graph of traced fibres, open in Avizo.167208_orientation.csv : 'x', 'y', 'z', 'fibre ID', 'theta', 'phi', orientation data for fibres output from TomoSAXS_initial_orientation.m.167208_pointcloud_spacecurve.mat : Output file from TomoSAXS_initial_orientation.m, for input into TomoSAXS_loaded_orientation.m. Contains fibre fitting data, can be opened in Matlab.167208_radcirc_strains.csv : Output from contourlines_strain.py: x, y, z, contour, strain_tangent (circumferential strain), strain_normal (radial strain), strain_through_plane, shear_tangent_normal, shear_tangent_z, shear_normal_z.167208_strain_direction.csv : Angles between strain eigenvectors and local fibre direction, output from angleofeigenvectors.m. 'x', 'y', 'z', 'ep1_alpha', 'ep3_alpha'167208_tissuestrain-sw75.Lstr.csv : Tissue level strain information output from iDVC strain executable. Input for contourlines_strain.py and eigenvectoranglewithfibre.py.167209_orientation.csv : Loaded orientation of fibres output from TomoSAXS_loaded_orientation.m. 167209_pointcloud_mask.csv : Points placed every voxel along loaded fibres, used for creating a binary mask for the loaded orientation tifs used for TomoSAXS reconstruction. Output from TomoSAXS_loaded_orientation.m.dvc_in_167208.txt : DVC input file for running iDVC.Processing files from SAXS experimentSAXS_mask.nxs: File containing mask used for processing of SAXS frames.SAXS_calibration.nxs: Axis calibration file for processing of SAXS frames. Outputs of CT/SAXS registrationFull_alpha_index_matrices.npy: numpy file comprising isolated α (vertical orientation) values for every SAXS voxel in a scan.Full_beta_index_matrices.npy: numpy file comprising isolated β (vertical orientation) values for every SAXS voxel in a scan.Full_count_index_matrices.npy: numpy file comprising isolated numbers of unique fibres for every SAXS voxel in a scan.Full_fibre_index_matrices.npy: numpy file comprising isolated fibre index values for every SAXS voxel in a scan.Full_wieght_index_matrices.npy: numpy file comprising isolated weighting values (proximity of fibre to beam centre) for every SAXS voxel in a scan.Outputs of flexible background correctionFIVD1_unloaded_1_processed.h5: hdf5 file containing background corrected SAXS frames for example SAXS slice, partitioned into individual sampling oreintations.Outputs of Intensity(chi) processing (first step of SVD analysis)FIVD1_unloaded_slice_1_fibril_params_raw.pkl: Python dictionary comprising entries for each indexed fibre found in a single SAXS slice.FIVD1_unloaded_slice_1_ichi_dict_params.pkl: Python dictionary comprising parameters used for sampling intensity across chi (I(chi).FIVD1_unloaded_slice_1_ichi_dict_raw.pkl: Python dictionary comprising sampled I(chi) for each frame in an example SAXS slice. FIVD1_unloaded_slice_1_rotation_beampaths.pkl: Python dictionary comprising Entries for each fibre, partitioned into individual SAXS beampaths for an example SAXS slice.FIVD1_unloaded_slice_1_svd_cake_params.pkl: Python dictionary comprising parameters for simulating Intensity(chi) data for example SAXS slice.Outputs of SVD estimation (second step of SVD analysis)FIVD1_unloaded_slice_1_fibril_params_svd_Arr_amps: copy of original “fibril_params” dictionary with initial estimates of scattering amplitude added for each fibre.FIVD1_unloaded_slice_1_rotation_beampaths_svd_amps.pkl: copy of original “rotation_beampaths” dictionary with initial estimates of scattering amplitude added for each fibre.