################################################### <<<< Introduction >>>> This README file describes the folder layout and data structures relevant to the following published article: "Vedula, V., Lee, J., Xu, H., Kuo, C.-C., Hsiai, T., and Marsden, A., “A method to quantify mechanobiologic forces during zebrafish cardiac development using 4-D light sheet imaging and computational modeling”, PLoS Computational Biology, 13 (10):e1005828, 2017." For any queries, please contact: ################################################### <<<< Folder layout: >>>> There are four subdirectories in the main folder corresponding to each fish type: (1) 01-wildtype : wild type or control zebrafish (2) 02-AG1478 : zebrafish chemically treated with AG1478 (3) 03-gata1aMO : zebrafish treated with Gata1aMO (4) 04-wea : weak atrium mutant zebrafish type Within each of these folders, are 4 sub-directories: (1) 01-image-data (2) 02-wall-motion (3) 03-flow-data (4) 04-shear-KE-data ################################################### <<<< File naming and data convention: >>>> (1) << 01-image-data >> Contains image data in vti format for one cardiac cycle. Images are named as image_#.vti, where # is an index corresponding to the time frame in the cardiac cycle. (2) << 02-wall-motion >> Contains ventricular surface data in vtk format for one cardiac cycle. Each file is named as markerNew_#.vtk, where # is the index corresponding to the time frame in the cardiac cycle. (3) << 03-flow-data >> Contains simulated flow field in .vtu format at selected time points in the cardiac cycle. Each file is named as result_t#.vtu, where # indicates dimensional time. (4) << 04-shear-KE-data >> Contains data related to hemodynamic shear (AWSS, TAWSS and OSI), and kinetic energy and viscous dissipation. (a) << AWSS_t.dat >> : Two column data, where first is the dimensional time (in secs) and second is AWSS in mm-g-s units. (b) << OSI.vtp >> : A VTK Polydata file that has OSI data on the surface of the ventricle. (c) << TAWSS.dat >> : Contains the TAWSS value in mm-g-s units. (d) << KE_Diss_t.dat >> : Four column data, where first is the dimensional time (in secs), second is the volume of the ventricle, third is KE and fourth is the viscous dissipation. All quantities are in mm-g-s units. AWSS: area-averaged wall shear stress; TAWSS: time-averaged wall shear stress; OSI: oscillatory shear index; KE: volume-averaged kinetic energy; Diss: volume-averaged viscous dissipation ################################################### Note: In general, (vti, vtk, vtu, vtp) data can be visualized with Paraview and metrics in .dat files can be loaded into Tecplot.