Pseudo-dynamic analysis of heart tube formation in the mouse reveals strong regional variability and early left-right asymmetry
Description
This Dataset contains: · Folders: "MT specimen collection" and "SMM specimen collection" contain segmentation images and 3D reconstructions of every tissue studied in Esteban et al., Nature Cardiovascular Research (2022). · Folder: "MSGs" contains the group of shapes referred to as "Mean Shape Group" (MSG) in Esteban et al., Nature Cardiovascular Research (2022). · Folder: "MSGs_3D+t" contains the group of shapes of the dynamic model elaborated with the MSG shapes in Esteban et al., Nature Cardiovascular Research (2022). · Folder: "RSGs_3D+t" contains the groups of shapes of the corresponding dynamic models elaborated with the SGR shapes in Esteban et al., Nature Cardiovascular Research (2022). · Folder: "Videos" contains the Videos described in Esteban et al., Nature Cardiovascular Research (2022).
Files
Steps to reproduce
To visualize the segmentation images (.nii.gz format), we recommend using ITK-SNAP. To visualize the meshes (.ply format), we recommend using ParaView. · In order to open a single mesh, select the file with the mouse and drop it in ParaView. It will appear listed in the "Pipeline Browser" window. Next, click on the eye icon, located at the left of the file name, and it will be displayed in the renderization window. · In order to open different meshes, repeat the former step for every mesh you want to open. · In order to visualize the dynamic models (i.e., temporal sequence of meshes), follow the next steps: 1. Uncompress the .tar.xz file of the specific description and tissue you want to see (e.g.: somatic mesoderm from RSG collection). 2. Select all the .ply files and drop them in ParaView. All the files are now loaded as a unique file. 3. Click on the closed eye icon and the meshes will be displayed in the rendering window. 4. Use the play button located at the top bar to play the simulation. 5. In order to visualize additional tissues simultaneously, repeat steps 2, 3 and 4. NOTE: the sequence of files is loaded in ParaView following the same order that is displayed in the folder that contains those files. Make sure to order them accordingly by name (t0, ..., t11). Otherwise, the simulation would run backwards. Each mesh, or group of meshes (e.g.: collection of myocardiums from the MSG) can be colored as follows: 1. Select the mesh or group of meshes. 2. Click on the gear icon, located in the "Properties" panel, at the left side of the ParaView window. 3. In "Coloring", select the "Solid Color" option. 4. In "Coloring", click on "Edit" and select the desired color from the emergent window.