DOI: 10.17608/k6.auckland.23647605
title: Rat uterus meshes

description: <b>Rat uterus meshes</b><b>General information</b>This item contains surface and volumetric meshes of the rat uterus (<b>AWA015_PTA_1_*</b>)<i> </i>and the ovarian segment <i>(</i><b>AWA015_PTA_2_Ova_</b><b>*</b>) along with the fibres identified with structure tensors. They were generated from the muscle segmentation of uCT images. The rat was in the oestrus phase of its cycle.This item also contains a .bin file containing the high-resolution ovarian segment surface mesh registered to the organ mesh and a figure showing the two meshes and the distances between them after registration.<b>Contents</b>In the meshes archives:The <b>AWA015_PTA_1_Rec_Trans_surface_mesh.stl </b>and <b>AWA015_PTA_1_Rec_Trans_surface_mesh.vtk</b> meshes are exported directly from ITK-SNAP (www.itksnap.org).The <b>AWA015_PTA_1_Rec_Trans_surface_mesh.stl</b> mesh was edited in Meshmixer 3.5.474 (Autodesk, Inc.) to correct issues in the surface mesh to generate a volumetric mesh. The exported file is <b>AWA015_PTA_1_Rec_Trans_surface_mesh_fixed.stl.</b>The <b>AWA015_PTA_1_Rec_Trans_volumetric_mesh.vtk</b> mesh was generated with Netgen (https://ngsolve.org/) from the fixed surface mesh.The <b>AWA015_PTA_1_Rec_Trans_volumetric_mesh_annotated.vtk</b> mesh is annotated with the thickness information obtained from the segmentation masks.The <b>AWA015_PTA_2_Ova_Rec_Trans_surface_mesh.stl </b>and <b>AWA015_PTA_2_Ova_Rec_Trans_surface_mesh.vtk</b> meshes are exported directly from ITK-SNAP (www.itksnap.org).The <b>AWA015_PTA_2_Ova_Rec_Trans_surface_mesh.stl</b> mesh was edited in Meshmixer 3.5.474 (Autodesk, Inc.) to correct issues in the surface mesh to generate a volumetric mesh. The exported file is <b>AWA015_PTA_2_Ova_Rec_Trans_surface_mesh_fixed.stl.</b>The <b>AWA015_PTA_2_Ova_Rec_Trans_volumetric_mesh.vtk</b> mesh was generated with Netgen (https://ngsolve.org/) from the fixed surface mesh.The <b>AWA015_PTA_2_Ova_Rec_Trans_volumetric_mesh_annotated.vtk </b>mesh is annotated with the thickness information obtained from the segmentation masks.In the fibres archives:The <b>AWA015_PTA_1_Rec_Trans_L4_fibres.exelem </b>file contains the elements of the streamlines representing the fibres of the entire uterus in Cmgui format.The <b>AWA015_PTA_1_Rec_Trans_L4_fibres.exnode </b>file contains the nodes of the streamlines representing the fibres of the entire uterus in Cmgui format.The <b>AWA015_PTA_12_Ova_Rec_Trans_L4_fibres.exelem </b>file contains the elements of the streamlines representing the fibres of the ovarian segment in Cmgui format.The <b>AWA015_PTA_2_Ova_Rec_Trans_L4_fibres.exnode </b>file contains the elements of the streamlines representing the fibres of the ovarian segment in Cmgui format.In the rest of the item:The <b>AWA015_mesh_registration.bin</b> file contains the full organ surface mesh (<b>AWA015_PTA_1_Rec_Trans_surface_mesh_fixed.stl</b>) and the registered ovarian segment surface mesh (<b>AWA015_PTA_2_Ova_Rec_Trans_surface_mesh_fixed</b>.<b>stl</b>).The <b>registration_figure.png</b> file shows two views from CloudCompare. In the top panel (A), the <b>AWA015_PTA_2_Ova_Rec_Trans_surface_mesh_fixed</b>.<b>stl </b>mesh color-coded to show the distance with the <b>AWA015_PTA_1_Rec_Trans_surface_mesh_fixed</b>.<b>stl</b>. The bottom panel (B) indicates the position of the <b>AWA015_PTA_2_Ova_Rec_Trans_surface_mesh_fixed</b>.<b>stl</b> mesh relative to the <b>AWA015_PTA_1_Rec_Trans_surface_mesh_fixed</b>.<b>stl</b> mesh.<b>Visualisation</b>The .vtk files can be viewed with software such as Paraview (https://www.paraview.org/). The .exnode and .exelem files exist for the original surface mesh exported from ITK-SNAP and the annotated volumetric mesh to be visualised in cmgui.The AWA015_mesh_registration.bin file can be viewed with Cloud Compare (https://www.cloudcompare.org/).