Rat uterus meshes

Rat uterus meshes

General information

This item contains surface and volumetric meshes of the rat uterus (AWA015_PTA_1_*) and the ovarian segment (AWA015_PTA_2_Ova_*) 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.

Contents

In the meshes archives:

• The AWA015_PTA_1_Rec_Trans_surface_mesh.stl and AWA015_PTA_1_Rec_Trans_surface_mesh.vtk meshes are exported directly from ITK-SNAP (www.itksnap.org).
• The AWA015_PTA_1_Rec_Trans_surface_mesh.stl 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 AWA015_PTA_1_Rec_Trans_surface_mesh_fixed.stl.
• The AWA015_PTA_1_Rec_Trans_volumetric_mesh.vtk mesh was generated with Netgen (https://ngsolve.org/) from the fixed surface mesh.
• The AWA015_PTA_1_Rec_Trans_volumetric_mesh_annotated.vtk mesh is annotated with the thickness information obtained from the segmentation masks.
• The AWA015_PTA_2_Ova_Rec_Trans_surface_mesh.stl and AWA015_PTA_2_Ova_Rec_Trans_surface_mesh.vtk meshes are exported directly from ITK-SNAP (www.itksnap.org).
• The AWA015_PTA_2_Ova_Rec_Trans_surface_mesh.stl 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 AWA015_PTA_2_Ova_Rec_Trans_surface_mesh_fixed.stl.
• The AWA015_PTA_2_Ova_Rec_Trans_volumetric_mesh.vtk mesh was generated with Netgen (https://ngsolve.org/) from the fixed surface mesh.
• The AWA015_PTA_2_Ova_Rec_Trans_volumetric_mesh_annotated.vtk mesh is annotated with the thickness information obtained from the segmentation masks.

In the fibres archives:

• The AWA015_PTA_1_Rec_Trans_L4_fibres.exelem file contains the elements of the streamlines representing the fibres of the entire uterus in Cmgui format.
• The AWA015_PTA_1_Rec_Trans_L4_fibres.exnode file contains the nodes of the streamlines representing the fibres of the entire uterus in Cmgui format.
• The AWA015_PTA_12_Ova_Rec_Trans_L4_fibres.exelem file contains the elements of the streamlines representing the fibres of the ovarian segment in Cmgui format.
• The AWA015_PTA_2_Ova_Rec_Trans_L4_fibres.exnode file contains the elements of the streamlines representing the fibres of the ovarian segment in Cmgui format.

In the rest of the item:

• The AWA015_mesh_registration.bin file contains the full organ surface mesh (AWA015_PTA_1_Rec_Trans_surface_mesh_fixed.stl) and the registered ovarian segment surface mesh (AWA015_PTA_2_Ova_Rec_Trans_surface_mesh_fixed.stl).
• The registration_figure.png file shows two views from CloudCompare. In the top panel (A), the AWA015_PTA_2_Ova_Rec_Trans_surface_mesh_fixed.stl mesh color-coded to show the distance with the AWA015_PTA_1_Rec_Trans_surface_mesh_fixed.stl. The bottom panel (B) indicates the position of the AWA015_PTA_2_Ova_Rec_Trans_surface_mesh_fixed.stl mesh relative to the AWA015_PTA_1_Rec_Trans_surface_mesh_fixed.stl mesh.

Visualisation

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/).