How the data was processed
(This report is written in the style of an instruction manual, for conciseness).
See the main Readme for a description of the data source.
- Download the data from this NITRC repository.
- In the segmentation software ITK-SNAP,
open the file
WHS_SD_rat_atlas_v2.nii.gzboth as the "Main Image" and as a "Segmentation".
- Generate a bunch of mesh files using
Segmentation > Export as surface mesh, creating a separate
.STLfile for each label. In the
Mesh file namefield, enter
- Open the resulting
.STLfiles in MeshLab.
- Apply the filters described in
mesh_processing/decimate_and_smooth.mlxto each mesh. This reduces the number of vertices by a factor ~10 (using Quadric Edge Collapse Decimation) and smooths the resulting mesh (using Taubin's algorithm).
- Export the filtered meshes as binary
.STLfiles. The total file size of all meshes has now been reduced by a factor ~37 (from 3 GB to 80 MB).