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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.

  1. Download the data from this NITRC repository.
  2. In the segmentation software ITK-SNAP, open the file WHS_SD_rat_atlas_v2.nii.gz both as the "Main Image" and as a "Segmentation".
  3. Generate a bunch of mesh files using Segmentation > Export as surface mesh, creating a separate .STL file for each label. In the Mesh file name field, enter label_.stl.
  4. Open the resulting .STL files in MeshLab.
  5. Apply the filters described in mesh_processing/decimate_and_smooth.mlx to 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).
  6. Export the filtered meshes as binary .STL files. The total file size of all meshes has now been reduced by a factor ~37 (from 3 GB to 80 MB).