Biomedical datasets

Biomedical datasets#

There are several public data-sets for meshing:

MRI to FEM Vol 2 - Chapter 2#

The following dataset: DOI: 10.5281/zenodo.14536217 contains the following surfaces (stl-files) for the patient known as Gonzo, (under Gonzo/outputs) for a subset of regions in the brain. Whenever there are files named a.stl, final-a.stl, it means that the initial surface a.stl has been processed, for instanced smoothened or perturbed for better surface quality with the resulting surface final-a.stl.

  • Brainstem (brainstem.stl): The surface describing the brainstem

  • Cerebellum (cerebellum.stl): The part of the brain known as “little brain”

  • The dura (dura.stl, final-dura.stl): The outer layer towards the skull.

  • The pial surfaces (lhpial.stl, rhpial.stl,final-lhpial.stl, final-rhpial.stl): The pial (outer) surface of the brain, separating grey-matter.

  • The ventricles (ventricles.stl, final-ventricles.stl): A network of fluid cavities within the brain parenchyma.

  • The white matter (lhwhite.stl, rhwhite.stl): The part of the brain parenchyma that is categorized as white matter. It lies within the grey matter.

The file final-fm.stlis a disk used to cut the brainstem. The file final-white.stl contains the surface describing the white matter, the cerebellum and the brain-stem as one surface file.

The data can be extracted with:

wget -nc https://zenodo.org/records/14536218/files/mri2femii-chp2-dataset.tar.gz
tar xvzf mri2femii-chp2-dataset.tar.gz

An example of a config file for wildmeshing is:

{
  "operation": "union",
  "left": "final-dura.stl",
  "right": {
    "operation": "union",
    "left": {
      "operation": "union",
      "left": "final-lhpial.stl",
      "right": "final-rhpial.stl"
    },
    "right": {
      "operation": "union",
      "left": "final-white.stl",
      "right": "final-ventricles.stl"
    }
  }
}

MRI to FEM Vol 2 - Chapter 3#

The following dataset: DOI: 10.5281/zenodo.10808333 contains surfaces (stl-files) for a subset of regions in the brain:

  • The dura (dura.final.stl): The outer layer towards the skull

  • Cisterna Magna (cisterna-magna.stl): A fluid cavity between the cerebellum and the brain-stem

  • The choroid plexus (lhchoroid.plexus.final.stl and rhchoroid.plexus.final.stl): A fluid cavity within the ventricles, where cells produce cerebrospinal fluid

  • The ventricles (ventricles.final.stl): A network of fluid cavities within the brain parenchyma.

  • The pial surface (lhpial.final.stl, rhpial.final.stl): The pial (outer) surface of the brain, separating grey-matter from cerebrospinal fluid in the sub-arachnoid spaces (the volume between the pial surface and the dura matter).

  • The white matter (white.final.stl): The part of the brain parenchyma that is categorized as white matter. It lies within the grey matter.

The data can be extracted with:

wget -nc https://zenodo.org/records/10808334/files/mhornkjol/mri2fem-ii-chapter-3-code-v1.0.0.zip
unzip mri2fem-ii-chapter-3-code-v1.0.0.zip

An example of a config file for wildmeshing is:

{
  "operation": "union",
  "left": "dura.final.stl",
  "right": {
    "operation": "union",
    "left": "white.final.stl",
    "right": {
      "operation": "union",
      "left": "ventricles.final.stl",
      "right": {
        "operation": "union",
        "left": "rhchoroid.plexus.final.stl",
        "right": "lhchoroid.plexus.final.stl"
      }
    }
  }
}

Data from the paper In-silico molecular enrichment and clearance of the human intracranial space#

Data DOI: 10.5281/zenodo.14749162 from the paper by Marius Causemann et al. 2025 DOI: 10.1101/2025.01.30.635680 .

There following regions of the brain has been marked:

  • The dura (skull.ply): The outer layer towards the skull

  • The brain parenchyma (parenchyma_incl_ventr.ply): The part of the brain containing white and grey matter, both the Cerebrum and the Cerebellum.

  • The lateral ventricles (LV.ply): The part of the ventricular network where cerebrospinal fluid is produced.

  • The third and fourth ventricles (V34.ply): The part of the ventricular network that connects the lateral ventricles to the subarachnoid space.

Other surfaces not used directly in the mesh generation is parenchyma.ply, which includes an interface towards the ventricles. The surface cerebrum.ply is also not used, as it does not contain the cerebellum (little brain).

The surfaces can be extracted with:

wget -nc https://zenodo.org/records/14749163/files/surfaces.zip
unzip surfaces.zip

An example configuration for wildmeshing would be

{
  "operation": "union",
  "left": "skull.ply",
  "right": {
    "operation": "union",
    "left": "parenchyma_incl_ventr.ply",
    "right": {
      "operation": "union",
      "left": "LV.ply",
      "right": "V34.ply"
    }
  }
}
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