fetal-umbilical-circulation

Fetal Anatomy Atlas

An MR-digitized fetal anatomy atlas (a single fetus, ~23 segmented anatomical structures) as a self-contained three.js viewer, with the geometry kept in a form that’s directly reusable for physiological simulation work rather than only for display.

Part of the companion repository for the manuscript “Anatomy-Informed Modeling of the Fetal Umbilical Circulation Across Gestation” (Tang, Peng and Ho, in preparation). The umbilical vessel geometry and flow viewers are in ../umbilical-geometry; the 1-D solver and calibration code are in ../solver. This folder covers only the whole-body anatomical atlas the umbilical geometry was extracted from.

Live viewer: https://hwe001.github.io/fetal-umbilical-circulation/atlas/viewers/fetus_atlas_viewer.html

Why rebuild it

The original page uses the legacy three.js JSON model format (formatVersion: 3, “Exported from LibZinc”) - a bitmask-encoded face format that modern three.js can no longer load directly (its JSONLoader was removed years ago). Rebuilding it required writing a real parser for that format (see scripts/parse_fetus_atlas.py), which also made it straightforward to export each anatomical part as a standard STL alongside the viewer geometry - useful for anything downstream (voxelization, CCO vessel growth, Poiseuille flow solves), not just rendering.

Structure

scripts/
  parse_fetus_atlas.py     # legacy three.js JSON -> per-part STL + combined viewer binary
  assemble_fetus_viewer.py # inlines three.js + geometry + manifest into one HTML file
data_in/
  source_json/             # the 26 original BasicMesh_*.json + metadata.json (unmodified)
data_out/
  stl/                     # one STL per original mesh part (e.g. BasicMesh_12.stl = portal vein)
  fetus_manifest.json      # part number -> organ group name -> vertex/triangle counts
  fetus_atlas_geometry.bin # combined position+normal binary for all 23 groups (no color baked in)
viewers/
  fetus_atlas_viewer.html  # the actual viewer - fully self-contained, open directly in a browser

The 23 anatomical structures

Grouped by system (see ORGAN_STYLE in assemble_fetus_viewer.py for the exact palette):

• Cardiovascular: aorta, heart, portal (vein), svc (superior vena cava)
• Umbilical: cord, placenta, uv (umbilical vein)
• Abdominal: bladder, kidney, liver, sex_organ_m
• Thoracic: lung
• Neuro: brain_left, brain_right, cerebellum, eye
• Maternal: womb
• Body shell: arm_left, arm_right, head, leg_left, leg_right, torso

Two of the original 26 mesh parts share a GroupName with another part at a much lower resolution (liver and torso each have two parts, both kept and merged; head has two parts but the higher-res one, BasicMesh_23.json at 45,216 triangles vs. BasicMesh_9.json at 11,448, was excluded from the merged viewer binary only - keeping both pushed the self-contained HTML too large. BasicMesh_23.stl is still written to data_out/stl/ for anyone who wants the higher-res head separately).

Design choices, since this is meant to be reused later

• Geometry has no color or scale baked in. fetus_atlas_geometry.bin is pure position + source vertex normal; organ color is assigned per-GroupName in assemble_fetus_viewer.py, so re-theming the viewer never requires rebuilding the binary.
• Real coordinates, untouched. No re-centering or rescaling happens before STL export (only the viewer recenters, for camera framing) - so data_out/stl/BasicMesh_12.stl (portal vein) and BasicMesh_6.stl/BasicMesh_10.stl (liver) sit in the same coordinate frame as every other part, ready to feed into a CCO growth or voxelization pipeline the same way the real donor portal-vein cohort was used elsewhere.
• Per-part STL, not just per-organ. Where an organ has more than one source part (liver, torso), each part keeps its own STL rather than being pre-merged, in case a future use only wants one of them.

Reproducing

python scripts/parse_fetus_atlas.py \
    --source-dir data_in/source_json \
    --stl-out-dir data_out/stl \
    --manifest-out data_out/fetus_manifest.json \
    --geometry-out data_out/fetus_atlas_geometry.bin

python scripts/assemble_fetus_viewer.py \
    --three-js path/to/three.min.js \
    --geometry data_out/fetus_atlas_geometry.bin \
    --manifest data_out/fetus_manifest.json \
    --out viewers/fetus_atlas_viewer.html

three.min.js (r160) isn’t vendored here - grab any recent three.js UMD build.

Provenance

Source data: a single fetus, MR-imaged in utero and manually segmented into 23 anatomical structures in 2018-2019. No patient identifiers are present in any file here.

Contact

Questions about this atlas: Dr Harvey Ho. (The live viewer builds the address at runtime.)

License

MIT.

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