The cardiovascular system — a still from ANATOMICA's surgical simulation film.
An open medical surgical and anatomy system: a 3D anatomical atlas, a physiology simulation engine, an imaging suite, a surgical procedure simulator, and a clinical case and hypothesis workbench — all reading one verified model of the human body.
ANATOMICA is an educational and simulation system. It is not a clinical device, it carries no real patient data, and it is not for diagnosis or treatment of real persons.
- One body, one truth. Every module derives from the same Body Model; modules never keep private copies of anatomy or physiology.
- Data before rendering. A structure exists because its record is verified — nomenclature, counts, and relations traceable to named sources. Uncertain items carry a visible verify flag instead of a silently chosen answer.
- Derived, never invented. Geometry comes from segmented human anatomy adopted under compatible licenses, tracked per file in a provenance ledger.
- Computed, not scripted. Vitals and labs are outputs of a running physiological state; complications in the operating theatre are computed by the engine.
- Open forever. The whole system is licensed AGPL-3.0.
| Path | Contents |
|---|---|
design/ |
Buildable design documents for every area of the system (10 documents) |
data/ |
Body Model data modules, one folder per body system; data/sources/ holds adopted source datasets with their provenance |
tools/ |
Verification tooling: provenance ledger builder, censuses, checkers, assemblers and record builders |
native/ |
The native application (flagship) — Rust + wgpu |
web/ |
The browser application (universal-access companion) — WebGL2 viewer |
physiology/ |
The deterministic physiology engine — Rust |
film-engine/ |
The surgical simulation film engine — Blender pipeline, geometry inputs, and the patient scene archive (see film-engine/README.md) |
research/ |
The research library the design rests on (3 rounds, 31 fronts) |
assets/ |
README and project imagery |
MILESTONE-*.md |
The milestone reports, one per landed milestone (listed below) |
Milestones 1–15 are complete and in this repository (plus the Milestone 7
pick-layer fix), recorded in MILESTONE-1.md through MILESTONE-15.md.
Body Model v1 is complete: 1,552 inventory records across all eleven body systems, with geometry for 1,545 of 1,552 — the only exceptions are the six auditory ossicles and the coccyx, which no adoptable dataset carries as separate structures. 361 sourced clinical records (Tier A 209 / Tier B 112 / Tier C 40).
Both shells render the real assembled geometry — the native Rust + wgpu flagship and the WebGL2 browser companion — and the deterministic physiology engine's resting cardiovascular outputs validate against published normal ranges.
Known dataset gaps are recorded on the records themselves, not smoothed over: nerves beyond cranial nerves II–V1, lymphatic vessels and nodes, thyroid and parathyroid geometry, kidney and urinary interior, the internal female reproductive tract, and skin layers / nails / glands have no concepts in BodyParts3D 4.0 + TotalSegmentator v1 and await a further source (a full FMA / Terminologia Anatomica pass is the named route).
| Milestone | Report | What landed |
|---|---|---|
| 1 | MILESTONE-1.md |
Design complete (10 design documents) + P2 geometry foundation and repo scaffold |
| 2 | MILESTONE-2.md |
Skeletal system: FMA-ID mapping and geometry conversion for all 206 bones |
| 3 | MILESTONE-3.md |
TotalSegmentator intake (10 subjects, full 1,204-subject index) + registered skeleton assembly: 199 records, 511,968 faces |
| 4 | MILESTONE-4.md |
Muscular system: 359 inventory / geometry records, 127 sourced clinical records |
| 5 | MILESTONE-5.md |
Cardiovascular system: 646 records, 69 clinical records + 8 variant records |
| 6 | MILESTONE-6.md |
Muscular assembly + Web Shell v2 rendering the real assembled skeleton and muscle layers |
| 7 | MILESTONE-7.md |
Native shell: Rust + wgpu application rendering the real Body Model packs |
| 7 (fix) | MILESTONE-7-FIX.md |
Web viewer pick-layer bug fix, with a regression check that executes the shipped decoder |
| 8 | MILESTONE-8.md |
Physiology engine v0: deterministic cardiovascular compartment model, 46 cited parameters, resting outputs inside all cited normal ranges |
| 9 | MILESTONE-9.md |
Nervous system: 133 records, 52 sourced clinical records; the nerve-concept gap quantified exactly |
| 10 | MILESTONE-10.md |
Respiratory system: 83 records, 37 clinical records (all Tier A) |
| 11 | MILESTONE-11.md |
Digestive system: 93 records, 31 clinical records, all eight Couinaud liver segments |
| 12 | MILESTONE-12.md |
Urinary system: 6 records, 6 clinical records (all Tier A) — the system's entire interior is absent from the source datasets |
| 13 | MILESTONE-13.md |
Lymphatic system (4 records, 4 clinical) + endocrine system (3 records, 6 clinical) |
| 14 | MILESTONE-14.md |
Reproductive system: 13 records, 16 clinical records — 14 male concepts vs 1 female concept in the source release |
| 15 | MILESTONE-15.md |
Integumentary system: 6 records, 13 clinical records — closes the eleven-system census: Body Model v1 |
All 246 files in this repository, by directory. Adopted source-dataset binaries (meshes, archives, GLBs) and build output are not tracked in git — see .gitignore; their provenance is recorded in data/sources/*/ledger.json and SOURCE.md.
.gitignoreLICENSEMILESTONE-1.mdMILESTONE-10.mdMILESTONE-11.mdMILESTONE-12.mdMILESTONE-13.mdMILESTONE-14.mdMILESTONE-15.mdMILESTONE-2.mdMILESTONE-3.mdMILESTONE-4.mdMILESTONE-5.mdMILESTONE-6.mdMILESTONE-7-FIX.mdMILESTONE-7.mdMILESTONE-8.mdMILESTONE-9.mdREADME.md
assets/anatomica-hero.jpg
data/cardiovascular/cardiovascular.jsondata/cardiovascular/cv-geometry.jsondata/cardiovascular/cv-inventory.jsondata/digestive/digestive-geometry.jsondata/digestive/digestive-inventory.jsondata/digestive/digestive.jsondata/endocrine/endocrine-geometry.jsondata/endocrine/endocrine-inventory.jsondata/endocrine/endocrine.jsondata/integumentary/integumentary-geometry.jsondata/integumentary/integumentary-inventory.jsondata/integumentary/integumentary.jsondata/lymphatic/lymphatic-geometry.jsondata/lymphatic/lymphatic-inventory.jsondata/lymphatic/lymphatic.jsondata/muscular/muscle-geometry.jsondata/muscular/muscle-inventory.jsondata/muscular/muscles-assembled.jsondata/muscular/muscles.jsondata/nervous/nervous-geometry.jsondata/nervous/nervous-inventory.jsondata/nervous/nervous.jsondata/reproductive/reproductive-geometry.jsondata/reproductive/reproductive-inventory.jsondata/reproductive/reproductive.jsondata/respiratory/respiratory-geometry.jsondata/respiratory/respiratory-inventory.jsondata/respiratory/respiratory.jsondata/skeletal/fma-mapping.jsondata/skeletal/gap-analysis.mddata/skeletal/skeleton-assembled.jsondata/skeletal/skeleton-geometry.jsondata/sources/bodyparts3d-4.0/SOURCE.mddata/sources/bodyparts3d-4.0/isa_element_parts.txtdata/sources/bodyparts3d-4.0/isa_inclusion_relation_list.txtdata/sources/bodyparts3d-4.0/isa_parts_list_e.txtdata/sources/bodyparts3d-4.0/ledger-summary.mddata/sources/bodyparts3d-4.0/ledger.jsondata/sources/bodyparts3d-4.0/partof_element_parts.txtdata/sources/bodyparts3d-4.0/partof_inclusion_relation_list.txtdata/sources/bodyparts3d-4.0/partof_parts_list_e.txtdata/sources/totalsegmentator-1.0/SOURCE.mddata/sources/totalsegmentator-1.0/index-census.jsondata/sources/totalsegmentator-1.0/labels.jsondata/sources/totalsegmentator-1.0/labels.mddata/sources/totalsegmentator-1.0/ledger-summary.mddata/sources/totalsegmentator-1.0/ledger.jsondata/sources/z-anatomy-glb/License.txtdata/sources/z-anatomy-glb/SOURCE.mddata/sources/z-anatomy-glb/ledger-summary.mddata/sources/z-anatomy-glb/ledger.jsondata/urinary/urinary-geometry.jsondata/urinary/urinary-inventory.jsondata/urinary/urinary.json
design/01-architecture.mddesign/02-body-model-schema.mddesign/03-geometry-pipeline.mddesign/04-physiology-engine.mddesign/05-theatre.mddesign/06-imaging.mddesign/07-cases.mddesign/08-native-shell.mddesign/09-web-shell.mddesign/10-governance.md
film-engine/README.mdfilm-engine/compose_still.pyfilm-engine/diag.pyfilm-engine/dump_groups.pyfilm-engine/fix_clip.pyfilm-engine/fix_islands.pyfilm-engine/fix_lung.pyfilm-engine/fix_lung2.pyfilm-engine/fix_mats.pyfilm-engine/fix_skin.pyfilm-engine/geometry/artery.npzfilm-engine/geometry/artery_keep.npzfilm-engine/geometry/bone.npzfilm-engine/geometry/bone_keep.npzfilm-engine/geometry/brain.npzfilm-engine/geometry/brain_keep.npzfilm-engine/geometry/cartilage.npzfilm-engine/geometry/cartilage_keep.npzfilm-engine/geometry/heart.npzfilm-engine/geometry/heart_keep.npzfilm-engine/geometry/liver.npzfilm-engine/geometry/liver_keep.npzfilm-engine/geometry/lung.npzfilm-engine/geometry/lung_keep.npzfilm-engine/geometry/muscle.npzfilm-engine/geometry/muscle_keep.npzfilm-engine/geometry/nerve.npzfilm-engine/geometry/nerve_keep.npzfilm-engine/geometry/organ.npzfilm-engine/geometry/organ_keep.npzfilm-engine/geometry/skin.npzfilm-engine/geometry/skin_keep.npzfilm-engine/geometry/vein.npzfilm-engine/geometry/vein_keep.npzfilm-engine/islands.pyfilm-engine/islands2.pyfilm-engine/islands3.pyfilm-engine/make_skin.pyfilm-engine/make_skin2.pyfilm-engine/patient.blend.xz.part-aafilm-engine/patient.blend.xz.part-abfilm-engine/patient.blend.xz.part-acfilm-engine/patient.blend.xz.part-adfilm-engine/patient.pyfilm-engine/plates.pyfilm-engine/probe.pyfilm-engine/probe2.pyfilm-engine/probe3.pyfilm-engine/restore_patient.shfilm-engine/restore_render_env.shfilm-engine/scene.py
native/Cargo.locknative/Cargo.tomlnative/src/camera.rsnative/src/lib.rsnative/src/main.rsnative/src/model.rsnative/src/pack.rsnative/src/render.rsnative/tests/pack_data.rs
physiology/Cargo.lockphysiology/Cargo.tomlphysiology/parameters.jsonphysiology/src/cases.rsphysiology/src/engine.rsphysiology/src/lib.rsphysiology/src/main.rsphysiology/src/params.rsphysiology/tests/engine_tests.rs
research/INDEX.mdresearch/round-01-state-of-the-art/SOURCE-AGENTS.mdresearch/round-01-state-of-the-art/fronts/00-overview.mdresearch/round-01-state-of-the-art/fronts/01-open-anatomical-data-and-ontologies/FRONT.mdresearch/round-01-state-of-the-art/fronts/02-surgical-simulation-state-of-the-art/FRONT.mdresearch/round-01-state-of-the-art/fronts/03-physiology-engines/FRONT.mdresearch/round-01-state-of-the-art/fronts/04-medical-imaging-tech/FRONT.mdresearch/round-01-state-of-the-art/fronts/05-clinical-reasoning-diagnosis-training/FRONT.mdresearch/round-01-state-of-the-art/fronts/06-web-3d-rendering-state-of-the-art-browser-tier/FRONT.mdresearch/round-01-state-of-the-art/fronts/07-native-real-time-3d-and-simulation-technology-supplement-1/FRONT.mdresearch/round-01-state-of-the-art/fronts/08-vr-ar-and-haptics-for-surgical-training-supplement-1/FRONT.mdresearch/round-01-state-of-the-art/fronts/09-native-vs-browser-ceiling-what-the-oss-community-actually-bu/FRONT.mdresearch/round-01-state-of-the-art/fronts/10-the-frontier-whole-body-digital-human-digital-twin-programme/FRONT.mdresearch/round-01-state-of-the-art/fronts/11-accuracy-and-validation-standards-supplement-3/FRONT.mdresearch/round-01-state-of-the-art/notes/front11-validation.mdresearch/round-01-state-of-the-art/notes/fronts7-10.mdresearch/round-01-state-of-the-art/report.mdresearch/round-02-medical-fields/SOURCE-AGENTS.mdresearch/round-02-medical-fields/fronts/00-overview.mdresearch/round-02-medical-fields/fronts/01-anatomy-science/FRONT.mdresearch/round-02-medical-fields/fronts/02-quantitative-physiology-and-pathophysiology/FRONT.mdresearch/round-02-medical-fields/fronts/03-surgery-and-perioperative-standards/FRONT.mdresearch/round-02-medical-fields/fronts/04-pharmacology-quantitative/FRONT.mdresearch/round-02-medical-fields/fronts/05-imaging-science/FRONT.mdresearch/round-02-medical-fields/fronts/06-diagnostic-reasoning-evidence/FRONT.mdresearch/round-02-medical-fields/fronts/07-disease-and-epidemiology-data/FRONT.mdresearch/round-02-medical-fields/fronts/08-medical-education-science/FRONT.mdresearch/round-02-medical-fields/fronts/09-special-populations-and-variation/FRONT.mdresearch/round-02-medical-fields/fronts/10-frontier-clinical-technology/FRONT.mdresearch/round-02-medical-fields/notes/sources-index.mdresearch/round-02-medical-fields/report.mdresearch/round-03-depth-specialization/SOURCE-AGENTS.mdresearch/round-03-depth-specialization/fronts/00-overview.mdresearch/round-03-depth-specialization/fronts/01-open-clinical-data-and-signals/FRONT.mdresearch/round-03-depth-specialization/fronts/02-anesthesia-and-critical-care-deep/FRONT.mdresearch/round-03-depth-specialization/fronts/03-emergency-and-resuscitation/FRONT.mdresearch/round-03-depth-specialization/fronts/04-surgical-subspecialty-evidence/FRONT.mdresearch/round-03-depth-specialization/fronts/05-tissue-biomechanics-and-surgical-physics/FRONT.mdresearch/round-03-depth-specialization/fronts/06-laboratory-medicine-and-pathophysiology-depth/FRONT.mdresearch/round-03-depth-specialization/fronts/07-infectious-disease-and-antimicrobials/FRONT.mdresearch/round-03-depth-specialization/fronts/08-human-factors-safety-and-debriefing-science/FRONT.mdresearch/round-03-depth-specialization/fronts/09-global-and-resource-tiered-medicine/FRONT.mdresearch/round-03-depth-specialization/fronts/10-regulatory-and-ethics-boundaries-for-educational-medical-sof/FRONT.mdresearch/round-03-depth-specialization/notes/coverage-log.mdresearch/round-03-depth-specialization/report.md
tools/assemble_muscles.pytools/assemble_skeleton.pytools/assembly_check.pytools/build_cv_records.pytools/build_dig_records.pytools/build_endo_records.pytools/build_integ_records.pytools/build_lymph_records.pytools/build_muscle_records.pytools/build_nerve_records.pytools/build_repro_records.pytools/build_resp_records.pytools/build_uri_records.pytools/census.jsontools/census.mdtools/census.pytools/cv_check.pytools/cv_map.pytools/dig_check.pytools/dig_map.pytools/endo_check.pytools/endo_map.pytools/fma_map.pytools/integ_check.pytools/integ_map.pytools/lymph_check.pytools/lymph_map.pytools/muscle_assembly_check.pytools/muscle_check.pytools/muscle_map.pytools/nerve_check.pytools/nerve_map.pytools/pack_web_geometry.pytools/provenance.pytools/register_sketch.mdtools/repro_check.pytools/repro_map.pytools/resp_check.pytools/resp_map.pytools/skeletal_check.pytools/ts_intake.pytools/uri_check.pytools/uri_map.pytools/verify_web.js
web/data/manifest.jsonweb/data/records.jsonweb/index.htmlweb/viewer.js
AGPL-3.0. See LICENSE. Adopted datasets keep their own licenses, recorded
per file in the provenance ledger under data/sources/.