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.
Get the code first: clone this repository or download it as an archive. There are no accounts, no server, and no telemetry — every module runs locally. ANATOMICA is for education and simulation only; never use it on a real patient.
Serve the web/ folder with any static file server and open it in a
browser (the viewer loads its data packs over HTTP, so opening the file
directly will not work):
cd web
python3 -m http.server 8000
# open http://localhost:8000- Move: drag to orbit, scroll to zoom, Shift-drag (or right/middle drag) to pan, pinch on touch screens. Reset view restores the starting camera.
- Find a structure: type in the Search box (name, Terminologia Anatomica name, or record id), filter by region, or click a row in the record list. Clicking a mesh in the 3D view selects it too — the selected structure highlights, the rest dim (toggleable), and its full record opens in the right-hand panel.
- Layers: toggle the eleven body systems on and off to build the view you need, from full body down to a single system. The labels and wireframe toggles sit in the header.
- Imaging: switch from Atlas to Imaging in the header. Step through slices with the slider or the slice buttons, adjust window/level with the presets or the Width/Level sliders, click a voxel to identify what it is, click a legend row to isolate a label, and use MPR planes for crosshair-linked axial, coronal, and sagittal views of the same volume. Imaging here is synthetic and derived from the Body Model, and is labelled as such.
Needs a Rust toolchain and a machine with a display and GPU:
cd native
cargo run --release -- view # windowed viewer
cargo run --release -- verify # headless check: loads the packs, runs
# the assertions, renders proof frames
# to native/frames/In the viewer: mouse orbit, wheel zoom, right-drag pan, left click picks a structure (its record prints to the console and the mesh highlights). Keys: S skeletal, M muscular, 1–0 toggle layers, I integumentary, A all layers, G glass shell (skin translucent), W wireframe, R reset view.
cd physiology
cargo run --release -- validate # resting outputs checked against
# every published normal range
cargo run --release -- run course # a −1,500 mL haemorrhage, untreated
# vs crystalloid / whole blood /
# component transfusion arms
cargo run --release -- run hormones # water, sodium, and ADH axes
cargo run --release -- run respiratory # respiratory and acid–base casesEvery run is deterministic: the same command always produces the same trace, and each run prints a trace hash and a PASS/FAIL line per output against its cited expectation.
cd theatre
cargo run --release -- validate # check every procedure, parameter,
# and instrument record
cargo run --release -- run-all # run all shipped attempt traces and
# write their scored debriefs
cargo run --release -- run <trace.json> [--out <debrief.json>]A procedure is a step graph over the atlas anatomy; an attempt is a
trace JSON (see theatre/traces/ for examples to copy). The runner
scores the attempt and emits a debrief. Safety gates are enforced as
the specialty defines them: in laparoscopic cholecystectomy, dividing
a structure before the Critical View of Safety is demonstrated fails
the attempt, because the model resolves the divided structure as the
common bile duct — the real injury mechanism. Scores are formative
only: the expert-review gate recorded in the procedure files is not
yet met, and the files say so.
python3 tools/case_run.py # score every shipped case and print its
# board, stage by stageEach case in cases/ presents in stages. To work one yourself, write
an attempt JSON alongside the examples in cases/attempts/: commit a
differential with explicit probabilities, update it as each stage's
findings arrive, and order tests knowing each carries cost and
information value. The runner recomputes the workbench board from the
cited likelihood ratios, evaluates the guideline criteria mechanically,
scores your board (per-stage Brier scores, rank of the true diagnosis —
there is deliberately no single composite score), and writes a
PEARLS-structured debrief to cases/debriefs/.
Nothing here asks to be taken on trust. The tools in tools/ recompute
the claims in this README from the data itself — tools/census.py
for the Body Model census, and a *_check.py beside every data module
and subsystem. If a checker and this README ever disagree, the checker
is right.
| 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 — every checker in the family exits 0 on this tree |
native/ |
The native application (flagship) — Rust + wgpu |
web/ |
The browser application (universal-access companion) — WebGL2 atlas/imaging viewer, the WebAssembly engine package (pkg/), and the case workbench; the full system runs in the browser |
wasm/ |
The physiology and Theatre engines as a wasm-bindgen crate, with its native-vs-wasm verification harness |
physiology/ |
The deterministic physiology engine — Rust |
theatre/ |
The surgical procedure simulator — Rust engine, procedure models, traces, debriefs |
cases/ |
The case and hypothesis workbench — cases, learner attempts, debriefs, FHIR export |
cases-harness/ |
Golden-debrief harness for the web case-workbench port |
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 |
milestones/ |
The milestone reports, one per milestone (listed below) |
Milestones 1–65 are complete and recorded in milestones/MILESTONE-1.md
through milestones/MILESTONE-65.md (plus the Milestone 7 pick-layer fix). The Body Model
stands at 2,236 inventory records across all eleven body systems, with
geometry for 1,566 of them. At the close of the concept-intake arc, 691
records carried no geometry (684 of them FMA 5.1.0 concept records, the
other 7 the six auditory ossicles and the coccyx, which no adoptable
dataset carries as separate structures); the Milestone 63 geometry
intake gave 21 of those records geometry. 670 concept records carry no
geometry. Clinical
coverage is 401 sourced clinical records (Tier A 239 / Tier B 121 / Tier C 41).
Concepts are complete; geometry was ruled on, and the ruled subset has been intaken. The concept gaps that the Body Model v1 status once listed — nerves beyond cranial nerves II–V1, lymphatic vessels and nodes, thyroid and parathyroid geometry, the kidney and urinary interior, the internal female reproductive tract, skin layers / nails / glands — were closed as concepts by the FMA 5.1.0 intake arc (Milestones 33–38: 684 records intaken, all concept-only). Geometry for those records was governed by the Z-Anatomy geometry audit (Milestone 34), which cleared provenance for 555 of 587 anatomical objects and validated a brain-assembly transform (held-out 0.27 mm), while global registration was refuted. The geometry ruling is made: Tier B geometry was intaken at Milestone 63 under the validated brain-assembly transform (236 objects clearing both bars; 19 FMA records gained geometry), and the deferent-duct meshes are claimed. Tier C remains gated on a validating derivation — its 285 objects clear provenance only, and no derivation that places them has yet passed the audit's held-out gates. Tier D is excluded permanently: its provenance cannot be separated from CC BY-NC-SA material. Six named structures have no FMA class at all (bulbourethral gland, paraurethral glands, cervical canal, isthmus of uterus, keratinocyte, crus of penis) and are recorded as gaps, not invented. The deferent-duct meshes exist in BodyParts3D 4.0 (FJ3135/FJ3140) and were claimed at Milestone 63 for the left and right deferent-duct records.
Expert review is the standing open gate. For every Theatre procedure and
every case, the expert-review gate is UNMET: no named independent reviewers
exist, so all content is dual-sourced-draft, all scores are
formative-only, and no composite score is published anywhere in the system.
Reviewers are never invented to fill the block.
Both shells render the real assembled geometry — the native Rust + wgpu flagship
and the WebGL2 browser companion — and the deterministic physiology engine's
resting outputs validate against published normal ranges (33 resting ranges
gated, all passing, resting trace hash 0x6369b10e9a71c872).
One inventory across eleven body systems, assembled from BodyParts3D 4.0 geometry (CC BY-SA 2.1 Japan governs the mesh headers; CC BY 4.0 per the DBCLS release page) and TotalSegmentator v1.0 labels (CC BY 4.0), with concepts intaken from FMA 5.1.0 (CC BY 4.0, hash-pinned in the provenance ledger). Every record carries its provenance; geometry is packed into one merged buffer set per layer (1 draw call per layer) — 8,285,791 triangles (311,136,996 bytes canonical, 125,760,132 bytes as gzip delivery).
| System | Inventory | With geometry | Clinical |
|---|---|---|---|
| skeletal | 206 | 199 | 0 |
| muscular | 359 | 359 | 127 |
| cardiovascular | 646 | 646 | 69 |
| nervous | 419 | 152 | 92 |
| respiratory | 83 | 83 | 37 |
| digestive | 93 | 93 | 31 |
| urinary | 73 | 6 | 6 |
| lymphatic | 135 | 4 | 4 |
| endocrine | 17 | 3 | 6 |
| reproductive | 146 | 15 | 16 |
| integumentary | 59 | 6 | 13 |
| Total | 2,236 | 1,566 | 401 |
Terminologia Anatomica 2 (TA2) Latin names are resolved for 854 of the 1,045 records the TA2 pass covers (361 clinical + 684 FMA concept records); 117 ambiguous and 74 not found, each carrying a dated reason. The nephron-segment records are among the not-found: TA2 carries no nephron-segment terms, and naming them awaits a Terminologia Histologica source decision.
A Rust compartment engine whose resting state validates against published normal ranges (MAP 73.1 mmHg, cardiac output 4.21 L/min, PaCO₂ 41.1 mmHg, PaO₂ 91.2 mmHg, pH 7.39, oxygen delivery 828 mL/min, ionized calcium 1.20 mmol/L, PTH 19.8 pg/mL). It carries 161 parameters from 80 sources (90 cited, 44 calibrated within cited ranges, 27 verify-flagged), 33 validation ranges, and 26 perturbation cases — circulation with a four-effector baroreflex and first-class Guyton venous return, renal excretion and the interstitial reservoir, the oncotic state with blood products as scenario inputs, the ADH and aldosterone axes, and a respiratory module (ventilation, gas exchange, chemoreflex, the Bohr shift, and chronic renal acid–base compensation on a days timescale) coupled one-way, and a calcium–PTH axis (PTH secretion on the Brown sigmoid; renal, bone and gut limbs) folded into the respiratory-side state — so the case-pinned circulation baseline is bit-identical by construction. Its validator reports ALL HARD GATES PASS.
Two synthetic DICOM CT series derived from TotalSegmentator subjects, each with a Body Model crosswalk: subject s0778 (431 DICOM instances, 262 × 262 × 431 voxels at 1.5 mm isotropic) and subject s1090 (439 DICOM instances, 257 × 257 × 439 voxels at 1.5 mm isotropic) — 870 instances in all. The series are synthetic throughout (watermarked "SYNTHETIC" in metadata and burned into every slice's pixels; no real patient data). 93 of the 104 labels mapped in both subjects; s0778's present labels reach 90 Body Model records; s1090's reach 88 Body Model records. The viewer offers tri-plane MPR (exact re-indexing reslice, no interpolation) and subject switching. A DICOM conformance defect in the series descriptions was found and repaired at Milestones 45–46 (an over-long SeriesDescription string in all 870 instances; the writer now refuses to emit a non-conforming value), and an independent toolkit pass (pydicom/nibabel) corroborates the derivation: pixel arrays exact against the sources, the watermark proven to be the only source-to-series alteration.
7 authored procedures, 63 phases / 97 steps / 323 microsteps, with 37 scripted traces and 37 generated debriefs: laparoscopic cholecystectomy (Critical View of Safety), laparoscopic appendicectomy (base identification), open carpal tunnel release (nerve identification), ulnar nerve decompression (nerve protection, transposition), laparoscopic inguinal hernia repair (triangle-of-doom / triangle-of-pain gate, two gated verbs: divide and fixate), total thyroidectomy (per-side recurrent laryngeal nerve identification and parathyroid preservation; nerve monitoring is an adjunct and cannot satisfy the gate), and upper gastrointestinal endoscopy (identify-classify-before-therapy gate: the bleeding source identified, its Forrest classification demonstrated and declared, and the airway–sedation account made, before any therapy; therapy first fails the attempt with a computed perforation; the Dieulafoy lesion is the authored variant). The Theatre carries 54 sources (T1–T54; T42–T48 added at Milestone 56 and T49–T54 at Milestone 62, both to the T1–T41), 18 parameters, 13 of them verify-flagged, and 39 instruments. Safety gates are scored exactly as the specialties define them — dividing an unidentified critical structure fails the attempt — and complications are computed by the engine against the physiology state. All seven procedures run on one generalized engine, and the checker family replays every trace (theatre_check: 872 checks, 0 failures). Expert review is UNMET for every procedure (see Status).
9 cases in the library, staged history → examination → tests → board, with a source register (70 sources, C1–C70), guideline criteria evaluated mechanically from the staged evidence, likelihood ratios only where sourced, and exactly one scored anchoring event per model-learner attempt. Case #2 is case #1's patient on postoperative day 4 after the Theatre's failed cholecystectomy, hash-linked to the trace itself; cases #4 and #5 localize lesions by branch anatomy; case #6 is the first cardiopulmonary case (pulmonary embolism, Wells/PERC/CURB-65/ESC blocks, A–a gradient re-derived by the checker); case #7 walks the pathway case #6 recorded but did not take — Wells 0.0 complete, PERC's gestalt precondition met, a D-dimer below the age-adjusted cutoff (560 against 620 µg/L, ADJUST-PE) — so PE is excluded without imaging, over-testing is the scored error, and the D-dimer LR− (0.0732) is registered for the negative direction. Case #8 is the trace-30 patient on postoperative day 1 — symptomatic hypocalcemia after the passed thyroidectomy whose parathyroid criterion went unaccounted — hash-linked to the Theatre debrief, with Trousseau's sign registered at the conservative end (LR+ 23.5) and the anchor an inherited anxiety/hyperventilation attribution, a real mechanism that cannot lower a total calcium. Case #9 is the bleeding case — a 71-year-old whose own "gastritis" diagnosis, carried untested across two winters, concealed a bleeding duodenal ulcer: the library's first score-and-classification pair (Glasgow-Blatchford 6 on admission values, never re-priced by the later count; Forrest IIa on the visible vessel), four likelihood ratios computed as reciprocals of one consulted review's figures, and the first physiology link to a perturbation arm — the hemorrhage runs, hash-pinned — rather than the resting baseline alone. Its endoscopy is hash-linked to the Theatre in the library's third form (Milestone 64): the case was written before the procedure existed, and trace 31 — authored on this case's own lesion — returns PASS on the course the case records. Cases hand off to Theatre procedures where one exists, and state the absence where none does. The FHIR-shaped export is checked against the case files by the same checker (case_check: 14,964 checks passed, 0 failed). Expert review is UNMET for every case (see Status).
Every number in this README that the tree can compute is asserted by
tools/readme_check.py, which recomputes the census, the TA2 ledger
totals, the pack totals, the physiology counts, the theatre and case
counts, the imaging counts, the milestone index, and the file index from
the data files themselves, and re-runs the sibling checkers to compare
their printed totals with the table below. Run it as
python3 tools/readme_check.py — exit 0 means the README agrees with the
tree.
| Check | Result |
|---|---|
tools/assembly_check_all.py |
ALL GATED CHECKS PASS |
tools/theatre_check.py |
872 checks, 0 failures |
tools/case_check.py |
14,964 checks passed, 0 failed |
tools/imaging_toolkit_check.py |
84 hard checks PASS, 0 conformance findings standing |
tools/verify_web.js |
ALL CHECKS PASS (W1–W10) |
physiology validate |
ALL HARD GATES PASS |
native verify |
99 data/pack assertions PASS, 0 FAIL |
all other tools/*_check.py |
exit 0 |
The native verifier's data/pack assertions run here (99 PASS, 0 FAIL).
Its GPU render stage needs a graphics adapter: where one exists — a
software GL stack such as llvmpipe suffices — the verifier also renders
its frames and prints 107 assertions (the 99 plus five frame silhouettes
against the CPU vertex projection, the Milestone 21 translucency proof,
and two picking checks), as observed on the instance that served this
tree before the 2026-11-07 VM replacement. On the current instance no
adapter can initialise (the GL/Vulkan driver libraries cannot be
loaded), so the render stage is asserted by the web checker (W1–W10)
and the pack/data checks instead, and the table carries the 99 the
verifier prints here; tools/readme_check.py re-derives the count on
every run.
| 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 |
| 16 | MILESTONE-16.md |
Shells integration: all 11 system layers assembled and packed (8,087,374 triangles), both shells render the full Body Model |
| 17 | MILESTONE-17.md |
Theatre v1: laparoscopic cholecystectomy — 9 phases / 21 steps / 86 microsteps, Critical View of Safety gate; divide-before-CVS is a Stewart–Way class III bile duct injury and fails the attempt |
| 18 | MILESTONE-18.md |
Physiology v1: venomotor recruitment + transcapillary refill; −750 mL haemorrhage lands inside the ATLS Class II band |
| 19 | MILESTONE-19.md |
Imaging v1: synthetic DICOM CT series of TotalSegmentator subject s0778 (431 instances), Body Model crosswalk, watermark in metadata and pixels |
| 20 | MILESTONE-20.md |
Case Workbench v1 + Case #1: acute cholecystitis, TG18 mechanically evaluated |
| 21 | MILESTONE-21.md |
Physiology: contractility effector (fourth baroreflex effector) + per-layer opacity in both shells |
| 22 | MILESTONE-22.md |
Case #2: post-operative bile duct injury — case #1's patient on postoperative day 4 after the Theatre's failed cholecystectomy, hash-linked to the trace |
| 23 | MILESTONE-23.md |
TA2 name pass: Terminologia Anatomica 2 Latin names over the clinical records (340/361 resolved) |
| 24 | MILESTONE-24.md |
Physiology: venous return first-class (Guyton readout); the −1,500 mL "decompensation" resolved as a sampling artifact — no parameter changed |
| 25 | MILESTONE-25.md |
Physiology: renal excretion + interstitial reservoir |
| 26 | MILESTONE-26.md |
Physiology: oncotic state + blood products as scenario inputs |
| 27 | MILESTONE-27.md |
Web delivery: gzip pack compression (290.3 → 117.6 MiB) via DecompressionStream, progressive per-layer loading |
| 28 | MILESTONE-28.md |
Theatre procedure #2: laparoscopic appendicectomy; base-identification gate; engine generalized, cholecystectomy debriefs byte-identical |
| 29 | MILESTONE-29.md |
Case #3: appendicitis — Alvarado 10/10 vs AIR 6/12 disagreement adjudicated per WSES Jerusalem 2020 |
| 30 | MILESTONE-30.md |
Physiology: hormonal volume axes (ADH + aldosterone) |
| 31 | MILESTONE-31.md |
Imaging MPR: tri-plane multiplanar reconstruction with exact re-indexing reslice, no interpolation |
| 32 | MILESTONE-32.md |
Imaging: second subject s1090 (439 instances) + viewer subject switching |
| 33 | MILESTONE-33.md |
FMA concept intake #1: 286 nervous-system concept records from FMA 5.1.0 (CC BY 4.0); nervous 133 → 419 records |
| 34 | MILESTONE-34.md |
Z-Anatomy geometry audit: provenance cleared for 555 of 587 anatomical objects; global registration refuted, brain-assembly transform validated (0.27 mm); no intake — the geometry decision is open |
| 35 | MILESTONE-35.md |
TA2 pass over the FMA nerve records (194/286 resolved) + muscle innervation re-pointing (2 → 69 nerve records linked) |
| 36 | MILESTONE-36.md |
FMA intake #2: lymphatic 4 → 135 records, endocrine 3 → 17 |
| 37 | MILESTONE-37.md |
FMA intake #3: urinary 6 → 73, female reproductive 13 → 70; six plexus records corrected on dual-parse evidence |
| 38 | MILESTONE-38.md |
FMA intake #4 (final): integumentary 6 → 59, male reproductive +76 — concept-intake arc closed at 684 FMA records; Body Model 2,236 |
| 39 | MILESTONE-39.md |
Major-nerve clinical tranche: 40 records (cranial, plexus, limb) — clinical records 361 → 401 |
| 40 | MILESTONE-40.md |
Deferent-duct checker repair: the M14 "absence" was a Latin-name probe miss (BP3D carries FJ3135/FJ3140); checker partition-scoped, regression gate added; zero data files changed |
| 41 | MILESTONE-41.md |
Case #4: carpal tunnel syndrome — first localization case; CTS-6; board 0.78 → 0.99 |
| 42 | MILESTONE-42.md |
Theatre procedure #3: open carpal tunnel release; nerve-identification gate; Case #4 hands off |
| 43 | MILESTONE-43.md |
Case #5: ulnar neuropathy localization (elbow vs wrist vs root) |
| 44 | MILESTONE-44.md |
Theatre procedure #4: ulnar nerve decompression, transposition authored with the equipoise scored as the evidence dictates; Case #5 hands off |
| 45 | MILESTONE-45.md |
Imaging toolkit pass: both DICOM series validated externally (pydicom/nibabel; 870 instances, 58.58M voxels exact); one conformance defect found (SeriesDescription 67 > 64 chars) |
| 46 | MILESTONE-46.md |
That defect repaired at the writer + permanent VR gate; both series re-derived, pixel identity 870/870, toolkit check clears with 0 findings |
| 47 | MILESTONE-47.md |
Physiology: respiratory module — ventilation + gas exchange; resting gases inside cited bands; pinned circulation baseline bit-identical |
| 48 | MILESTONE-48.md |
Case #6: acute dyspnoea — pulmonary embolism; Wells/PERC/CURB-65/ESC blocks, A–a gradient re-derived by the checker |
| 49 | MILESTONE-49.md |
Theatre procedure #5: laparoscopic inguinal hernia repair (TAPP) — triangle-of-doom / triangle-of-pain gate over two gated verbs (divide + fixate) |
| 50 | MILESTONE-50.md |
README reconciliation: the public index brought current through M49, with tools/readme_check.py guarding it against drift |
| 51 | MILESTONE-51.md |
Physiology: two-way coupling — hypoxic ventilatory drive + metabolic–circulatory feedback, both exactly zero at the resting equilibrium; pinned baseline bit-identical |
| 52 | MILESTONE-52.md |
Physiology: the Bohr shift — pH-dependent P50 anchored exactly on the resting pH; resting readouts bit-identical; the M47 deferral list (hypoxic drive, metabolic feedback, Bohr shift) closed |
| 53 | MILESTONE-53.md |
Physiology: chronic acid–base compensation — a slow renal bicarbonate state on the cited chronic relations (direction-specific) and a days timescale; sustained arms recover pH toward, not to, normal; resting baseline and Bohr anchor bit-identical |
| 54 | MILESTONE-54.md |
Case #7: pulmonary embolism rule-out — the pathway case #6 recorded but did not walk: Wells 0.0 complete, PERC precondition met, D-dimer 560 below the age-adjusted 620 cutoff (ADJUST-PE); PE excluded without imaging, over-testing scored as the error, D-dimer LR− 0.0732 registered |
| 55 | MILESTONE-55.md |
README reconciliation, final pass: the "How to use" section Chase added on main (ca36d943) merged verbatim, all figures brought current through M54, file index regenerated; readme_check fully green — the imaging-toolkit harness failure diagnosed as the environment's missing pinned toolkits (pydicom 3.0.2 / nibabel 5.4.2), restored |
| 56 | MILESTONE-56.md |
Theatre procedure #6: total thyroidectomy — per-side recurrent laryngeal nerve identification and parathyroid preservation gate; nerve monitoring is adjunct-only and cannot satisfy the gate (a probe pins it); extralaryngeal branching variant at cited prevalence, the 0.7% non-recurrent nerve below the authoring gate and not authored; the bilateral gate exposed a first-demonstration criteria bug, fixed with all 25 prior debriefs byte-identical |
| 57 | MILESTONE-57.md |
Case #8: post-thyroidectomy hypocalcemia — the trace-30 patient on postoperative day 1, hash-linked to the Theatre debrief; Trousseau LR+ 23.5 registered at the conservative end; the anchor an inherited anxiety/hyperventilation attribution |
| 58 | MILESTONE-58.md |
Physiology: the calcium–PTH axis — PTH secretion on the Brown four-parameter sigmoid, renal/bone/gut limbs; resting ionized calcium and PTH inside cited normals, the PTH-loss arm reproducing Case #8's postoperative-day-2 values; resting circulation baseline bit-identical |
| 59 | MILESTONE-59.md |
README final pass: figures and file index brought current through M58 and the landed browser build (web/wasm/cases-harness on main), the merged "How to use" section re-proven byte-identical; readme_check fully green |
| 60 | MILESTONE-60.md |
Case #8's physiology link: the case pinned to the calcium–PTH axis's PTH-loss arm — POD2 consonance near-exact (corrected 1.830 against 1.83 mmol/L), the POD1 gap (+0.146) disclosed in-case; correction of record: the arm is secretion capacity 9 percent, not capacity-0 as the M58 dossier's prose stated |
| 61 | MILESTONE-61.md |
Case #9: acute upper gastrointestinal bleeding — Glasgow-Blatchford and Forrest blocks, four reciprocal likelihood ratios, the patient-installed anchor (the ninth shape), the first perturbation-arm physiology link; the README drift closed (case_check figure, milestone rows 60–61, file index) |
| 62 | MILESTONE-62.md |
Theatre procedure #7: upper gastrointestinal endoscopy — identify-classify-before-therapy gate (source identified, Forrest classification demonstrated and declared, airway–sedation account); therapy before classification is a critical fail with a computed perforation; Dieulafoy variant authored; traces 31–37, all 30 prior debriefs byte-identical |
| 63 | MILESTONE-63.md |
Tier B geometry intake under the Milestone 34 audit's validated brain-assembly transform: 19 FMA records gain geometry, and the deferent-duct mesh pair (FJ3135/FJ3140) claimed — records with geometry 1,545 → 1,566, concept-only 691 → 670; atlas packs rebuilt (8,285,791 faces); Tier C gated, Tier D excluded |
| 64 | MILESTONE-64.md |
Case #9's Theatre hash-link: the case's endoscopic act pinned to trace 31 (authored on the case's own lesion), debrief SHA-256 recomputed and matched field-by-field, verdict PASS — the loop's third form (case first, procedure after); case_check 14,964; cases #1–#8 byte-identical |
| 65 | MILESTONE-65.md |
README reconciliation through M64: the endoscopy, geometry-intake and hash-link figures and indexes brought current; the geometry ruling recorded in the Status section, and the guard's R12 status statements moved to the ruled facts with it; readme_check fully green |
All 680 files in this repository, by directory. Adopted source-dataset binaries (meshes, archives, GLBs, segmentation masks) and build output are not tracked in git — see .gitignore; their provenance is recorded in data/sources/*/ledger.json and SOURCE.md. Regenerable artifacts (geometry packs and their gzip variants, DICOM series and web slice bins) are likewise not tracked: they are products of the shipped derivation and packing tools, and their identity is asserted by the checkers.
.gitignoreLICENSEREADME.md
assets/anatomica-hero.jpg
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AGPL-3.0. See LICENSE. Adopted datasets keep their own licenses, recorded
per file in the provenance ledger under data/sources/.