# Anatomy inventory and asset audit

Status: anatomical review pending. Inspected 2026-09-22.

## Reference build and packaging

The live reference is https://www.leezhaomd.org/urethral-stricture-atlas/. Its publication.json identifies source commit `7f5ca300e52799dd936eb399f43b430dd48b5df3`. The local atlas.json and atlas.bin hashes exactly match that live publication record:

- atlas.json: `4efae28377dcad95f7fc1042d111085bb890419830cf64a5a109367a5cda42b5`
- atlas.bin: `3f2d9c5ef19279995443501670bc5081023987186d197e7a81656e57028f5d17`

The reference source uses Three.js, OrbitControls, Vite/vinext, static exported client assets, scoped asset paths, and a file-hash publication manifest. The parent `leezhaomd-www` repository is Astro with Vite teaching apps and `build:website` scripts. This separate prototype follows the Vite teaching-app convention and prepares a static package for `/penile-replantation-atlas/`. The existing urethral atlas files are unchanged. The initial prototype was built separately; Lee subsequently authorized publication through the main website.

Viewer reuse: Three.js OrbitControls, the reference lighting/material approach, the restrained palette, and the atlas triangle-clipping helper (`src/atlas-clip.ts`). Procedure-specific state and disease geometry were not imported. The new teaching timeline derives all segment positions from a single progress value; it does not accumulate translations.

## Coordinate contract

The original atlas records X left, Y superior, Z anterior, with centimetre model units. The rigid registration here maps `(X,Y,Z)` to `(-Y,Z-6.5,-X)`. Thus the teaching shaft axis is +x distal, +y dorsal, and +z anatomical right. The constructed cut is at x=1.7 in that registered frame. These are model coordinates, not a patient measurement or a proposed clinical injury level. The proximal piece stays fixed; the distal piece translates along +x without reflection or rotation.

The proximal cut view looks proximally from +x: anatomical right appears at screen left. The distal view looks distally from -x: anatomical right appears at screen right. Labels explicitly state both viewing directions. Separate dorsal-artery identities preserve laterality.

## Structure audit

| Structure | Available before modeling | Prototype treatment | Review limitation |
|---|---|---|---|
| Skin | Absent from the source atlas crop | Constructed sleeve with outer and inner surfaces and a real annular cut face | Schematic thickness, proximal transition, and relationship to the glans |
| Superficial fascia/dartos | Absent as a distinct volume | Constructed sleeve between skin and Buck fascia; separate hole for superficial vein | Branching superficial vascular and neural networks omitted |
| Buck fascia | Constructed source viewer surface, not a closed tissue volume | New nested wall and cut annulus | Elliptical contour is schematic, especially ventrally; no claim of surgical fidelity |
| Right/left corpora cavernosa | Open3DAnatomy outer meshes, split at the medial plane in atlas preparation | Original surface shape reused; cropped shaft, separately identified right/left cores, triangulated cross-sections | Constructed medial closure; original medial surface is open; trabecular architecture omitted |
| Tunica albuginea | Thin constructed offset surface in the reference viewer | Outer atlas corporal surface plus inner core and cut annulus | Thickness and septum schematic; complete longitudinal tunical wall is not yet validated |
| Corpus spongiosum | Open3DAnatomy outer mesh; source bulbar disease interval altered | Shaft reused, constructed inner bore and cross-sectional tissue around urethral wall | Clean shaft level avoids the original disease interval; distal bore continuity needs refinement |
| Urethral wall/lumen | Atlas reference surface and a constructed disease-bearing lumen in reference app | New curved patent tube without stricture, with inner wall and annular ends | Both injury-plane openings are ray-tested; uninterrupted lumen through the source glans/meatus is not established |
| Glans | Open3DAnatomy mesh | Reused with the amputated segment | Atlas meatus is not reconstructed as a validated continuation of the new lumen |
| Scrotum | Absent from the source atlas crop | Constructed continuous external envelope, retained with the proximal anatomy throughout | Contour, folds, size, and attachment are schematic; testes and internal scrotal anatomy are not modeled |
| Cavernosal arteries | Paired atlas surfaces | Reused with independent right/left identity, open wall cross-sections | Not a claim that these arteries will be repaired; no full longitudinal intratissue bore validation |
| Dorsal arteries | Combined paired atlas mesh | Split into right/left selections; translated dorsally by 0.2 model units to clear the tunica at this section; open cut walls | Explicit constructed registration correction, requires anatomical review; original source intersects tunica at this plane |
| Deep dorsal vein | Atlas mesh | Same dorsal registration correction and a patent cut wall | Caliber and longitudinal course require review |
| Dorsal nerves | Constructed source viewer tubes | Paired curved courses fitted to the dorsal vein profile, retaining lateral positions and solid cut faces | Nerve branching, fascicles, and regional variation omitted |
| Superficial dorsal vein | No suitable source shaft mesh | Constructed course in the superficial fascial layer, with a real open cut wall | A representative channel, not a universal count or operative target |
| Intervening connective tissue | No segmented volume | Constructed planar tissue partition around major structures on both cut faces | Provides tissue-filled sections; not a validated longitudinal connective-tissue mesh |
| Proximal context | Atlas pubic rami, symphysis, bulb, proximal corporal/spongiosal tissue | Retained in the model data; hidden in the current external-anatomy sequence | Not a complete pelvis, skin envelope, or organ system |

The urethral course follows sampled spongiosal sections. Its inner wall, outer wall, and surrounding bore share the same curve. The proximal tube is cropped with the shaft, and the distal tube ends before the narrow spongiosal tip. The nerves follow the longitudinal bend of the atlas dorsal vein while retaining their paired lateral positions. A small proximal dorsal offset separates the nerves from arterial branches and fades before the injury plane. These are fitted teaching paths, not traced nerve anatomy. The injury-plane centers and radii remain fixed; an explicit ring at that plane keeps each curved wall aligned with its cut face.

The binary retains the source atlas parts, including unused pelvic structures. `public/anatomy/atlas.json` is the per-mesh source-name and offset manifest. No third-party textures, patient photographs, or new anatomical scans are included. All colors are programmatic materials.

The current opening view shows the external penis and scrotum. Pelvic context is hidden. Distal sleeves now taper with an oblique transition beneath the source glans; the injury-plane contours are unchanged. Small constructed neurovascular surface paths are hidden beneath the intact skin view and shown when outer layers are opened. Their cut faces remain available in the matching sections.

## Requested animation extension

Lee requested a visible cutting animation, a scrotum, and then a continuous normal-anatomy to amputation to replantation sequence. A schematic blade reveals a narrow cut behind its leading edge. The segment separates only after the stroke is complete. Replantation returns the segment along the same axis, closes the display gap, highlights internal repair objectives, and restores skin with illustrative stitches. The stitch count and placement are drawing choices, not an operative prescription. This sequence does not simulate sutured microvascular anastomoses, debridement, tissue viability, reperfusion, or healing.

The temporary display kerf uses the existing injury-plane contours on its two offset faces. It is a visibility construction, not a new anatomical resection or a validated tissue-loss model. Reverse scrubbing restores the original appearance; the scrotal envelope remains outside the cutting region.

The caidao silhouette follows a user-supplied visual reference: a broad steel blade, metal collar, and black handle. Its reference dimensions use the atlas's centimetre units: approximately 18 cm blade length, 9 cm blade height, and 32 cm overall length. The size reference is the manufacturer's specification for the [ZWILLING Pro Chinese chef's knife, 38419-181-0](https://www.zwilling.com/uk/zwilling-pro-18-cm-chinese-chefs-knife-38419-181-0/38419-181-0.html), accessed 2026-09-22. This establishes a representative caidao size, not the identity or measured size of the photographed knife. At Lee's request, the displayed knife is uniformly scaled to 50% of that size, including the handle and blade thickness. The cutting edge retains its original path. Blade thickness remains a thin display construction within the existing kerf. The camera fits the knife and anatomy throughout the stroke. Geometry and surface grain are constructed; the original reference image is not redistributed.

## Cut-face construction

Actual mesh-plane intersections provide the corporal, spongiosal, and source-vessel contours. The open medial corporal contours are closed with a documented constructed septal edge. Tissue regions are triangulated with holes for the urethra and vessels. Matching faces use the same coordinates. Geometry tests cast rays through the apertures from both sides, sample the section for overlapping tissue, verify the half-space partition, and check right/left identities.

Initial independent review found overlapping nerve/tunica/fascial contours that caused the connective-tissue triangulation to cover vessel openings. The source dorsal bundle was repositioned, nerve courses adjusted, and the enclosing layers enlarged. The repaired section passes aperture and overlap checks. This numerical result does not constitute anatomical approval.

## Attribution and license

Primary reused mesh source: Marco C. DeRuiter, Eungyeol Lee, Daniël Jansma, O. Paul Gobée and colleagues, LUMC, [Open3DAnatomy pelvic floor and perineum](https://anatomytool.org/content/open3danatomy-3d-model-pelvic-floor-and-perineum-english-labels), CC BY-SA 4.0. Source ancestry includes [Z-Anatomy](https://github.com/Z-Anatomy/Models-of-human-anatomy), Gauthier Kervyn and contributors, and [BodyParts3D/DBCLS](https://dbarchive.biosciencedbc.jp/en/bodyparts3d/), Kousaku Okubo and collaborators. Inherited BodyParts3D attribution remains intact. The atlas also retains Anatria notices for the bundled source atlas.

All adapted geometry, constructed geometry, and the derived SVG section in this project are offered under [CC BY-SA 4.0](https://creativecommons.org/licenses/by-sa/4.0/). Retain attribution, modification notices, and ShareAlike when distributing adapted geometry. This license does not establish clinical validity. The original attribution record is retained in `reference-atlas-sources.md`; inherited notices are under `public/licenses/`.

The source viewer has no separately identified blanket code license in the inspected tree. Reuse of the user-owned viewer helper is scoped to this requested project; no third-party code relicensing is asserted. Three.js/OrbitControls retain the Three.js MIT notice. The application is published as an educational review model.

## Review decisions

Review the injury plane and paired corpus contours, constructed septum and fascia, dorsal registration changes, urethral position and distal lumen, and nerve and vessel courses. Review the separate repair models below. Their teaching order does not select an operative sequence. Publication is authorized; anatomical and clinical review remain open.

The scrotal envelope was enlarged by 30% in each model dimension for this publication, keeping its upper attachment level fixed and its entire surface proximal to the injury plane. This is a display adjustment, not a normative measurement.

## Continuous movie on the original anatomy

The main movie keeps the same proximal and distal meshes from intact anatomy through division, separation, each repair, and coverage. The camera magnifies the actual injury plane. It does not substitute the supplementary cylindrical models.

Tunical closure comes first in this teaching sequence. The urethra and spongiosum, dorsal arteries, deep vein, and dorsal nerves retain local gaps until their own repair. Retraction is confined to the cut ends; anatomy beyond that band remains registered to its shaft half. The main scene keeps the proximal half fixed while the distal half returns. The scrotum remains stationary.

Native sutures follow the original noncircular tunical contours and the curved urethral and vascular walls. The dorsal vessels receive a short constructed inner wall fitted to their source sections and existing cut apertures. The rest of each vessel retains its original surface. A curved catheter lies within the urethral channel. Completed sutures remain in place as the camera moves on.

Both original dorsal nerves receive a schematic two-leaf Nerve Tape wrap. The device follows each nerve's local curve. The left wrap opens dorsally; axial display length is shortened to clear nearby arterial branches. These display dimensions are not a device-size recommendation. Native nerves remain filled; no fascicular dissection or functional recovery is simulated.

The teaching order does not prescribe operative order. As in the supplementary models, wall thickness, thread size, stitch count, retraction, and device proportions are illustrative. Needle handling, knot tying, preparation, tissue loss, clamps, and flow are omitted. The cavernosal arteries and superficial vein are identified but their repairs are not animated.

## Separate repair models

The corporal repair reuses the full paired tunica surfaces from the main atlas model. The other close-ups use constructed display geometry. None is a patient-specific reconstruction.

- Corpora cavernosa: the original atlas outer triangles retain their curvature, taper, extent, and paired position. Missing medial and proximal crop faces are constructed. Inner tissue and wall thickness are illustrative. Sutures follow the local noncircular contours on both sides of the repair. Shared septal closure is not animated. The full-tunica view retains the entire model; a removable dorsal window exposes the closure.
- Pending repairs during tunical closure: urethra with its surrounding spongiosum, paired dorsal arteries, deep dorsal vein, and paired dorsal nerves reuse the main model geometry and registration. Only their cut ends retract as the corpora meet, retaining a visible gap. The shaft outside that short transition remains attached in its original position. This display adjustment does not model tissue loss or specify a surgical gap. Urethral and vessel apertures remain open; nerve ends remain filled. This context is hidden when the separate magnified lessons begin.
- Urethra: a hollow wall with a surrounding spongiosal layer and a separate catheter. Full-thickness bites reach the inner wall surface locally without spanning the lumen or capturing the catheter. Circular ends omit spatulation; mucosal preparation and separate spongiosal closure are not animated.
- Microvascular: the camera starts with a dorsal context map, then magnifies one matched artery or vein. Paired arteries flank the central vein. The selected vessel is enlarged for identification; neighboring structures fade during magnification. Separate arterial and venous models use hollow walls and full-thickness, wall-local thread paths.

The constructed tube shapes in the other lessons, wall thicknesses, catheter size, thread diameter, stitch count, and spacing are display choices. They do not specify clinical dimensions or calibrated magnification. The moving marker traces a thread path. It is not a needle simulation; knot tying, clamps, preparation, and grafts are omitted. Direct approximation assumes matching ends without modeled tissue loss. Cutaway mode removes a window or wedge and its stitches, so it shows only part of the circumferential repair. An open rendered lumen is not proof of perfusion or durable patency.

Geometry checks verify filled corporal cores, open central channels, matching edge approximation, bites in both walls, local inner-surface engagement for hollow structures, catheter clearance, and reset of all sutures on reverse seeking. These checks establish geometric behavior, not clinical validation.

## Focused repair journey and Nerve Tape mechanism

The four repair lessons share a scene. The camera zooms to tunical closure first, moves ventrally to the urethral wall, then dorsally to an artery and across to the deep dorsal vein. Corporal cores and tunica are translucent by default. Skin and fascia are absent; the urethral view also hides surrounding spongiosum. Completed repairs persist as faint context. Small structures are enlarged relative to the corpora, so the scene is an anatomical teaching map rather than a calibrated specimen.

The final close-up moves laterally to a constructed, tissue-filled dorsal nerve. A translucent two-leaf wrap surrounds aligned ends; the shorter leaf closes before the longer overlapping leaf. Nitinol hook profiles engage the epineurial shell outside the modeled fascicular core. Corporal context is hidden here so the enlarged open leaf does not pass through visible tissue. The device surrounds only the nerve. No axonal growth, conduction, or functional recovery is animated. Device dimensions and hook profiles are illustrative; measurement, preparation, handling, and optional securing sutures are omitted.

The Nerve Tape illustration is based on the manufacturer IFU and FDA device description listed in the source manifest. It is a device-mechanism illustration applied to a dorsal nerve, not evidence of a penile indication or a validated penile replantation technique. No manufacturer artwork or patient imagery was copied.