3.2 · M07 model · NAV / Ruberte 2025

Mouse lung explorer · v3.3 Lite

Stationary ventral view. Reference lobe positions are preserved. Day 14 / 30 buttons show exploratory shape-based plane candidates, not established 3D registration.

Lobes keep their measured positions. The two small ventral lobes can be isolated without moving them.

Scientific plane address

M07 local frame (mm): +X right, +Y ventral, +Z cranial; plane n·x = d. Direction names follow NAV terminology discussed by Ruberte et al. (2025). The origin and dimensions belong to this M07 mesh, not to Ruberte et al. or Xenium.

Alveoli / air-sac data

No individual alveolar geometry is loaded. m07 provides near-acini compartments, which are not alveolar sacs. Independent micron-scale alveolar datasets cannot be placed into m07 without registration.
m07 same-specimen data
1.1 µm alveolar ROI study
LungVis data

Section planeM07 frame · mm

Offset normal distancemm0.00

Azimuth right ↔ ventral°15°

Elevation cranial ↔ caudal°0°

Drag to tilt

azimuth → · elevation ↑

Slide plane

0.00 mm

M07 model plane

Oblique sagittal plane

Display

Lobe opacity95%

Airway surfaceLung lobes

Alveoli · schematic

Sources · measured vs schematic

M07 reference: deposited lapdMouse gross lung and airway geometry. No measured alveolar atlas is present in this model. M07 source.

E02 measured-data ROI: independently reconstructed projection data, with exploratory thresholded tissue surfaces. Different specimen; not registered to M07. Source dataset. This is not ground-truth alveolar segmentation.

Schematic airspaces: generated enlarged polyhedra (0.40 mm diameter, 0.65 mm spacing), not acquired anatomy. Positions, dimensions and counts are illustrative. Their 2D contours are geometric cuts of these same artificial shapes. Method: alveolar notebook, versions 2.9 and 3.0. No paper is cited as evidence for these invented dimensions.

Left lung

Right cranial

Right middle

Right caudal

Right accessory

Trachea / airway

Info

Model & sources

M07 is a reference lung, not a registration of either Xenium section. The whole-lung airspaces are schematic; the E02 alveolar ROI is a separate measured specimen.

Current plane · M07 coordinates (mm)

Virtual 2D sections are computed from intersections of the selected plane with the M07 reference mesh; they are not measured histology sections. Schematic airspaces are illustrative.

Sources

Bauer et al. (2020) — M07 lung anatomy.
Beichel et al. — source geometry archive.
Bolaños et al. (2021) — illustrative whole-body CT context.
Ruberte et al. (2025) — quadruped orientation terms.
Lovric et al. (2017) — independent alveolar ROI.

How to cite

Arash Bagherabadi and Abel Lopez. Mouse Lung Explorer (v3.3) [Software]. arashabadi.github.io/mlung3d/

Acknowledgements

Thank you to Abel Lopez for helping build the 3D lung and airway model, and to Codex (GPT-6) for assistance with implementation and documentation.

Anatomical orientation

Ventral view. Mouse left appears on the right side of the image; cranial points up.

R / L · Right / Left
V / D · Ventral / Dorsal
Cr / Cd · Cranial / Caudal

Ventral view: screen-left = mouse RIGHT lung · screen-right = mouse LEFT lung

Loading Lite lung model…

Preparing 3D engine

Independent alveolar-region reconstruction

Measured-data ROI · exploratory reconstruction

BALB/c · mouseE02 · 10 cmH₂O · 2.2 µm sampling · not registered to m07

Loading reconstructed surface…

Measured-volume section

Slice axis Cut 3D surfaceTissue overlay

Copy / restore ROI slice

Source & reconstruction limits

Reconstructed from Lovric et al. public projection data. Surface = exploratory thresholded tissue interface, not individually segmented alveoli. Propagation fringes, missed thin septa and crop edges remain. Slice positions use ROI acquisition coordinates; they have no anatomical registration to the whole-lung model. Paper.