README.md

---
license: cc-by-nc-4.0
pretty_name: "SpineDepth (preprocessed) — CT & RGB-D lumbar vertebrae"
tags:
- medical-imaging
- rgbd
- depth-camera
- computed-tomography
- spine
- point-cloud
- registration
- orthopedics
size_categories:
- n<1K
---

# SpineDepth (preprocessed) — CT ↔ RGB-D lumbar vertebrae

A **preprocessed** version of the **SpineDepth** dataset (Liebmann et al., 2021) for
multi-modal **CT ↔ intraoperative RGB-D** bone-surface registration of lumbar vertebrae.
Each vertebra is provided as a preoperative CT bone mesh together with two intraoperative
RGB-D point clouds (one per depth-camera view). It accompanies the *Medical Image
Analysis* 2026 paper (see [Citation](#citation)).

## Dataset summary
- **7 cadaveric specimens** (IDs `2`–`8`), lumbar levels **L1–L5**.
- **35 preoperative CT bone meshes** (`.stl`) — one vertebra model per (specimen, level).
- **70 intraoperative RGB-D point clouds** (`.xyz`) — **two camera views**
  (`camera0`, `camera1`) per vertebra, ~30k–40k points each (XYZ in millimetres).
- Every vertebra is thus one CT mesh + two RGB-D clouds: a ready CT↔RGB-D registration set.

## Excluded specimens
The original SpineDepth comprises **ten** cadaveric specimens (1–10). **Specimens 1, 9, and
10 are excluded** from this release because they provide **insufficient anatomical
coverage** for intraoperative surface registration (see [Liebmann et al., 2021](https://doi.org/10.3390/jimaging7090164) and [Massalimova et al., 2025](https://doi.org/10.1080/24699322.2025.2511126)). For specimen 1, the original
recordings used a standard midline approach with the soft tissue left intact (pedicle
screws instrumented from TH12–S1 prior to the experiment), exposing too little bone
surface; for specimen 9 the depth views observe too little of each vertebra to
disambiguate its near-symmetric pose. The released set is therefore specimens 2–8.

For completeness, the preprocessed data for the excluded specimens is still provided under
`excluded_specimens/` (mirroring the main `preoperative/` + `intraoperative/` layout): CT bone
meshes for specimens 1, 9, and 10, plus RGB-D clouds for specimens 9 and 10 (specimen 1's bone
surface is too occluded to reconstruct usable intraoperative clouds). This data is **not** part of
the released registration set and is **not** loaded by the default pipeline.

## Preprocessing
This is **not** the raw SpineDepth release. Starting from the original SpineDepth RGB-D
recordings (tracked video sequences) and CT data, we provide **level-wise segmentation
for both modalities**: each lumbar vertebra (L1–L5) is isolated into its own
intraoperative RGB-D point cloud *and* its own preoperative CT bone mesh, rather than a
whole-spine scan. Each RGB-D cloud is built by **merging the tracked frames** of a
recording into one point cloud per camera view, **downsampling** it, and **segmenting it
per vertebral level**; the matching preoperative mesh is that vertebra's CT bone surface.
See our paper for the full procedure.

## Directory structure
```
SpineDepth/
├── README.md
├── preoperative/                 # CT bone meshes
│   └── 2_L1.stl  2_L2.stl  ...  8_L5.stl          # <specimen>_<level>.stl              (35 files)
├── intraoperative/               # merged + downsampled RGB-D point clouds
│   └── 2_L1_camera0.xyz  2_L1_camera1.xyz  ...     # <specimen>_<level>_camera<0|1>.xyz  (70 files)
└── excluded_specimens/           # specimens 1, 9, 10 (excluded above) — provided for completeness
    ├── preoperative/             # CT bone meshes for 1, 9, 10
    └── intraoperative/           # RGB-D clouds for 9 and 10 (specimen 1: CT only)
```
`specimen ∈ {2..8}`, `level ∈ {L1..L5}`, `camera ∈ {0,1}`. Each `.xyz` is plain XYZ
coordinates in millimetres, one point per line; each `.stl` is a triangle mesh of the
CT-segmented vertebra.

## Usage
Each `preoperative/<s>_<L>.stl` (CT model) pairs with the two
`intraoperative/<s>_<L>_camera{0,1}.xyz` (RGB-D) clouds of the same vertebra for
CT↔RGB-D bone-surface registration (e.g. with NeuralBoneReg).

## Citation
If you use this dataset, please cite **both** our paper and the original SpineDepth:

```bibtex
@article{wu2026neuralbonereg,
  title   = {NeuralBoneReg: An instance-specific label-free point cloud-based method for multi-modal bone surface registration},
  author  = {Wu, Luohong and Seibold, Matthias and Cavalcanti, Nicola A. and Ao, Yunke and Flepp, Roman and Massalimova, Aidana and Calvet, Lilian and F{\"u}rnstahl, Philipp},
  journal = {Medical Image Analysis},
  year    = {2026},
  doi     = {10.1016/j.media.2026.104133}
}

@article{liebmann2021spinedepth,
  title   = {{SpineDepth}: A Multi-Modal Data Collection Approach for Automatic Labelling and Intraoperative Spinal Shape Reconstruction Based on {RGB-D} Data},
  author  = {Liebmann, Florentin and St{\"u}tz, David and Suter, Daniel and Jecklin, Sascha and Snedeker, Jess G. and Farshad, Mazda and F{\"u}rnstahl, Philipp and Esfandiari, Hooman},
  journal = {Journal of Imaging},
  volume  = {7},
  number  = {9},
  pages   = {164},
  year    = {2021},
  doi     = {10.3390/jimaging7090164}
}
```