Legacy example · Python · Version 0.2.0

G-SHARP: Gaussian Splatting for Holographic Anatomical Reconstruction Pipeline

Real-time surgical scene reconstruction using Gaussian Splatting: DA2 depth, MedSAM3 segmentation, VGGT poses, and GSplat training in a five-phase pipeline.

Authors	Holoscan Team (NVIDIA)
Supported platforms	x86_64
Language	Python
Version	0.2.0
Compatibility	HSDK 3.8
Contribution level	Level 2 · Quality code
Source	HoloHub

Legacy HoloHub application

This application comes from HoloHub and was last tested with Holoscan SDK (HSDK) 3.8. It runs with the HoloHub CLI, ./holohub.

This application demonstrates real-time 3D surgical scene reconstruction by combining Holoscan SDK for high-performance streaming, 3D Gaussian Splatting for neural 3D representation, and temporal deformation networks for accurate modeling of dynamic tissue.

G-SHARP Rendering — Ground Truth vs Reconstructed (CMR surgical video)

The application provides a complete end-to-end pipeline — from raw surgical video frames to real-time 3D reconstruction — with no manual preprocessing. Researchers and developers can use it to train custom models on their own endoscopic data and visualize results with GPU-accelerated rendering.

Features of this application include:

Fully Automated Pipeline: Five-phase pipeline (depth, segmentation, poses, training, rendering) with zero manual preprocessing
Real-time Visualization: Stream reconstructed scenes at >30 FPS using Holoscan HoloViz
High-Quality Reconstruction: Achieves 35+ dB PSNR with ~50,000 Gaussians on surgical video
Temporal Deformation: Per-frame tissue modeling captures dynamic deformation over time
Tool Segmentation: MedSAM3-based tool masks automatically exclude instruments from reconstruction
Auto-Download: Sample data and all model checkpoints download automatically on first build

It takes input from a directory of sequential PNG frames (e.g., endoscopic video). It processes the input through DA2 depth estimation, MedSAM3 segmentation, VGGT camera pose estimation, and GSplat training. And it outputs a real-time 3D Gaussian Splatting reconstruction with temporal deformation.

It is ideal for use cases such as:

Surgical scene understanding and visualization
Tool-free tissue reconstruction for analysis
Research in surgical vision and 3D reconstruction
Development of real-time surgical guidance systems

Quick Start

Step 1: Clone the HoloHub Repository

git clone https://github.com/nvidia-holoscan/holohub.git
cd holohub

Step 2: Read and Agree to the Terms and Conditions of the EndoNeRF Sample Dataset

Read and agree to the Terms and Conditions for the EndoNeRF dataset.
The EndoNeRF sample dataset, DA2 checkpoint, and MedSAM3 checkpoint are downloaded automatically when building the application.
Optionally, for manual download of the dataset, refer to the Data section below.
Optionally, if you do not agree to the terms and conditions, set the HOLOHUB_DOWNLOAD_DATASETS environment variable to OFF and manually download the dataset and place it in the correct location by following the instructions in the Data section below.
```
export HOLOHUB_DOWNLOAD_DATASETS=OFF
```

Step 3: Run the Full Pipeline

To run the complete pipeline (depth + segmentation + poses + training + live viewer):

./holohub run surgical_scene_recon full

The first run builds the Docker container and downloads all data and checkpoints automatically. This may take several minutes.

Step 4: View Results

After training completes, the live render viewer opens automatically, showing side-by-side ground truth and reconstructed frames at 30 FPS. Close the window to exit.

To re-render from existing training output without re-training:

./holohub run surgical_scene_recon render

Pipeline Overview

G-SHARP runs five sequential phases to reconstruct a 3D scene from surgical video frames:

Phase	Component	Framework	Description
1	DA2 depth + MedSAM3 segmentation	Holoscan streaming	Dense monocular depth estimation and surgical tool segmentation
2	VGGT camera pose estimation	Standalone PyTorch	Batch camera extrinsic and intrinsic estimation
3	EndoNeRF format assembly	Python script	Assembles depth, masks, and poses into training-ready format
4	GSplat training with deformation network	Standalone PyTorch	Two-stage Gaussian Splatting: coarse (static) then fine (deformation)
5	Live render viewer	Holoscan streaming	Real-time side-by-side GT vs rendered visualization

Phase 1: DA2 Depth + MedSAM3 Segmentation

Phase 1 runs as a Holoscan streaming application. Each frame passes through Depth Anything V2 for dense monocular depth and MedSAM3 for surgical tool segmentation, all in a single streaming pass.

Phase 1 — Source | Depth | Mask (CMR surgical video)

Pipeline Progress Monitor

The pipeline reports progress through a live monitor window:

Pipeline Progress Monitor

Run Modes

All commands are from the HoloHub repo root:

Mode	Command	Description
Full pipeline	`./holohub run surgical_scene_recon full`	All five phases: DA2+MedSAM3 → VGGT → EndoNeRF → training → live viewer.
Train only	`./holohub run surgical_scene_recon train`	Phases 1–4 (no viewer; exits after training).
Render only	`./holohub run surgical_scene_recon render`	Phase 5 only (live viewer on existing output).
Verify train	`./holohub run surgical_scene_recon verify_train`	Short run for CI/testing: 20 training iters, 5 coarse, no viewer, headless.

Examples:

# Full pipeline with live viewer (requires display)
./holohub run surgical_scene_recon full

# Train only, then later run the viewer
./holohub run surgical_scene_recon train
./holohub run surgical_scene_recon render

# Quick sanity check (no display needed)
./holohub run surgical_scene_recon verify_train

To pass extra arguments to the app (e.g. more iterations), use --run-args:

./holohub run surgical_scene_recon full --run-args="--training-iterations 7000 --coarse-iterations 1000"

Data

Automatic Download (Default)

All data and checkpoints are downloaded automatically on first build:

Asset	Source	License	Size
EndoNeRF "pulling" frames (50 images)	Google Drive	Terms	~20 MB
Depth Anything V2 (Small)	HuggingFace	Apache-2.0	~95 MB
MedSAM3 checkpoint	HuggingFace	MIT	~9.3 GB

The application downloads the EndoNeRF "pulling" dataset by default, providing a ready-to-run experience out of the box.

Dataset Layout

<HOLOHUB_ROOT>/data/surgical_scene_recon/
├── frames/          ← PNG images (downloaded or your own)
├── da2/depth_anything_v2_vits.pth
└── medsam3/checkpoint.pt

Using Your Own Data

To use your own surgical video frames instead of the default EndoNeRF dataset:

Place your PNG frames in data/surgical_scene_recon/frames/. Filenames should sort alphabetically in temporal order (e.g., frame-000000.color.png, frame-000001.color.png, ...).
Checkpoints (DA2 and MedSAM3) are downloaded automatically. If they already exist on disk, the download is skipped.

mkdir -p data/surgical_scene_recon/frames
cp /path/to/your/*.png data/surgical_scene_recon/frames/

Manual Download

To skip automatic downloads and supply your own data manually:

export HOLOHUB_DOWNLOAD_DATASETS=OFF
mkdir -p data/surgical_scene_recon/frames data/surgical_scene_recon/da2 data/surgical_scene_recon/medsam3
cp /path/to/your/*.png data/surgical_scene_recon/frames/
wget -O data/surgical_scene_recon/da2/depth_anything_v2_vits.pth \
  https://huggingface.co/depth-anything/Depth-Anything-V2-Small/resolve/main/depth_anything_v2_vits.pth
# Download MedSAM3 checkpoint (~9.3 GB) from https://huggingface.co/ChongCong/Medical-SAM3

Automatically managed (do not place in your data dir): VGGT-1B is downloaded from HuggingFace on first run (cache at ~/.cache/huggingface). VGG-16 for LPIPS is pre-cached in the Docker image at build time.

Models Used by the `surgical_scene_recon` Application

The surgical_scene_recon application uses a five-model pipeline:

Model	Purpose	License
Depth Anything V2 (Small)	Dense monocular depth estimation	Apache-2.0
MedSAM3	Surgical tool segmentation	MIT
VGGT-1B	Camera pose estimation (extrinsics + intrinsics)	Meta License
4D Gaussian Splatting	Neural 3D scene representation	MIT / Apache-2.0
HexPlane Deformation Network	Temporal tissue deformation modeling	MIT / Apache-2.0

Gaussian Splatting Model

Architecture: 3D Gaussians with learned position, scale, rotation, opacity, and color
Initialization: Multi-frame point cloud (~30,000–50,000 points)
Renderer: gsplat library (CUDA-accelerated differentiable rasterization)
Spherical Harmonics degree 3 (16 coefficients per Gaussian for view-dependent color)

Temporal Deformation Network

Architecture: HexPlane 4D spatiotemporal grid + MLP decoder
Input: 3D position + normalized time value [0, 1]
Output: Deformed position, scale, rotation, and opacity per Gaussian
Training: Two-stage (coarse: static base, fine: with deformation)

About the Model Training Process

The application trains in two stages:

Coarse Stage — learns the base static Gaussian model without deformation.
Fine Stage — adds the temporal deformation network for dynamic tissue modeling.

The training uses:

Multi-modal Data: RGB images, depth maps, tool segmentation masks
Loss Functions: RGB loss, depth loss, TV loss, masking losses
Optimization: Adam optimizer with batch-size scaled learning rates
Tool Removal: Segmentation masks applied during training for tissue-only reconstruction

Training outputs are saved to <output-dir>/phase4_training/trained_model/:

ckpts/fine_best_psnr.pt — Best checkpoint (use for rendering)
ckpts/fine_step00XXX.pt — Regular step checkpoints
renders/ — Saved render frames

Performance

Tested Configuration:

GPU: NVIDIA RTX 6000 Ada Generation
Container: Holoscan SDK 4.0.0

Pipeline Timing

Phase	Description	Time
Phase 1	DA2 + MedSAM3 streaming inference	~24 s (63 frames)
Phase 2	VGGT batch pose estimation	~15 s
Phase 3	EndoNeRF format conversion	~1.5 s
Phase 4	GSplat training (1400 iter)	~2.5 min
Phase 5	Live render viewer	Real-time
Total	End-to-end (63 frames)	~3.5 min

Quality Metrics

Metric	Value
PSNR	35–38 dB
Rendering FPS	>30 FPS (real-time)
Gaussians	~35,000–65,000 splats
Training iterations	1400 (200 coarse + 1200 fine)

EndoNeRF "Pulling" Dataset Results

The default EndoNeRF "pulling" dataset (50 frames, 640×512) provides a ready-to-run benchmark:

EndoNeRF Pulling — Ground Truth vs Reconstructed

Output Structure

After a full run, <output-dir>/ contains:

<output-dir>/
├── phase1_raw/
│   ├── images/          # Resized input frames
│   ├── depth/           # DA2 depth maps (*.npy)
│   └── masks/           # MedSAM3 segmentation masks (*.png)
├── phase2_vggt/
│   ├── poses.npy        # Camera extrinsics (4x4 matrices)
│   └── intrinsics.npy   # Camera intrinsics
├── phase3_endonerf/
│   ├── images/          # Final frames in EndoNeRF layout
│   ├── depth/           # Scaled depth maps
│   ├── masks/           # Binary masks
│   └── poses_bounds.npy # LLFF-format camera parameters
├── phase4_training/
│   └── trained_model/
│       └── ckpts/
│           ├── fine_best_psnr.pt   # Best checkpoint by PSNR
│           └── fine_step*.pt       # Step checkpoints
└── progress.json        # Live progress (updated during run)

Requirements

Hardware

NVIDIA GPU with CUDA 12+ and Vulkan support (tested on RTX 6000 Ada)
~30 GB free disk space for Docker containers
Display configured for X11 (for Phase 1 / Phase 5 visualization)

Software

Docker with NVIDIA Container Toolkit
Holoscan SDK 3.8.0 or later (automatically provided in containers)

Application Integration Testing

We provide integration tests.

To test the application, run:

./holohub test surgical_scene_recon --verbose

Run a single test by name:

./holohub test surgical_scene_recon --ctest-options="-R surgical_scene_recon_test_all_imports -VV"

Command Line Arguments

Argument	Description	Default
`--data-dir`	Directory containing input PNG frames	Required
`--output-dir`	Base output directory for all pipeline artifacts	Required
`--training-iterations`	Total GSplat training iterations	`1400`
`--coarse-iterations`	Coarse stage iterations (fixed camera)	`200`
`--no-deformation`	Disable deformation network (static scene)	`False`
`--batch-size`	VGGT batch size (frames per batch)	`30`
`--depth-scale`	Depth scale factor (100 = centimeters)	`100.0`
`--fps`	Render viewer playback FPS	`30`
`--headless`	Run Holoscan apps without visualization	`False`
`--skip-phase1`	Skip Phase 1 (reuse existing depth/masks)	`False`
`--skip-phase2`	Skip Phase 2 (reuse existing VGGT poses)	`False`
`--skip-phase3`	Skip Phase 3 (reuse existing EndoNeRF data)	`False`
`--skip-training`	Skip Phase 4 (no training)	`False`
`--skip-viewer`	Skip Phase 5 (no live viewer)	`False`
`--da2-checkpoint`	DA2 `.pth` checkpoint	Auto (data dir)
`--da2-encoder`	DA2 encoder variant (`vits`, `vitb`, `vitl`)	`vits`
`--sam3-checkpoint`	MedSAM3 `.pt` checkpoint	Auto (data dir)

Incremental Runs

Use --skip-* flags to re-run only specific phases. For example, to re-train with more iterations while reusing Phase 1–3 output:

./holohub run surgical_scene_recon full --run-args="--skip-phase1 --skip-phase2 --skip-phase3 --training-iterations 7000 --coarse-iterations 1000"

Troubleshooting

Problem: "FileNotFoundError: No PNG files found"

Cause: Frames not in the correct location
Solution: Ensure PNG frames are in data/surgical_scene_recon/frames/
Verify: ls data/surgical_scene_recon/frames/*.png | head

Problem: "Unable to find image holohub-surgical_scene_recon"

Cause: Container not built yet
Solution: Remove --no-docker-build flag (let CLI build automatically)
Or: Manually build: ./holohub build-container surgical_scene_recon

Problem: Holoviz window doesn't appear

Cause: X11 forwarding not enabled
Solution: Run xhost +local:docker before running
Verify: Check echo $DISPLAY shows a value

Problem: GPU out of memory

Cause: Another process using GPU memory
Solution: Check nvidia-smi and stop other processes
Or: Reduce training batch or frame count

Problem: MedSAM3 checkpoint download fails or is 0 bytes

Cause: Network issue or HuggingFace rate limiting
Solution: Manually download from ChongCong/Medical-SAM3 and place at data/surgical_scene_recon/medsam3/checkpoint.pt
Verify: ls -lh data/surgical_scene_recon/medsam3/checkpoint.pt (should be ~9.3 GB)

Problem: Google Drive data download fails

Cause: Google Drive rate limiting for automated downloads
Solution: Download the EndoNeRF "pulling" images manually from Google Drive and place them in data/surgical_scene_recon/frames/

Acknowledgements

Citation

If you use this work, please cite the following:

G-SHARP:

@article{nath2025g,
  title={G-SHARP: Gaussian Surgical Hardware Accelerated Real-time Pipeline},
  author={Nath, Vishwesh and Tejero, Javier G and Li, Ruilong and Filicori, Filippo and Azizian, Mahdi and Huver, Sean D},
  journal={arXiv preprint arXiv:2512.02482},
  year={2025}
}

EndoNeRF:

@inproceedings{wang2022endonerf,
  title={EndoNeRF: Neural Rendering for Stereo 3D Reconstruction of Deformable Tissues in Robotic Surgery},
  author={Wang, Yuehao and Yifan, Wang and Tao, Rui and others},
  booktitle={MICCAI},
  year={2022}
}

3D Gaussian Splatting:

@article{kerbl20233d,
  title={3d gaussian splatting for real-time radiance field rendering},
  author={Kerbl, Bernhard and Kopanas, Georgios and Leimk{\"u}hler, Thomas and Drettakis, George},
  journal={ACM Transactions on Graphics},
  year={2023}
}

gsplat Library:

@software{ye2024gsplat,
  title={gsplat},
  author={Ye, Vickie and Turkulainen, Matias and others},
  year={2024},
  url={https://github.com/nerfstudio-project/gsplat}
}

Third-Party Dependencies and Licenses

This application uses several third-party libraries. By building and running this application, you acknowledge and accept the license terms of these libraries.

VGGT (Visual Geometry Grounded Transformer)

Source: https://github.com/facebookresearch/vggt
License: Meta License (see repository for license terms)
Installation: Pip-installed from source at Docker build time
Model weights: facebook/VGGT-1B from HuggingFace

Important: The VGGT code and model weights are released under a custom Meta license. By using VGGT, you agree to be bound by its terms. The facebook/VGGT-1B checkpoint is licensed for non-commercial use only. A separate facebook/VGGT-1B-Commercial checkpoint is available for commercial use — see the VGGT repository for details.

SAM3 (Segment Anything Model 3)

Source: https://github.com/facebookresearch/sam3
License: SAM License
Installation: Pip-installed from source at Docker build time

Important: SAM3 is released under a custom SAM License. By using SAM3, you agree to be bound by its terms. A MedSAM3 checkpoint suitable for this pipeline can be downloaded from ChongCong/Medical-SAM3 on Hugging Face.

Depth Anything V2

Source: https://github.com/DepthAnything/Depth-Anything-V2
License: Apache-2.0 (code and Small model)
Bundled: models/depth_anything_v2/

The Small model (depth_anything_v2_vits.pth) used by this application is Apache-2.0 licensed. Base/Large/Giant models are CC-BY-NC-4.0.

EndoGaussian / GSplat Training

Source: Derived from EndoGaussian
License: MIT (upstream EndoGaussian) + Apache-2.0 (NVIDIA modifications)
Bundled: training/

The bundled training code is a custom derivative that replaces the original CUDA rasterizer with the gsplat library. It is not a direct copy of the upstream repository.

Additional Python Libraries

Library	License	URL
PyTorch	BSD-3-Clause	https://github.com/pytorch/pytorch
CuPy	MIT	https://github.com/cupy/cupy
gsplat	Apache-2.0	https://github.com/nerfstudio-project/gsplat
LPIPS	BSD-2-Clause	https://github.com/richzhang/PerceptualSimilarity
HuggingFace Hub	Apache-2.0	https://github.com/huggingface/huggingface_hub
einops	MIT	https://github.com/arogozhnikov/einops
timm	Apache-2.0	https://github.com/huggingface/pytorch-image-models

License

This application is licensed under Apache 2.0. See individual files for specific licensing:

Application code: Apache 2.0 (NVIDIA)
Training utilities: MIT License (EndoGaussian Project)
Spherical harmonics utils: BSD-2-Clause (PlenOctree)

All examples

G-SHARP: Gaussian Splatting for Holographic Anatomical Reconstruction Pipeline

Quick Start

Step 1: Clone the HoloHub Repository

Step 2: Read and Agree to the Terms and Conditions of the EndoNeRF Sample Dataset

Step 3: Run the Full Pipeline

Step 4: View Results

Pipeline Overview

Phase 1: DA2 Depth + MedSAM3 Segmentation

Pipeline Progress Monitor

Run Modes

Data

Automatic Download (Default)

Dataset Layout

Using Your Own Data

Manual Download

Models Used by the surgical_scene_recon Application

Gaussian Splatting Model

Temporal Deformation Network

About the Model Training Process

Performance

Pipeline Timing

Quality Metrics

EndoNeRF "Pulling" Dataset Results

Output Structure

Requirements

Hardware

Software

Application Integration Testing

Command Line Arguments

Incremental Runs

Troubleshooting

Problem: "FileNotFoundError: No PNG files found"

Problem: "Unable to find image holohub-surgical_scene_recon"

Problem: Holoviz window doesn't appear

Problem: GPU out of memory

Problem: MedSAM3 checkpoint download fails or is 0 bytes

Problem: Google Drive data download fails

Acknowledgements

Citation

Third-Party Dependencies and Licenses

VGGT (Visual Geometry Grounded Transformer)

SAM3 (Segment Anything Model 3)

Depth Anything V2

EndoGaussian / GSplat Training

Additional Python Libraries

License

Models Used by the `surgical_scene_recon` Application