GaussianPile: A Unified Sparse Gaussian Splatting Framework for Slice-based Volumetric Reconstruction
Authors: Di Kong, Yikai Wang, Wenjie Guo, Yifan Bu, Boya Zhang, Yuexin Duan, Xiawei Yue, Wenbiao Du, +3 more
Organizations: Tsinghua University · Zhongguancun Academy · Beijing Normal University · Nankai University · Beijing Institute of Technology · Beihang University
Slice-based volumetric imaging is widely applied and it demands representations that compress aggressively while preserving internal structure for analysis. We introduce GaussianPile, unifying 3D Gaussian splatting with an imaging system-aware focus model to address this challenge. Our proposed method introduces three key innovations: (i) a slice-aware piling strategy that positions anisotropic 3D Gaussians to model through-slice contributions, (ii) a differentiable projection operator that encodes the finite-thickness point spread function of the imaging acquisition system, and (iii) a compact encoding and joint optimization pipeline that simultaneously reconstructs and compresses the Gaussian sets. Our CUDA-based design retains the compression and real-time rendering efficiency of Gaussian primitives while preserving high-frequency internal volumetric detail. Experiments on microscopy and ultrasound datasets demonstrate that our method reduces storage and reconstruction cost, sustains diagnostic fidelity, and enables fast 2D visualization, along with 3D voxelization. In practice, it delivers high-quality results in as few as 3 minutes, up to 11x faster than NeRF-based approaches, and achieves consistent 16x compression over voxel grids, offering a practical path to deployable compression and exploration of slice-based volumetric datasets.
Figures & tables
Figure 1: Panel (a) is the average PSNR-fps-minute comparison (circle radius encodes minutes of training). Our method achieves the highest accuracy at far lower compute cost than prior work. Panels (b–d) are the comparisons of Gaussian rendering models under different imaging physics. (b) All-in-focus ( σz→∞ ): no axial falloff; primitives contribute regardless of its depth, appropriate for all-in-focus pinhole rendering (e.g., original 3DGS [ 14 ] ) or line-integral modalities (e.g., X-ray [ 4 ] ). (c) Zero-thickness ( σz→0 ): delta-like axial response; primitives contribute only at the exact plane, suitable for dense slicing (e.g., MRI [ 20 ] ). (d) Finite-thickness Focus Gaussian (ours): finite axial sensitivity ( σz finite); primitives contribute within a focal zone determined by σz , modeling anisotropic PSF in slice-based modalities (e.g., ultrasound, light-sheet microscopy).
Figure 2: Focus-aware rendering pipeline of GaussianPile. Given 3D Gaussians and a sensitivity map defining the focal zone, the rendering process consists of three stages: (1) Scan : project Gaussians onto slices at different depths; (2) Axial re-parameterization and Opacity modulation : apply axial weighting to attenuate off-focal contributions, yielding Focus Gaussians, while modulating opacity based on distance from the focal plane; (3) Screen-space projection and Additive rasterization : compute 2D marginal distributions and additively accumulate weighted Gaussian footprints to form final rendered images.
Figure 3: Reconstruction results of our GaussianPile at different iterations, visualized on the 3D data of a noisy Tribolium castaneum embryo by confocal microscopy with high laser power, demonstrating high 3D fidelity throughout the optimization process.
Figure 4: Qualitative comparison of reconstruction results. Slice examples of different methods with PSNR (dB) shown at the bottom right of each image. The up three rows are from the TDSC-ABUS dataset [ 24 ] and the down three rows are from the rDL-LSM dataset [ 30 ] . Our method shows superior performance in modeling different regions (e.g. breast fibroglandular tissues and tumors) while preserving finer details compared to existing approaches.
Method
ABUS
rDL-LSM
TNNI1
hiPSC
Tribolium
PSNR ↑
SSIM ↑
Time ↓
PSNR ↑
SSIM ↑
Time ↓
PSNR ↑
SSIM ↑
Time ↓
PSNR ↑
SSIM ↑
Time ↓
PSNR ↑
SSIM ↑
Time ↓
HEVC [ 34 ]
29.67
0.729
-
29.34
0.615
-
35.76
0.863
-
19.73
0.450
-
35.51
0.710
-
INIF [ 8 ]
24.84
0.608
1h24m
17.54
0.372
54m
30.89
0.826
27m
18.49
0.322
29m
31.55
0.517
27m
CoordNet [ 12 ]
23.32
0.517
60m
31.98
0.631
47m
30.12
0.827
32m
24.78
0.627
60m
29.42
0.687
46m
NeurComp [ 22 ]
19.85
0.341
2h41m
30.32
0.602
52m
39.25
0.915
11m
21.61
0.670
43m
32.59
0.719
21m
3DGS [ 14 ]
27.41
0.794
24m
28.63
0.749
10m
38.17
0.931
12m
20.15
0.522
26m
27.81
0.715
1h4m
Table 1: 2D quantitative comparison of GaussianPile and other methods.
Method
ABUS
rDL-LSM
TNNI1
hiPSC
Tribolium high
Tribolium low
Tribolium very low
Mem. ↓
Comp. ↑
Mem. ↓
Comp. ↑
Mem. ↓
Comp. ↑
Mem. ↓
Comp. ↑
Mem. ↓
Comp. ↑
Mem. ↓
Comp. ↑
Mem. ↓
Comp. ↑
INIF [ 8 ]
7.8
15 ×
4.9
15 ×
1.8
18 ×
4.7
15 ×
3.1
16 ×
3.1
16 ×
3.1
16 ×
CoordNet [ 12 ]
10.7
11 ×
5.2
14 ×
3.2
10 ×
5.5
13 ×
5.6
9 ×
5.6
9 ×
5.6
9 ×
NeurComp [ 22 ]
7.4
16 ×
4.5
16 ×
2.0
16 ×
4.5
16 ×
3.0
16 ×
3.0
16 ×
3.0
16 ×
3DGS [ 14 ]
691.7
0.2 ×
50.2
1.5 ×
10.6
3 ×
173.6
0.4 ×
28.2
1.7 ×
378.4
0.1 ×
45.0
1.1 ×
Ours w/o Quant.
49.8
2 ×
22.6
3 ×
9.7
3 ×
21.8
3 ×
9.3
5 ×
11.3
4 ×
11.0
4 ×
Table 2: Compression comparison of GaussianPile and other methods. Memory size is reported in megabytes (MB).
Method
ABUS
rDL-LSM
TNNI1
hiPSC
Tribolum
PSNR
SSIM
PSNR
SSIM
PSNR
SSIM
PSNR
SSIM
PSNR
SSIM
CoordNet [ 12 ]
18.75
0.454
32.03
0.689
29.26
0.716
22.23
0.642
28.56
0.693
NeurComp [ 22 ]
19.38
0.248
31.08
0.586
39.53
0.940
22.54
0.653
32.51
0.667
3DGS [ 14 ]
28.49
0.828
25.39
0.665
26.75
0.780
15.20
0.349
21.46
0.583
Ours
33.22
0.876
34.47
0.814
40.17
0.952
33.73
0.752
35.05
0.860
Table 3: 3D quantitative results of baselines and our method.
Figure 5: Results of 3DGS and our method with PSNR (dB) indicated on each image. We show slices of 3DGS queried from elevational angle (z-axis). Although 3DGS can produce plausible 2D projections, its reconstructed volume exhibits poor quality.
Tribolium high
PSNR ↑
SSIM ↑
Time ↓
Gau.
σz=δz/10
34.25
0.927
8m9s
215k
σz=δz/2
36.44
0.942
8m18s
214k
σz=δz
36.67
0.944
7m23s
211k
σz=2δz
36.12
0.940
8m8s
162k
σz=10δz
23.05
0.858
9m17s
66k
M=50k
34.12
0.932
7m28s
85k
Table 4: Ablation results with our choices in bold.
Figure 6: Qualitative comparison of reconstruction results on three cellular datasets. Slice examples of different methods with PSNR (dB) shown at the bottom of each image.
Figure 7: 3D reconstruction results on cellular datasets, presented by depth-encoded color rendering of volumes.
Figure 8: Convergence analysis of baseline methods and GaussianPile. We visualize the intermediate snapshots at different iterations. GaussianPile shows faster and better convergence.
Figure 9: Qualitative results on industrial CeraMIRScan MIR-OCT data, validating GaussianPile’s applicability to diverse slice-based imaging modalities.
Figure 10: Generalization to highly anisotropic ssEM (CREMI 1 , ISBI12 [ 1 ] , 10×/12.5× anisotropy respectively). We visualize three consecutive slices for each dataset.
Figure 11: Scalability analysis on the large-scale EPFL CA1 EM dataset [ 23 ] .
Method
ISBI12
CREMI
2D PSNR ↑
2D SSIM ↑
3D PSNR ↑
3D SSIM ↑
CR ↑
Time ↓
2D PSNR ↑
2D SSIM ↑
3D PSNR ↑
3D SSIM ↑
CR ↑
Time ↓
CoordNet [ 12 ]
25.19
0.708
24.98
0.715
3 ×
51m
22.66
0.620
20.80
0.589
6 ×
2h34m
NeurComp [ 22 ]
24.45
0.695
25.19
0.728
8 ×
5m
19.81
0.428
17.62
0.333
10 ×
11h
Ours
28.79
0.815
28.98
0.881
8 ×
6m
29.50
0.831
28.27
0.752
10 ×
25m
Table 5: Quantitative comparison on highly anisotropic ssEM datasets. We report 2D slice fidelity, 3D volumetric fidelity, and compression/runtime metrics on ISBI12 [ 1 ] and CREMI 1 .
Recent work has shown that implicit neural representations (INRs) can be trained to effectively compress structured and unstructured volume data, allowing for direct data querying with a reduced memory footprint. However, as existing INRs for unstructured volumes do not encode geometry, they require partial mesh storage for later sampling, limiting achievable compression. At the same time, novel view synthesis methods have shown that explicit collections of 3D Gaussians can be used to accurately visualize volume data. In this work, we introduce an explicit model for volume data compression based on 3D Gaussian primitives. We reinterpret collections of 3D Gaussians as an explicit representation of a scalar field and use a sampling strategy that reconstructs scalar values at spatial locations through weighted aggregation of intersecting Gaussians. We develop optimized CUDA-accelerated pipelines for structured and unstructured model sampling, loss functions that encourage accurate domain encoding by our models, and a novel sampling-error based densification strategy. Our explicit formulation naturally encodes domain geometry, eliminating the need for mesh storage in unstructured volumes and introducing significantly higher compression opportunities. Compared to existing INRs, we demonstrate that our explicit model achieves competitive reconstruction quality with significant training speedups on structured volumes, while markedly outperforming in all metrics on unstructured volumes.
3D Gaussian Splat (3DGS) enables high-fidelity, real-time novel view synthesis by representing scenes with large sets of anisotropic primitives, but often requires millions of Splats, incurring significant storage and transmission costs. Most existing compression methods rely on GPU-intensive post-training optimization with calibrated images, limiting practical deployment. We introduce NanoGS, a training-free and lightweight framework for Gaussian Splat simplification. Instead of relying on image-based rendering supervision, NanoGS formulates simplification as local pairwise merging over a sparse spatial graph. The method approximates a pair of Gaussians with a single primitive using mass preserved moment matching and evaluates merge quality through a principled merge cost between the original mixture and its approximation. By restricting merge candidates to local neighborhoods and selecting compatible pairs efficiently, NanoGS produces compact Gaussian representations while preserving scene structure and appearance. NanoGS operates directly on existing Gaussian Splat models, runs efficiently on CPU, and preserves the standard 3DGS parameterization, enabling seamless integration with existing rendering pipelines. Experiments demonstrate that NanoGS substantially reduces primitive count while maintaining high rendering fidelity, providing an efficient and practical solution for Gaussian Splat simplification. Our project website is available at https://saliteta.github.io/NanoGS/.
Butian Xiong, Rong Liu, Tiantian Zhou +3
USC Institute for Creative Technologies · Texas A&M University
Medical image visualization requires volumetric rendering algorithms that preserve anatomical fidelity while maintaining high rendering speeds. To address the high computational cost of large volumetric datasets, we propose a Gaussian-based volumetric representation for efficient visualization of dense medical volumes without compromising structural and radiometric details. We optimize the proposed representation using Monte Carlo volumetric estimation, which enables training on a highly sparse subset of voxels while maintaining consistency with the dense volumetric objective. In addition, we introduce a curriculum learning strategy that progressively incorporates structured slice-based sampling during training. Sparse voxel samples provide an early global coverage of the volume, while slice samples capture spatially correlated regions that aid geometric structure and texture continuity. This combination enables the Gaussian representation to learn anatomical details of various structures and corresponding textures from sparse supervision while significantly reducing the computational cost associated with dense voxel processing. The learned representation supports slice-based rendering methods such as shear-warp volume rendering, enabling efficient visualization of multimodal medical datasets including MRI and Cryosection volumes while preserving anatomical structures. Using sparse supervision, our method achieves up to 43.86 FPS rendering with a compression ratio of 11.31:1.
Mayuri Mathur, Ojaswa Sharma
Indraprastha Institute of Information Technology Delhi · Indraprastha Institute of Information Technology Delhi, New Delhi, India