Recent advances in volumetric super-resolution (SR) have demonstrated strong performance in medical and scientific imaging, with transformer- and CNN-based approaches achieving impressive results even at extreme scaling factors. In this work, we show that much of this performance stems from training on downsampled data rather than real low-resolution scans. This reliance on downsampling is partly driven by the scarcity of paired high- and low-resolution 3D datasets. To address this, we introduce VoDaSuRe, a large-scale volumetric dataset containing paired high- and low-resolution scans. When training models on VoDaSuRe, we reveal a significant discrepancy: SR models trained on downsampled data produce substantially sharper predictions than those trained on real low-resolution scans, which smooth fine structures. Conversely, applying models trained on downsampled data to real scans preserves more structure but is inaccurate. Our findings suggest that current SR methods are overstated - when applied to real data, they do not recover structures lost in low-resolution scans and instead predict a smoothed average. We argue that progress in deep learning-based volumetric SR requires datasets with paired real scans of high complexity, such as VoDaSuRe. Our dataset and code are publicly available through: https://augusthoeg.github.io/VoDaSuRe/
Figures & tables
Figure 1: Example from VoDaSuRe: (a) volume of bamboo showing the cropped area in red, (b) high resolution crop, (c) 4 × downsampled, (d) scan at 4 × lower resolution, (e) SR of bamboo, (f) SR of cardboard. The top row in (e) and (f) is trained on downsampled HR-LR pairs, the bottom row is trained on actual LR data.
Figure 2: VoDaSuRe sample overview, including zoom-ins shown in red-framed cubes. From left to right: bamboo, cardboard, elm, larch, MDF, oak, cypress, animal bone, human vertebrae, and human femur. High- and low-resolution scans are interleaved in the zoom-in cubes.
Table 1: Overview of volumetric image datasets, including single-resolution and paired multi-resolution datasets. In terms of total corresponding LR-HR voxel pairs and mean volume shape, VoDaSuRe is several times larger than existing paired resolution 3D datasets.
Figure 3: Illustration of our data curation pipeline for VoDaSuRe. We collect multi-resolution nested CT scans of the same sample, after which we crop and register the LR data to the downsampled HR volumes. LR and HR volumes are masked and their intensity histograms are matched. All scans are saved to OME-Zarr with up to four resolution levels, using separate groups for HR, LR, and registered data.
Figure 4: Visual comparison of SR predictions on CTSpine1K, LIDC-IDRI and VoDaSuRe at scale 4× . From top to bottom: CTSpine1K, LIDC-IDRI, VoDaSuRe (downsampled), and VoDaSuRe (registered) – two examples. The LR inputs and corresponding HR ground truth images are shown on the left, separated by the red line.
\Block 2-1 Method
\Block 2-1 CTSpine1K
\Block 2-1 LiTS
\Block 2-1 LIDC-IDRI
\Block 2-1 VoDaSuRe
(Downsampled)
\Block 2-1 VoDaSuRe
(Registered)
Scale 2×
PSNR / SSIM / NRMSE / LPIPS
PSNR / SSIM / NRMSE / LPIPS
PSNR / SSIM / NRMSE / LPIPS
PSNR / SSIM / NRMSE / LPIPS
PSNR / SSIM / NRMSE / LPIPS
HAT
35.94 / .9258 / .0430 / .0571
38.11 / .9713 / .0339 / .0257
33.92 / .9062 / .0419 / .0614
23.32 / .8921 / .1638 / .1571
17.44 / .4755 / .3377 / .4661
RCAN
36.62 / .9282 / .0402 / .0505
39.04 / .9736 / .0309 / .0218
35.01 / .9111 / .0379 / .0549
23.28 / .8687 / .1654 / .1575
17.40 / .4691 / .3337 / .4807
EDDSR
37.04 / .9292 / .0380 / .0597
39.87 / .9752 / .0274 / .0268
34.40 / .9096 / .0395 / .0651
24.86 / .9066 / .1445 / .1563
17.63 / .4755 / .3277 / .4527
Table 2: Quantitative comparison of state-of-the-art SR models on datasets CTSpine1K, LiTS, LIDC-IDRI and VoDaSuRe using downsampled and registered LR input data. The best performance metrics PSNR ↑ / SSIM ↑ / NRMSE ↓ / LPIPS ↓ are highlighted in bold .
\Block 1-1 Training
\Block 1-2 VoDaSuRe (Downsampled)
\Block 1-1 Evaluation
\Block 1-1 VoDaSuRe
(Registered) 2×
\Block 1-1 VoDaSuRe
(Registered) 4×
Method
PSNR / SSIM / NRMSE / LPIPS
PSNR / SSIM / NRMSE / LPIPS
HAT
16.38 / .4806 / .3606 / .5220
14.58 / .3118 / .4445 / .5132
RCAN
16.38 / .4337 / .3644 / .5208
14.57 / .3429 / .4433 / .4894
Table 3: Quantitative results for cross-domain experiments on VoDaSuRe registered and downsampled at 2× and 4× upscaling.
Figure 5: Visualizations from VoDaSuRe. Top row: HR data, middle row: SR predictions using downsampled LR data, bottom row: SR predictions using real LR data. All outputs are obtained at 4× upscaling using RRDBNet3D. Total variation (TV) is shown for each slice.
Figure 6: SR prediction obtained using different combinations of training/test data. From left to right: HR data, training/testing on downsampled data, training/testing on registered data, training on downsampled and testing using registered data. Predictions are obtained using RRDBNet3D at scale 4× .
Figure 9: Ablation experiments on VoDaSuRe.
Figure 10: Visualization of the intensity matching procedure used in VoDaSuRe. The intensity distribution of registered LR slices is adjusted to match the distribution of downsampled HR slices.
Figure 11: LAM comparisons of SR models. Top row: example from CTSpine1K, middle and bottom row: examples from VoDaSuRe. The highest DI ↑ is highlighted in bold .
Figure 12: Diffusion index (DI) averages using datasets CTSpine1K, LiTS and LIDC-IDRI for all SR models. The highest DI ↑ scores for each dataset are highlighted in bold .
Figure 13: Illustration of the data loading pipeline for VoDaSuRe based on the OME-Zarr data format.
Figure 14: Visualizations from VoDaSuRe. From top to bottom: HR data, model predictions using downsampled LR data, model predictions using real LR data, and model predictions obtained by training on downsampled data but evaluating using real LR data input. All outputs are obtained at 4× upscaling using RRDBNet3D. Total variation (TV) is shown for each slice.
Method
\Block 1-1RCAN
\Block 1-1HAT
\Block 1-1EDDSR
\Block 1-1SuperFormer
\Block 1-1MFER
\Block 1-1mDCSRN
\Block 1-1MTVNet
\Block 1-1RRDBNet3D
No. of parameters
15.6M
20.8M
0.8M
20.4M
1.7M
1.7M
67.0M
26.1M
Avg. training time
9.47 h
5.64 h
8.09 h
32.85 h
50.65 h
7.76 h
31.05 h
16.48 h
Table 6: Average training time of SR methods at 4× upscaling. The measured times is the average time to complete 100K training iterations across datasets CTSpine1K, LiTS, LIDC-IDRI and VoDaSuRe.
Figure 15: Evaluation of HR-LR registrations in VoDaSuRe. From left to right: Full HR slice, cropped HR slice, cropped registered LR slice, checkerboard image, and absolute difference image between HR and interpolated LR slice.
Figure 16: Orthogonal slices from VoDaSuRe, including high-resolution (left), registered (middle) and unregistered LR slices (right).
Figure 17: Comparison of spatial frequency distributions for HR images, and SR predictions using downsampled and real LR images from VoDaSuRe using RRDBNet3D at scale 4× . The bottom row shows the log 2 power spectra computed from the FFTs of the corresponding images in the top row. Radially averaged power profiles (right) show the relative distribution of power as a function of spatial frequency.
School of Informatics, Xiamen University Xiamen, China · School of Computer Science and Informatics, Cardiff Universiy Cardiff, England · Faculty of Computing, Harbin Institute of Technology Harbin, China +2