Frequency-Aware Dual-Stream Learning for Balanced Realism and Fidelity in Electron Microscopy Imaging

Electron microscopy enables nanoscale cellular visualization but faces a trade-off between imaging resolution and acquisition speed. Existing learning-based methods rely on single-stream architectures that struggle to balance perceptual realism and quantitative fidelity, either over-smoothing details or generating unrealistic hallucinations. This work introduces a frequency-adaptive dual-stream architecture to resolve this conflict. Using discrete wavelet transform, we decompose images into low-frequency structures and high-frequency details, then employ a conditional diffusion model for realistic global synthesis and a transformer network for precise detail recovery. Experiments on the EMDiffuse dataset show the method achieves superior LPIPS and resolution ratio, substantially outperforming existing approaches. The method also shows strong generalization across diverse biological samples, supporting fast and reliable electron microscopy imaging for structural biology and nanotechnology applications. The source code and associated dataset are publicly available to facilitate further research.

ConnectomeBench2: A Unified Benchmark for Automated Connectomic Proofreading

Proofreading--correcting segmentation errors in 3D brain reconstructions--is the rate-limiting step in synapse-resolution connectomics. We release ConnectomeBench2, a unified multi-species dataset of over 716,485 expert-labeled proofreading decisions with >4,500,000 associated images spanning four major open connectomes (mouse, human, zebrafish, fly), spanning both split and merge error correction. Trained on this dataset, a single Vision Transformer with shared encoders for mesh geometry and electron microscopy reaches human-level accuracy across species for split error correction and merge error identification, with performance scaling with data size and modality. Beyond accuracy, we show that the model is well-calibrated within distribution, that measures of distribution distance predict where calibration and accuracy will degrade on unseen data, and that connectomics-specific pretraining and active learning-based sample selection show potential to substantially reduce the labeling effort needed to extend to new species and brain regions. The benchmark provides the infrastructure to train and evaluate increasingly capable vision models for connectomic proofreading. Data and code availability. The ConnectomeBench2 dataset is released on Hugging Face at https://huggingface.co/datasets/jeffbbrown2/ConnectomeBench2. The accompanying codebase is available on GitHub at https://github.com/timfarkas/ConnectomeBench2.

CRIS: Cross-Plane Self-Supervised Isotropic Restoration for Anisotropic Volumetric Imaging Across Modalities

Anisotropic volumetric acquisitions are common in clinical MRI and volume electron microscopy (vEM), where sparse through-plane sampling creates thick slices or sections that degrade orthogonal reformats and downstream analysis. We present CRIS, a cross-plane self-supervised framework for isotropic restoration without paired isotropic ground truth. CRIS casts 3D restoration as 2D stripe completion on orthogonal reformats of an isotropic grid: high-resolution in-plane slices are synthetically degraded and periodically masked for training, while at inference blank slices define the isotropic grid, two orthogonal reformats are restored, and predictions are fused by multi-view averaging. We evaluate CRIS on two MRI cohorts and two microscopy benchmarks up to 8x anisotropy. On brain MRI, CRIS achieves 32.921 +/- 0.436 dB PSNR and 0.963 +/- 0.003 SSIM, outperforming interpolation, ECLARE, SMORE4, SIMPLE, SA-INR, and ATME, and gives the best segmentation consistency (Dice 0.940 +/- 0.004, ASSD 0.245 +/- 0.014 mm, HD99 1.275 +/- 0.061 mm). On reference-free abdominal MRI, CRIS reduces FID/KID to 48.71/0.023, outperforming interpolation, ECLARE, SMORE4, and SIMPLE. On vEM, CRIS achieves 29.100 dB/0.830 3D PSNR/SSIM at 4x and 26.874 dB/0.722 at 8x on EPFL, and 21.935 +/- 0.437 dB/0.696 +/- 0.024 on noisy hemibrain data. In a dedicated robustness experiment, one variable-gap CRIS model evaluated across gap factors 3-7 and coronal, axial, and sagittal degradations maintained higher PSNR/SSIM than interpolation (36.36-31.14 dB and 0.977-0.932 vs. 33.07-27.85 dB and 0.951-0.853). These results support CRIS as a modality-flexible route to isotropic restoration without paired isotropic targets or configuration-specific retraining. Code is available at https://github.com/adi-hatav/CRIS.