Papers for
brain imaging teams
Papers whose findings have a practical use for this group, as judged from the abstract. Open a paper to read what it means in practice.
Deep learning speeds up electron microscopy brain imaging dramatically
ZoomSEM: accelerating large-scale brain connectomics with intelligent SEM super-resolution
Abstract: Serial electron microscopy (EM) is essential for large-volume biological imaging and connectomics, yet its throughput remains a major bottleneck, with cubic-millimeter-scale brain imaging requiring months or years. Existing deep learning-based EM super-resolution methods are limited to small upscaling factors or rely on synthetic data, offering modest acceleration and limited practical impact. We introduce ZoomSEM, a deep learning-based super-resolution method to dramatically accelerate SEM imaging. Trained on real low- and high-resolution scanning electron microscopy (SEM) pairs, ZoomSEM enables reliable recovery of 4$\times$, 8$\times$, and up to 16$\times$ higher-resolution images from fast low-resolution scans while preserving fine neuronal structures critical for connectomic analysis, achieving up to 30-fold effective acceleration. Extensive experiments across datasets of diverse biological samples demonstrate robust generalization under realistic low-resolution acquisition. This advance enables high-resolution, large-volume serial EM imaging at unprecedented speed, poised to transform connectomics and related fields.
Multimodal model predicts diverse brain responses to stimuli accurately
MultiFlow: Vision-Driven Multimodal fMRI Encoding via Stimulus-Informed Source Flow Matching
Abstract: Current fMRI encoding models frame prediction as deterministic regression, yet identical stimuli evoke a distribution of neural responses (arising from physiological noise, hemodynamic variability, and cognitive fluctuations) that a single point estimate cannot capture. This work introduces MultiFlow, a generative fMRI encoding framework based on Conditional Flow Matching (CFM) and a formulation termed Stimulus-Informed Source Flow Matching (SISFM). SISFM generalises CFM by conditioning the source distribution on the stimulus: a learnable temporal convolution shapes the source mean with an HRF-length receptive field, while a variance head shrinks its scale, shortening the expected transport path. SISFM is instantiated with a Diffusion Transformer (DiT-X) decoder parameterising the velocity field, with sub-layer Attention Residuals, heterogeneous fusion of ten frozen vision, audio, language, and audiovisual backbones, and per-subject Yeo-network heads. On the Algonauts 2025 dataset, a single MultiFlow checkpoint recovers most of the benefit of large deterministic ensembles: it trails the 1000-model TRIBE ensemble in-distribution by 0.003 PCC (0.3163 vs. 0.3195), and the strongest in- and out-of-distribution ensembles (VIBE-20, MedARC-50) by 0.010 and 0.009 PCC, using a single trained model rather than an ensemble of 20-1000. The same checkpoint also provides stimulus-conditioned uncertainty estimates and sample-based diversity.