biomedical imaging developers

Abstract: Spatial transcriptomics maps gene expression across tissue sections and, when integrated with whole slide images, jointly captures both morphological architecture and molecular activity to provide a rich, multimodal view of tissue biology. ML approaches combining spatial transcriptomics and WSIs typically learn a mapping from morphological features to molecular profiles via contrastive alignment or supervised fine-tuning of pathology foundation models. In both cases, transcriptomics serves as a training signal rather than a true input modality, leaving inference fundamentally image-driven. We propose an early-fusion vision transformer architecture in which transcript tokens are constructed at arbitrary spatial resolution, merged with image patch tokens, and jointly processed through a shared transformer stack for deep cross-modal interaction. Starting from a pretrained vision-only pathology foundation model, we train HistoTx by continuing self-supervised pretraining on paired image and spatial transcriptomics data and demonstrate that: 1) at inference with image only, performance remains on par with the baseline on most tasks while improving on tasks that inherently benefit from molecular knowledge, such as gene expression prediction; 2) when both modalities are available at inference, jointly providing image and transcript inputs outperforms either modality alone.

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.