Biology subjects

Xue, H.-C.

Publications and source records attributed to Xue, H.-C..

2 recordsLinked to original sources

bioRxiv2026

AtlasMap: enabling low-cost, map-style exploration of million-cell single-cell atlases

Interactive visualization is critical for interpreting single-cell atlases, yet existing web-based tools struggle to handle the growing scale of multimillion-cell datasets, often constrained by browser memory limits and rendering latency. Here, we present AtlasMap, a scalable visualization framework that overcomes these bottlenecks through a multi-resolution, tile-based architecture. Unlike conventional systems that transfer cell-level data to the client, AtlasMap employs an offline preprocessing module to generate quadtree-based spatial aggregations stored in compressed Zarr v3 formats. A high-performance Go backend dynamically renders these summaries as PNG tiles, allowing a lightweight frontend to support fluid pan-and-zoom exploration similar to digital geographic maps. Systematic benchmarking against leading tools (including cellxgene and UCSC Cell Browser) demonstrates that AtlasMap decouples visualization performance from dataset size. While point-based approaches incurred prohibitive client-side memory costs or failed entirely at the 11-million-cell scale, AtlasMap maintained sub-second startup latency and a negligible browser footprint (<5 MB). By shifting computational pressure from the browser to an optimized server-side pipeline, AtlasMap enables accessible, high-fidelity exploration of ultra-scale single-cell datasets on standard hardware.

bioinformatics↗

bioRxiv2025

FX-Cell: a method for single-cell RNA sequencing on difficult-to-digest and cryopreserved plant samples

Single-cell RNA sequencing (scRNA-seq) in plants requires the isolation of high-quality protoplasts-- cells devoid of cell walls. However, many plant tissues and organs are resistant to enzymatic digestion, posing a significant barrier to advancing single-cell multi-omics research in plants. Furthermore, for many field-grown crops, the lack of immediate laboratory access presents another major challenge for protoplast preparation. To address these limitations, we developed the FX-Cell method and its derivatives, FXcryo-Cell and cryoFX-Cell, to enable scRNA-seq with both difficult-to-digest and cryopreserved plant samples. By optimizing the fixation buffer and minimizing RNA degradation, our approach ensures efficient cell wall digestion at high temperatures while maintaining high-quality single cells, even after long-term storage at -80{degrees}C, and circumvents use of nuclei, which are not representative of the pool of translatable mRNAs. Using these methods, we successfully constructed high-quality cell atlases for rice tiller nodes, rhizomes of wild rice, and maize crown roots grown in field conditions. Moreover, these methods enable the accurate reconstruction of plant acute wounding responses at single-cell resolution. Collectively, these advancements expand the applicability of plant single-cell genomics across a wider range of species and tissues, paving the way for comprehensive Plant Cell Atlases for plant species.

plant biology↗