用GPU加速生物图像处理,让科研分析更快更顺手。
cubic: CUDA-accelerated 3D Bioimage Computing
- 基于CuPy和cuCIM,无缝对接SciPy/scikit-image API
- 2D/3D图像处理速度显著提升,保持算法准确性
- 适合需要高速分析的生物成像研究者使用
多维生物图像的定量分析有助于理解复杂细胞表型并推动生物医学研究。随着现代显微镜生成越来越大的2D和3D数据集,现有计算方法在可扩展性、效率及与现代科学计算工作流集成方面日益受限。现有生物图像分析工具常缺乏应用编程接口(API)、不支持图形处理器(GPU)加速、3D图像处理能力有限,或在计算密集型任务中互操作性差。本文介绍cubic,一个开源Python库,通过将广泛使用的SciPy和scikit-image API与CuPy和RAPIDS cuCIM提供的GPU加速替代方案结合,解决上述问题。cubic的API具备设备无关性,当数据位于设备上时自动调度至GPU执行,否则在CPU上运行,从而无缝加速广泛的图像处理流程。该方法可实现从预处理到分割和特征提取的全流程加速,涵盖2D和3D数据。我们通过基准测试单个操作及复现现有的去卷积与分割流程验证了其性能,实现了显著提速且保持算法保真度。这些进展为可扩展、可复现的生物图像分析奠定了坚实基础,并与更广泛的Python科学计算生态(包括其他GPU加速方法)集成,支持交互式探索与自动化高通量分析。cubic可在https://github.com/alxndrkalinin/cubic公开获取。
原文摘要 · Abstract (English)
Quantitative analysis of multidimensional biological images is useful for understanding complex cellular phenotypes and accelerating advances in biomedical research. As modern microscopy generates ever-larger 2D and 3D datasets, existing computational approaches are increasingly limited by their scalability, efficiency, and integration with modern scientific computing workflows. Existing bioimage analysis tools often lack application programmable interfaces (APIs), do not support graphics processing unit (GPU) acceleration, lack broad 3D image processing capabilities, and/or have poor interoperability for compute-heavy workflows. Here, we introduce cubic, an open-source Python library that addresses these challenges by augmenting widely used SciPy and scikit-image APIs with GPU-accelerated alternatives from CuPy and RAPIDS cuCIM. cubic's API is device-agnostic and dispatches operations to GPU when data reside on the device and otherwise executes on CPU, seamlessly accelerating a broad range of image processing routines. This approach enables GPU acceleration of existing bioimage analysis workflows, from preprocessing to segmentation and feature extraction for 2D and 3D data. We evaluate cubic both by benchmarking individual operations and by reproducing existing deconvolution and segmentation pipelines, achieving substantial speedups while maintaining algorithmic fidelity. These advances establish a robust foundation for scalable, reproducible bioimage analysis that integrates with the broader Python scientific computing ecosystem, including other GPU-accelerated methods, enabling both interactive exploration and automated high-throughput analysis workflows. cubic is openly available at https://github$.$com/alxndrkalinin/cubic
Thank you to arXiv for use of its open access interoperability. PaperDance 不是 arXiv 官方产品;中文卡片由大模型生成,请以原文为准。