Faubert Andre C, Wang Shang
Department of Biomedical Engineering, Stevens Institute of Technology, Hoboken, NJ 07030, United States.
Bioinformatics. 2024 Dec 26;41(1). doi: 10.1093/bioinformatics/btae761.
Time-lapse 3D imaging is fundamental for studying biological processes but requires software able to handle terabytes of voxel data. Although many multidimensional viewing applications exist, they mostly lack support for heterogeneous voxel counts, datatypes, and modalities in a single timeline. Open Chrono-Morph Viewer provides a straightforward graphical user interface to quickly investigate multi-timescale datasets represented as separate volume files in the common NRRD format for compatibility between toolchains. It features dynamic clipping surfaces for rapid investigation of 3D morphology and a scriptable animation API for quantitative, repeatable, publication-quality visualization. It is implemented in pure Python using common libraries to facilitate community-driven development.
OCMV is available at https://github.com/ShangWangLab/OpenChronoMorphViewer for Windows, Linux, and macOS. Supporting tutorials, documentation, and installation instructions can be found in the supplementary information. Our modified Fiji I/O plugin for up to 5D NRRD file conversion is available at https://github.com/afaubert/IO.
延时三维成像对于研究生物过程至关重要，但需要能够处理数TB体素数据的软件。尽管存在许多多维查看应用程序，但它们大多缺乏对单个时间轴上异构体素计数、数据类型和模态的支持。开放式时间形态查看器提供了一个直观的图形用户界面，可快速研究以常见NRRD格式表示为单独体积文件的多时间尺度数据集，以实现工具链之间的兼容性。它具有动态裁剪表面，可快速研究三维形态，还有一个可编写脚本的动画应用程序编程接口，用于进行定量、可重复、具有发表质量的可视化。它使用通用库以纯Python实现，以促进社区驱动的开发。
OCMV可在https://github.com/ShangWangLab/OpenChronoMorphViewer上获取，适用于Windows、Linux和macOS。支持教程、文档和安装说明可在补充信息中找到。我们修改后的用于高达5D NRRD文件转换的Fiji I/O插件可在https://github.com/afaubert/IO上获取。
