PDF(Pubmed)
Abstract：
The management and processing of synchrotron and neutron computed tomography data can be a complex, labor-intensive and unstructured process. Users devote substantial time to both manually processing their data (i.e. organizing data/metadata, applying image filters etc.) and waiting for the computation of iterative alignment and reconstruction algorithms to finish. In this work, we present a solution to these problems: TomoPyUI, a user interface for the well known tomography data processing package TomoPy. This highly visual Python software package guides the user through the tomography processing pipeline from data import, preprocessing, alignment and finally to 3D volume reconstruction. The TomoPyUI systematic intermediate data and metadata storage system improves organization, and the inspection and manipulation tools (built within the application) help to avoid interrupted workflows. Notably, TomoPyUI operates entirely within a Jupyter environment. Herein, we provide a summary of these key features of TomoPyUI, along with an overview of the tomography processing pipeline, a discussion of the landscape of existing tomography processing software and the purpose of TomoPyUI, and a demonstration of its capabilities for real tomography data collected at SSRL beamline 6-2c.
摘要：
同步加速器和中子计算机断层扫描数据的管理和处理可能是复杂的，劳动密集型和非结构化过程。用户投入大量时间来手动处理他们的数据（即组织数据/元数据，应用图像过滤器等。），并等待迭代对齐和重建算法的计算完成。在这项工作中,我们提出了解决这些问题的方法：TomoPyUI，用于众所周知的断层摄影数据处理包TomoPy的用户界面。这个高度可视化的Python软件包指导用户通过层析成像处理管道从数据导入，预处理,对齐，最后进行3D体积重建。TomoPyUI系统的中间数据和元数据存储系统改善了组织，以及检查和操作工具（在应用程序中内置）有助于避免工作流中断。值得注意的是,TomoPyUI完全在Jupyter环境中运行。在这里，我们提供了TomoPyUI的这些关键功能的摘要，以及层析成像处理管道的概述，讨论了现有层析成像处理软件的概况和TomoPyUI的目的，并演示了其在SSRL光束线6-2c上收集的真实层析成像数据的能力。
