Data_Sheet_3_Nutil: A Pre- and Post-processing Toolbox for Histological Rodent Brain Section Images.PDF

With recent technological advances in microscopy and image acquisition of tissue sections, further developments of tools are required for viewing, transforming, and analyzing the ever-increasing amounts of high-resolution data produced. In the field of neuroscience, histological images of whole rodent brain sections are commonly used for investigating brain connections as well as cellular and molecular organization in the normal and diseased brain, but present a problem for the typical neuroscientist with no or limited programming experience in terms of the pre- and post-processing steps needed for analysis. To meet this need we have designed Nutil, an open access and stand-alone executable software that enables automated transformations, post-processing, and analyses of 2D section images using multi-core processing (OpenMP). The software is written in C++ for efficiency, and provides the user with a clean and easy graphical user interface for specifying the input and output parameters. Nutil currently contains four separate tools: (1) A transformation toolchain named “Transform” that allows for rotation, mirroring and scaling, resizing, and renaming of very large tiled tiff images. (2) “TiffCreator” enables the generation of tiled TIFF images from other image formats such as PNG and JPEG. (3) A “Resize” tool completes the preprocessing toolset and allows downscaling of PNG and JPEG images with output in PNG format. (4) The fourth tool is a post-processing method called “Quantifier” that enables the quantification of segmented objects in the context of regions defined by brain atlas maps generated with the QuickNII software based on a 3D reference atlas (mouse or rat). The output consists of a set of report files, point cloud coordinate files for visualization in reference atlas space, and reference atlas images superimposed with color-coded objects. The Nutil software is made available by the Human Brain Project (https://www.humanbrainproject.eu) at https://www.nitrc.org/projects/nutil/.

随着显微镜和切片图像采集技术的近期技术进步，对于查看、转换和分析日益增长的高分辨率数据，需要进一步开发相关工具。在神经科学领域，全脑切片的病理图像常被用于研究脑连接以及正常和病变脑中的细胞和分子组织结构，但对于缺乏或有限编程经验的典型神经科学家来说，分析所需的预处理和后处理步骤构成了一个问题。为满足这一需求，我们设计了Nutil，这是一款开放获取且独立的可执行软件，能够通过多核处理（OpenMP）实现二维切片图像的自动化转换、后处理和分析。该软件采用C++编写，以提高效率，并为用户提供简洁易用的图形用户界面，用于指定输入和输出参数。Nutil目前包含四个独立的工具：（1）名为“Transform”的转换工具链，允许对非常大的拼贴TIFF图像进行旋转、镜像、缩放、调整大小和重命名。（2）“TiffCreator”工具能够从PNG和JPEG等其他图像格式生成拼贴TIFF图像。（3）“Resize”工具完善了预处理工具集，允许以PNG格式对PNG和JPEG图像进行下采样。（4）第四个工具是名为“Quantifier”的后处理方法，它能够在基于3D参考图谱（小鼠或大鼠）的脑图谱映射（QuickNII软件生成）定义的区域上下文中，实现对分割对象的量化。输出包括一系列报告文件、用于在参考图谱空间中可视化的点云坐标文件，以及叠加了彩色编码对象的参考图谱图像。Nutil软件由人类脑计划（https://www.humanbrainproject.eu）在https://www.nitrc.org/projects/nutil/提供。