Nutil: A Pre- and Post-processing Toolbox for Histological Rodent Brain Section Images

被引：37

作者：

Groeneboom, Nicolaas E. ^{[1
]}

Yates, Sharon C. ^{[1
]}

Puchades, Maja A. ^{[1
]}

Bjaalie, Jan G. ^{[1
]}

机构：

[1] Univ Oslo, Inst Basic Med Sci, Neural Syst Lab, Oslo, Norway

来源：

FRONTIERS IN NEUROINFORMATICS | 2020年 / 14卷

基金：

欧盟地平线“2020”;

关键词：

image processing; rodent atlas; brain; QuickNII; QUINT; workflow; WAXHOLM SPACE ATLAS; RECONSTRUCTION; MAPS;

D O I：

10.3389/fninf.2020.00037

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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 designedNutil, 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.Nutilcurrently 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 theQuickNIIsoftware 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. TheNutilsoftware is made available by the Human Brain Project (https://www.humanbrainproject.eu) at https://www.nitrc.org/projects/nutil/.

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