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

Nicolaas E Groeneboom1, Sharon C Yates1, Maja A Puchades1

  • 1Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.

Frontiers in Neuroinformatics
|September 25, 2020
PubMed
Summary

Nutil is new open-access software designed for neuroscientists to easily process and analyze high-resolution 2D brain section images. It automates transformations and quantification, simplifying complex pre- and post-processing tasks.

Keywords:
QUINTQuickNIIbrainimage processingrodent atlasworkflow

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Area of Science:

  • Neuroscience
  • Bioinformatics
  • Computational Biology

Background:

  • Advances in microscopy generate large, high-resolution histological datasets for neuroscience research.
  • Neuroscientists often lack programming expertise for pre- and post-processing these complex image datasets.
  • Existing tools are insufficient for efficient analysis of whole rodent brain sections.

Purpose of the Study:

  • To develop an accessible, stand-alone software tool, Nutil, for automated image processing and analysis in neuroscience.
  • To provide neuroscientists with user-friendly tools for transforming, pre-processing, and quantifying 2D brain section images.
  • To facilitate the analysis of large-scale histological data for studying brain organization and disease.

Main Methods:

  • Nutil is an open-access, stand-alone executable software written in C++ with a graphical user interface.
  • It utilizes multi-core processing (OpenMP) for efficient handling of large image files.
  • Includes four tools: Transform (rotation, scaling, renaming), TiffCreator (format conversion), Resize (downscaling), and Quantifier (object quantification using brain atlas maps).

Main Results:

  • Nutil enables automated transformations, pre-processing (resizing, format conversion), and post-processing (quantification) of 2D histological images.
  • The Quantifier tool integrates with QuickNII software for atlas-based analysis, generating reports and visualization files.
  • The software supports large tiled TIFF images and various common image formats (PNG, JPEG).

Conclusions:

  • Nutil provides a crucial, user-friendly solution for neuroscientists to analyze complex brain imaging data.
  • The software streamlines pre- and post-processing workflows, enhancing research efficiency and accessibility.
  • Nutil is available via the Human Brain Project, promoting open science and collaborative research.