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nutil

https://nutil.readthedocs.io/en/latest/

https://github.com/neural-systems-at-uio/nutil

Science Score: 39.0%

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    CITATION.cff file
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    Found codemeta.json file
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    Found .zenodo.json file
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    DOI references
    Found 2 DOI reference(s) in README
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    Academic publication links
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    Scientific vocabulary similarity
    Low similarity (16.6%) to scientific vocabulary
Last synced: 9 months ago · JSON representation

Repository

https://nutil.readthedocs.io/en/latest/

Basic Info
  • Host: GitHub
  • Owner: Neural-Systems-at-UIO
  • License: gpl-3.0
  • Language: C++
  • Default Branch: master
  • Homepage:
  • Size: 241 MB
Statistics
  • Stars: 13
  • Watchers: 8
  • Forks: 7
  • Open Issues: 22
  • Releases: 31
Created over 8 years ago · Last pushed 12 months ago
Metadata Files
Readme License Support Codemeta

README.md

Nutil

Nutil aims to simplify and streamline the mechanism of pre-and-post processing 2D brain imaging data from mouse and rat. It is an integral part of the QUINT workflow for regional quantification of labelled objects such as cells in histological imaging data.

For installation and user instructions see: https://nutil.readthedocs.io/en/latest/

Getting started

Download here on github or from https://www.nitrc.org/projects/nutil/

Nutil is written in C++ using standard Qt libraries, and is optimised for parallel operations on multiple CPUs. Nutil does not require any installation, and does not currently utilise any GPU extensions. The external libraries that are used in Nutil are: - Libtiff for fast and efficient TIFF file handling (http://www.libtiff.org/) - LibXLNT for Excel file I/O (https://github.com/tfussell/xlnt/)

Compiling from source (Windows)

  1. In order to compile from scratch, the following software components are also required:
    • On Windows, Microsoft Visual C++ 2019 compiler (MSVC), community version (https://visualstudio.microsoft.com/vs/features/cplusplus/)
    • On macOS, XCode (Clang)
    • On Linux, Gnu C++ compiler
  2. Download and install Qt Creator for open source users (https://www.qt.io/download) Install the Qt framework version 6 or above (create a user account, custom install, select newest version and MSVC 2019).
  3. Install git (https://desktop.github.com/)
  4. Clone this repository to a folder (in github desktop: file->clone repository)
  5. Open the project file in Qt (file->open file or project)
  6. Set up a build path to the project (projects->build->build directory)
  7. Compile and run! (ctrl+r)

Compiling from source on linux (debian-based)

  1. git clone https://github.com/Neural-Systems-at-UIO/nutil.git
  2. Move to the nutil directory : cd nutil
  3. Install the required packages: sudo apt-get install qt5-default qtchooser
  4. Run Qmake: qmake
  5. Compile: make -j 8 (number of threads)

You can now run Nutil from the command line / bash scripts by simply running ./Nutil myProject.nut 8 or ./Nutil to use the GUI

Acknowledgements

Nutil is an integral part of the QUINT workflow and is developed by the Neural Systems Laboratory at the Institute of Basic Medical Sciences, University of Oslo, Norway. Nutil was developed with support from the EBRAINS infrastructure, and funding from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Framework Partnership Agreement No. 650003 (HBP FPA) and the European Union’s Horizon Europe Programme for Research Infrastructures Grant Agreement No. 101147319 (EBRAINS 2.0).

Authors

Nicolaas E Groeneboom, Sharon C Yates, Maja A Puchades, Gergely Csucs and Jan G Bjaalie.

Licence

  • Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International
  • GNU General Public License v3

Download

  • https://www.nitrc.org/projects/nutil/

Current version

v1.1

Cite

Groeneboom NE, Yates SC, Puchades MA and Bjaalie JG (2020) Nutil: A Pre- and Post-processing Toolbox for Histological Rodent Brain Section Images. Front. Neuroinform. 14:37. doi: 10.3389/fninf.2020.00037

Also described in

Yates SC, Groeneboom NE, Coello C, et al. & Bjaalie JG (2019) QUINT: Workflow for Quantification and Spatial Analysis of Features in Histological Images From Rodent Brain. Front. Neuroinform. 13:75. doi: 10.3389/fninf.2019.00075

Contact us

Report issues here on github or email: support@ebrains.eu

Owner

  • Name: NeSys at UiO
  • Login: Neural-Systems-at-UIO
  • Kind: organization
  • Location: University of Oslo, Norway

Neurale Systemer at UiO

CodeMeta (codemeta.json) 

{
  "@context": "https://w3id.org/codemeta/3.0",
  "type": "SoftwareSourceCode",
  "applicationCategory": "Neurosciences",
  "codeRepository": "https://github.com/Neural-Systems-at-UIO/nutil",
  "contributor": [
    {
      "id": "https://orcid.org/0000-0002-3001-8725",
      "type": "Person",
      "affiliation": {
        "type": "Organization",
        "name": "University of Oslo, Norway"
      },
      "email": "s.c.yates@medisin.uio.no",
      "familyName": "Yates",
      "givenName": "Sharon C."
    },
    {
      "id": "https://orcid.org/0000-0002-4536-8197",
      "type": "Person",
      "affiliation": {
        "type": "Organization",
        "name": "University of Oslo, Norway"
      },
      "email": "m.a.puchades@medisin.uio.no",
      "familyName": "Puchades",
      "givenName": "Maja A."
    },
    {
      "id": "_:contributor_3",
      "type": "Person",
      "familyName": "Groeneboom",
      "givenName": "Nicolaas"
    }
  ],
  "dateCreated": "2019-05-03",
  "dateModified": "2025-01-20",
  "datePublished": "2019-05-03",
  "description": "Nutil is an integral part of the QUINT workflow for regional quantification of labelled objects such as cells in histological imaging data.",
  "downloadUrl": "https://github.com/Neural-Systems-at-UIO/nutil/releases/download/v1.0.11/nutil_win_v1.1.zip",
  "funder": {
    "type": "Organization",
    "name": "EU"
  },
  "identifier": "SCR_017183",
  "keywords": [
    "cell count",
    "atlas",
    "QUINT"
  ],
  "name": "Nutil",
  "operatingSystem": "Windows",
  "programmingLanguage": [
    "C++",
    "C#",
    "Makefile",
    "C",
    "HTML",
    "Pascal"
  ],
  "releaseNotes": "Major Nutil release. This version contains Nutil Quantifier only (Transform has been removed, it will not be supported in future versions).\n\nSupported atlases:\n\n-Allen Mouse Brain Atlas Common Coordinate Framework version 3 (CCFv3) (delineations from 2017 or 2015).\n-Waxholm Atlas of the Spraque Dawley Rat (WHS) (version 2, 3 and 4).\n-Kim Unified Adult Mouse Brain Atlas (version 1, 2019).\n-Developmental Mouse Brain Atlas for ages P4-P56 (DeMBA) with Allen CCFv3 delineations from 2017.\n-Developmental Mouse Brain Atlas for ages P4-P56 (DeMBA) with Kim Lab developmental delineations (KimLabDev CCFv001).\n\nChange log:\n\n-Atlas hierarchy and custom region files are included for all the listed atlases.\n-The \"object_splitting\" feature in Nutil has been renamed to \"Counts or Area Fraction\". The terminology has changed but the calculations are the same as before. To replicate \"Object_splitting\" = no, select \"Counts\". To replicate \"Object_splitting = yes, select \"Area Fraction\".\n-Improved error messaging.\n",
  "version": "1.1",
  "licence": "GPL-3.0 license",
  "funding": "H2020-EU FPA 650003 (HBP FPA) and HORIZON-INFRA (EBRAINS 2.0) 101147319",
  "referencePublication": "https://doi.org/10.3389/fninf.2020.00037"
}

GitHub Events

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Last Year
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Issues and Pull Requests

Last synced: 10 months ago

All Time
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  • Average comments per issue: 1.0
  • Average comments per pull request: 0
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  • Bot issues: 0
  • Bot pull requests: 0
Past Year
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  • Pull requests: 0
  • Average time to close issues: 7 days
  • Average time to close pull requests: N/A
  • Issue authors: 2
  • Pull request authors: 0
  • Average comments per issue: 1.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
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Dependencies

.github/workflows/auto-add-issue-to-proj.yml actions
  • actions/add-to-project main composite
.github/workflows/ebrains.yml actions
  • wei/git-sync v3 composite
.github/workflows/nutil_windows_build.yml actions
  • actions/checkout v2 composite
  • actions/create-release latest composite
  • actions/upload-release-asset v1 composite
  • jurplel/install-qt-action v2 composite
  • mathieudutour/github-tag-action v5.1 composite
  • microsoft/setup-msbuild v1 composite
  • papeloto/action-zip v1 composite