Metadata-Version: 2.4
Name: nipoppy
Version: 0.3.4
Summary: Standardized organization and processing of neuroimaging-clinical datasets
Author: Nipoppy developpers
License: MIT License
        
        Copyright (c) 2022 NeuroDataScience
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
        in the Software without restriction, including without limitation the rights
        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
        copies of the Software, and to permit persons to whom the Software is
        furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all
        copies or substantial portions of the Software.
        
        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
        SOFTWARE.
License-File: LICENSE
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved
Classifier: Operating System :: POSIX
Classifier: Operating System :: Unix
Classifier: Programming Language :: Python
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Software Development
Requires-Python: >=3.9
Requires-Dist: boutiques
Requires-Dist: click
Requires-Dist: pandas
Requires-Dist: pybids!=0.18.0
Requires-Dist: pydantic
Requires-Dist: pydicom!=3.0.0
Requires-Dist: requests
Requires-Dist: rich
Requires-Dist: rich-click
Requires-Dist: typing-extensions
Provides-Extra: dev
Requires-Dist: fids>=0.1.0; extra == 'dev'
Requires-Dist: furo; extra == 'dev'
Requires-Dist: mdit-py-plugins; extra == 'dev'
Requires-Dist: myst-parser; extra == 'dev'
Requires-Dist: packaging; extra == 'dev'
Requires-Dist: pre-commit; extra == 'dev'
Requires-Dist: pytest-cov; extra == 'dev'
Requires-Dist: pytest-mock; extra == 'dev'
Requires-Dist: pytest>=6.0.0; extra == 'dev'
Requires-Dist: sphinx; extra == 'dev'
Requires-Dist: sphinx-autoapi; extra == 'dev'
Requires-Dist: sphinx-click; extra == 'dev'
Requires-Dist: sphinx-copybutton; extra == 'dev'
Requires-Dist: sphinx-design; extra == 'dev'
Requires-Dist: sphinx-github-changelog; extra == 'dev'
Requires-Dist: sphinx-hoverxref; extra == 'dev'
Requires-Dist: sphinx-jsonschema; extra == 'dev'
Requires-Dist: sphinx-togglebutton; extra == 'dev'
Provides-Extra: doc
Requires-Dist: furo; extra == 'doc'
Requires-Dist: mdit-py-plugins; extra == 'doc'
Requires-Dist: myst-parser; extra == 'doc'
Requires-Dist: sphinx; extra == 'doc'
Requires-Dist: sphinx-autoapi; extra == 'doc'
Requires-Dist: sphinx-click; extra == 'doc'
Requires-Dist: sphinx-copybutton; extra == 'doc'
Requires-Dist: sphinx-design; extra == 'doc'
Requires-Dist: sphinx-github-changelog; extra == 'doc'
Requires-Dist: sphinx-hoverxref; extra == 'doc'
Requires-Dist: sphinx-jsonschema; extra == 'doc'
Requires-Dist: sphinx-togglebutton; extra == 'doc'
Provides-Extra: test
Requires-Dist: fids>=0.1.0; extra == 'test'
Requires-Dist: packaging; extra == 'test'
Requires-Dist: pytest-cov; extra == 'test'
Requires-Dist: pytest-mock; extra == 'test'
Requires-Dist: pytest>=6.0.0; extra == 'test'
Provides-Extra: tests
Requires-Dist: fids>=0.1.0; extra == 'tests'
Requires-Dist: packaging; extra == 'tests'
Requires-Dist: pytest-cov; extra == 'tests'
Requires-Dist: pytest-mock; extra == 'tests'
Requires-Dist: pytest>=6.0.0; extra == 'tests'
Description-Content-Type: text/markdown

# Nipoppy

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8084759.svg)](https://doi.org/10.5281/zenodo.8084759)
[![PyPI - Version](https://img.shields.io/pypi/v/nipoppy)](https://pypi.org/project/nipoppy/)
[![License](https://img.shields.io/badge/license-MIT-blue.svg)](https://opensource.org/license/mit)
[![codecov](https://codecov.io/gh/nipoppy/nipoppy/graph/badge.svg?token=SN38ITRO4M)](https://codecov.io/gh/nipoppy/nipoppy)
[![https://github.com/psf/black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://black.readthedocs.io/en/stable/)
[![Documentation Status](https://readthedocs.org/projects/nipoppy/badge/?version=latest)](https://nipoppy.readthedocs.io/en/latest/?badge=latest)

<img alt="Nipoppy logo" src="https://raw.githubusercontent.com/nipoppy/nipoppy/refs/heads/main/logo/logo_square.svg" width=100px style="float:right">

Nipoppy is a lightweight framework for standardized organization and processing of neuroimaging-clinical datasets. Its goal is to help users adopt the
[FAIR](https://www.go-fair.org/fair-principles/) principles
and improve the reproducibility of studies.

The framework includes three components:

1. A protocol for data organization, curation and processing, with steps that include the following:
    - **Organization** of raw data, including conversion of raw DICOMs (or NIfTIs) to [BIDS](https://bids.neuroimaging.io/)
    - **Processing** of imaging data with existing or custom pipelines
    - **Tracking** of data availability and processing status
    - **Extraction** of imaging-derived phenotypes (IDPs) for downstream statistical modelling and analysis

    ![Nipoppy protocol](https://raw.githubusercontent.com/nipoppy/nipoppy/main/docs/source/_static/img/nipoppy_protocol.jpg)

2. A specification for dataset organization that extends the [Brain Imaging Data Structure (BIDS) standard](https://bids.neuroimaging.io/) by providing additional guidelines for tabular (e.g., phenotypic) data and imaging derivatives.

    ![Nipoppy specification](https://raw.githubusercontent.com/nipoppy/nipoppy/main/docs/source/_static/img/nipoppy_specification.jpg)

3. A **command-line interface** and **Python package** that provide user-friendly tools for applying the framework. The tools build upon existing technologies such as the [Apptainer container platform](https://apptainer.org/) and the [Boutiques descriptor framework](https://boutiques.github.io/). Several existing containerized pipelines are supported out-of-the-box, and new pipelines can be added easily by the user.
    - We have also developed a [**web dashboard**](https://digest.neurobagel.org) for interactive visualizations of imaging and phenotypic data availability.
