Brain Imaging Python Packages

nibabel

Python package to access a cacophony of neuro-imaging file formats

nipype

Workflows and interfaces for neuroimaging packages

nilearn

Machine learning for NeuroImaging in Python

templateflow

A python client to query TemplateFlow via pyBIDS

nireports

The NiPreps' Reporting and Visualization system - report templates and "reportlets"

netneurotools

Useful tools from the Network Neuroscience Lab

tedana

TE-dependent analysis of multi-echo fMRI

snirf

Python package for reading, writing and validating Shared Near Infrared Spectroscopy Format (SNIRF) files

fmriprep

fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.

fmriprep-docker

fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.

deepslice

A python package which aligns histology to the Allen Brain Atlas and Waxholm rat atlas using deep learning.

neuromaps

A toolbox for comparing brain maps

clinicadl

Python library for the reproducible processing of neuroimaging data with deep learning methods

explorepy

Python API for Mentalab biosignal aquisition devices

nidataset

Python package to manage NIfTI images dataset

frat-brain

An analysis tool that uses per-voxel statistical maps in conjunction with FSL atlases to create per-region statistical maps. Current usage includes the creation of regional maps of temporal signal to noise ratio.

nipype-ancp

Workflows and interfaces for neuroimaging packages

convert-source

Converts and organises source MR image data-sets in accordance with the Brain Imaging Data Structure (BIDS)

pysnirf2

Python package for reading, writing and validating Shared Near Infrared Spectroscopy Format (SNIRF) files

quicknat-pytorch

QuickNAT, Brain segmentation.

niftiview

View volumetric images in Python 🧠

mni-to-atlas

A simple Python-based tool for finding brain atlas regions based on MNI coordinates.

niftiai

Train neural nets on 3D images (e.g. MRIs) 🧠

niftiview-app

Standalone app for viewing volumetric images 🧠 based on Python