Nifti Python Packages

nibabel

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

dcm2niix

dcm2nii DICOM to NIfTI converter: compiled versions available from NITRC

med-imagetools

Transparent and reproducible medical image processing pipelines in Python.

auxiliary

helpful functions for handling biomedical-imaging data in DICOM or NIfTI format

zarrnii

Package for working with OME-Zarr and NIFTI images in a unified manner, with a focus on spatial transformations

imio

Loading and saving of image data.

niivue-streamlit

A Streamlit component for NiiVue neuroimaging viewer

nii2dcm

nii2dcm: NIfTI to DICOM creation with Python

data-tracking

This project contains scripts to extract metadata from DICOM files, NIFTI files and spreadsheets, and import them into a database.

vids-validator

Open standard for structuring, validating, and delivering annotated medical imaging datasets for AI/ML

som

Stanford open modules for python

convert-source

Convert source DICOM, PAR REC or NIFTI image data to BIDS directory layout

nekton

A python package for DICOM to NifTi and NifTi to DICOM-SEG and GSPS conversion

nii2png

🖼 A lightweight neuroimaging .nii to .png converter for Matlab and Python users

niftiai

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

pyvoxel

Fast Pythonic data structures and tools for wrangling medical images.

erwin

Toolbox to generate quantitative maps from MRI images

nii-info

Display NIfTI image information in a tabular format

batch-niistats

Calculate descriptive statistics for large numbers of 3D .nii files and return the output as a .csv file. Pure python code that works very quickly on all operating systems.

retinex-for-mri

Retinex algorithm for MRI data.

biswebpython

This is the repository for the BioImage Suite Web Project

pydcm2niix

DCM2NIIX Python package

zarrnii-plugin-api

Package for working with OME-Zarr and NIFTI images in a unified manner, with a focus on spatial transformations

iphigen

A command-line program for n-dimensional image enhancement and color balancing.