PlatiPy
PlatiPy: Processing Library and Analysis Toolkit for Medical Imaging in Python - Published in JOSS (2023)
small_gicp
small_gicp: Efficient and parallel algorithms for point cloud registration - Published in JOSS (2024)
PyCPD
PyCPD: Pure NumPy Implementation of the Coherent Point Drift Algorithm - Published in JOSS (2022)
mrivis
mrivis: Medical image visualization library for neuroscience in python - Published in JOSS (2018)
QMRTools
QMRTools: a Mathematica toolbox for quantitative MRI analysis. - Published in JOSS (2019)
BrainGlobe Atlas API
BrainGlobe Atlas API: a common interface for neuroanatomical atlases - Published in JOSS (2020)
simpleitk
SimpleITK: a layer built on top of the Insight Toolkit (ITK), intended to simplify and facilitate ITK's use in rapid prototyping, education and interpreted languages.
mcmicro
An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.
globalmatch
GlobalMatch: Registration of forest terrestrial point clouds by global matching of relative stem positions [ISPRS 2023]
https://github.com/brainglobe/brainreg-napari
Automated 3D brain registration in napari with support for multiple species and atlases.
https://github.com/dipy/dipy
DIPY is the paragon 3D/4D+ medical imaging library in Python. Contains generic methods for spatial normalization, signal processing, machine learning, statistical analysis and visualization of medical images. Additionally, it contains specialized methods for computational anatomy including diffusion, perfusion and structural imaging.
visualqc
VisualQC : assistive tool to ease the quality control workflow of neuroimaging data.
https://github.com/antsx/antsr
R interface to the ANTs biomedical image processing library
microaligner
Image registration (alignment) software for large microscopy images
https://github.com/ait-assistive-autonomous-systems/2d_nonrigid_tricubic_pointcloud_registration
Prototype implementation of a non-rigid point cloud registration algorithm using piece-wise tricubic polynomials as transformation model.
brainreg
Automated 3D brain registration with support for multiple species and atlases.
craniumpy
A tool for the alignment and basic analysis of 3D meshes, focused on craniofacial applications.
pituitary-segmentation-tool
This repository contains code that normalizes head MRIs segments the pituitary gland.
slicer
Multi-platform, free open source software for visualization and image computing.
https://github.com/ait-assistive-autonomous-systems/3d_nonrigid_tricubic_pointcloud_registration
Non-rigid ICP-like point cloud registration algorithm using piece-wise tricubic polynomials as transformation model.
https://github.com/cea-metrocarac/images_alignment
Application to re-align images