Software

Here are Python packages and stand-alone software for Tissue level analysis, Organ level analysis, and Data management created by the ORMIR community
You can also find other packages and tools that are available online

Tissue level analysis

Ciclope

Processing of micro computed tomography data to generate finite element models

ITKIOScanco

An ITK module to read and write Scanco microCT .isq files

ORMIR_XCT

Segmentation and morphometric analyses of HR-pQCT images

vtkbone

VTK classes for processing Scanco’s AIM file format




Organ level analysis

ALBA

Agile Library for Biomedical Applications

Dafne

Annotating MRI images and training machine learning models

OAI analysis 2

An open source analysis approach for the OsteoArthitis Initiative (OAI) dataset

pyKNEEr

Segment and analyze femoral knee cartilage images




Data management

MUSCLE-BIDS

An open data standard for Muscle MR imaging

ORMIR-MIDS

An open data standard for MSK imaging




More packages

QMRITools

A toolbox for quantitative magnetic resonance imaging



Cannot find your package or software in this page? Contact us!