ORMIR Packages

Here are the Python packages created by members of the ORMIR community
Note: Code standardization across packages is work in progress!

Tissue image analysis

ORMIR XCT

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Segmentation and morphometric analyses of HR-pQCT images

code

ITKIOScanco

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

code

Organ image analysis

OAI analysis 2

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

publication

pyKNEEr

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An open and reproducible workflows to segment and analyze femoral knee cartilage

code jupyter notebooks documentation data publication

Dafne

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Annotate MRI images
and
training machine learning models

code jupyter notebooks documentation publication

Mechanical analysis

Ciclope

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Processing of micro computed tomography data to generate finite element models

code jupyter notebooks data publication

Image data management

Muscle-BIDS

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An open data standard for Muscle MR imaging

code jupyter notebooks data documentation



More packages

Here are some more packages with MSK applications

QMRITools

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A toolbox for analysis of quantitative magnetic resonance imaging data

code