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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
uniGradICON
Accurate, easy registration using a pretrained foundation model
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
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