pyKNEEr

An image analysis workflow for open and reproducible research on femoral knee cartilage

• See the video on Youtube for presentation, installation, and demo:

• Try pyKNEEr on Binder:

  • Example #1:
  • Example #2:

• Documentation at sbonaretti.github.io/pykneer/

• Paper: S. Bonaretti ,G.E. Gold, G.S. Beaupre pyKNEEr: An image analysis workflow for open and reproducible research on femoral knee cartilage Plos one 15.1 (2020): e0226501.

• Release on Zenodo (with DOI for citation):

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Contributors

Project and new code:

• Serena Bonaretti

Open source code included in pyKNEEr:

• Intensity preprocessing by Liang Shan and Marc Niethammer
• Elastix for registration in atlas-based segmentation by Stefan Klein
• Cylinder fitting for cartilage flattening by https://github.com/xingjiepan/cylinder_fitting

User feedbacks and suggestions for improvements:

• Tijmen Van Zadelhoff
• Piyush Kumar Prajapati
• Tadiwa Waungana

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Changelog

v 0.0.6.3: (Complicated version number due to issues while uploading to Pypi)

• Substituted the filter sitk.BinaryDilate() with the filter sitk.BinaryDilateImageFilter() in the function dilate_mask() of the module sitk_functions (-> Closure of issues 13 and 15)
• Added raise FileNotFoundError in the elastix_transformix module to provide feedback during the registration process

v 0.0.5:

• Solved ITK bug about the Orient function in preprocessing - different way to set direction in ITK4.13
• Added option to show images with slider in notebooks
• Added demo_v3 to Zenodo (added sliders to notebooks)

v 0.0.4:

• Added test functions
• Added relative and absolute imports within pyKNEEr package for easier debug, code extension, and testing
• Changed all variable names to python convention (e.g. from fileName to file_name)
• Improved dependences print outs in notebooks (added pyKNEEr, watermark itself, and date)
• Added demo_v2 to Zenodo (minor changes, listed in Zenodo)
• Added page Development.html in the website

v 0.0.3:

• Reduced mask file size
• Added check to end of string in input .txt files
• Fixing issue with ITK version to download for image orientation in preprocessing
• Added demo_v1 to Zenodo

v 0.0.2:

• Minor

v 0.0.1:

• First release