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

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pyKNEEr

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



📣 pyKNEEr IS UNDER REFACTORING AND EXTENSION! STAY TUNED!




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

Video


Contributors

Project and new code:

Open source code included in pyKNEEr:

User feedbacks and suggestions for improvements:

  • Tijmen Van Zadelhoff
  • Piyush Kumar Prajapati
  • Tadiwa Waungana

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

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

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