sbonaretti/pyKNEEr

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

Jupyter NotebookGPL-3.0

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:

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):

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

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