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🔬 Syntax - the arrangement of whole-slide-images and their image tiles to create well-formed computational pathology pipelines.
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jgamper/compay-syntax
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fromsyntax.slideimportSlidefromsyntax.transformers.tissue_maskimportOtsuTissueMaskfromsyntax.transformers.tilingimportSimpleTilingfromsyntax.transformersimportPipeline,visualize_pipeline_resultsslide=Slide(slide_path=slide_path)pipeline=Pipeline([OtsuTissueMask(),SimpleTiling(magnification=40,tile_size=224,max_per_class=10)])slide=pipeline.fit_transform(slide)visualize_pipeline_results(slide=slide,transformer_list=pipeline.transformers,title_list=['Tissue Mask','Random Tile Sampling'])
pip install compay-syntax==0.4.0
You will need to install openslide. This is included in the dependencies so may be automatically installed. If not I found this to help:
#!/bin/bashsudo apt-get install openslide-toolspip install openslide-pythonAbout
🔬 Syntax - the arrangement of whole-slide-images and their image tiles to create well-formed computational pathology pipelines.
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