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from syntax.slide import Slide from syntax.transformers.tissue_mask import OtsuTissueMask from syntax.transformers.tiling import SimpleTiling from syntax.transformers import Pipeline, visualize_pipeline_results slide = 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/bash
sudo apt-get install openslide-tools
pip install openslide-python