compay-syntax 0.4.1

Syntax - the arrangement of whole-slide-images and their image tiles to create well-formed computational pathology pipelines.

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Quick Start

Tissue mask and tiling pipeline

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'])

Install

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