Metadata-Version: 2.1
Name: compay-syntax
Version: 0.4.1
Summary: Syntax - the arrangement of whole-slide-images and their image tiles to create well-formed computational pathology pipelines.
Home-page: https://github.com/jgamper/compay-syntax
Author: Jevgenij Gamper & Peter Byfield
Author-email: jevgenij.gamper5@gmail.com
License: UNKNOWN
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            <a href="https://github.com/jgamper/compay-syntax/blob/master/LICENSE">
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        # Help building our code and community!
        
        [![](https://sourcerer.io/fame/jgamper/jgamper/compay-syntax/images/0)](https://sourcerer.io/fame/jgamper/jgamper/compay-syntax/links/0)[![](https://sourcerer.io/fame/jgamper/jgamper/compay-syntax/images/1)](https://sourcerer.io/fame/jgamper/jgamper/compay-syntax/links/1)[![](https://sourcerer.io/fame/jgamper/jgamper/compay-syntax/images/2)](https://sourcerer.io/fame/jgamper/jgamper/compay-syntax/links/2)[![](https://sourcerer.io/fame/jgamper/jgamper/compay-syntax/images/3)](https://sourcerer.io/fame/jgamper/jgamper/compay-syntax/links/3)[![](https://sourcerer.io/fame/jgamper/jgamper/compay-syntax/images/4)](https://sourcerer.io/fame/jgamper/jgamper/compay-syntax/links/4)[![](https://sourcerer.io/fame/jgamper/jgamper/compay-syntax/images/5)](https://sourcerer.io/fame/jgamper/jgamper/compay-syntax/links/5)[![](https://sourcerer.io/fame/jgamper/jgamper/compay-syntax/images/6)](https://sourcerer.io/fame/jgamper/jgamper/compay-syntax/links/6)[![](https://sourcerer.io/fame/jgamper/jgamper/compay-syntax/images/7)](https://sourcerer.io/fame/jgamper/jgamper/compay-syntax/links/7)
        
        * All contributions are welcome! Please raise an issue for a bug, feature or pull request!
        
        * <a href="https://twitter.com/share?" class="twitter-share-button" data-text="Check out compay-syntax for custom computational pathology pipelines! " data-url="https://github.com/jgamper/compay-syntax" data-show-count="false">Tweet</a> about this repo!
        
        * Give this repo a star! :star:
        
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        <p>
        
        # Quick Start
        
        ### Tissue mask and tiling pipeline
        ```python
        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'])
        ```
        <p align="center">
            <img src="https://raw.githubusercontent.com/jgamper/compay-syntax/master/docs/source/imgs/simple_pipeline.png?token=ADDZO4ISOOTTRG4MMPNYCXS6ZPXPS" width="600"/>
        <p>
        
        # 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:
        
        ```bash
        #!/bin/bash
        
        sudo apt-get install openslide-tools
        pip install openslide-python
        ```
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3.6
Description-Content-Type: text/markdown
