https://github.com/jgamper/compay-syntax

:microscope: Syntax - the arrangement of whole-slide-images and their image tiles to create well-formed computational pathology pipelines.
https://github.com/jgamper/compay-syntax

computational-pathology medical-imaging openslide pathology-image slide-images whole-slide-image whole-slide-imaging wsis

Last synced: about 1 month ago
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:microscope: Syntax - the arrangement of whole-slide-images and their image tiles to create well-formed computational pathology pipelines.

• Host: GitHub
• URL: https://github.com/jgamper/compay-syntax
• Owner: jgamper
• License: mit
• Created: 2018-02-08T18:29:21.000Z (almost 7 years ago)
• Default Branch: master
• Last Pushed: 2022-11-22T06:22:15.000Z (about 2 years ago)
• Last Synced: 2024-10-22T09:49:07.315Z (2 months ago)
• Topics: computational-pathology, medical-imaging, openslide, pathology-image, slide-images, whole-slide-image, whole-slide-imaging, wsis
• Language: Python
• Homepage:
• Size: 43.5 MB
• Stars: 55
• Watchers: 3
• Forks: 1
• Open Issues: 6
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

• awesome-pathology - compay-syntax - Tissue mask and tiling pipeline. (Software / Image IO)

README

        


    


    

    






    

        

    

    

        

    

    

        

    



# Help building our code and community!

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* All contributions are welcome! Please raise an issue for a bug, feature or pull request!

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# 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'])

```



    



# 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

```