https://github.com/kaczmarj/model-inference-plugin-rdf

Python plugin to write cell segmentation/classification model outputs to RDF file.
https://github.com/kaczmarj/model-inference-plugin-rdf

Last synced: about 2 months ago
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Python plugin to write cell segmentation/classification model outputs to RDF file.

• Host: GitHub
• URL: https://github.com/kaczmarj/model-inference-plugin-rdf
• Owner: kaczmarj
• Created: 2021-09-23T03:04:55.000Z (over 3 years ago)
• Default Branch: main
• Last Pushed: 2023-01-12T15:30:42.000Z (over 2 years ago)
• Last Synced: 2025-02-10T03:22:19.306Z (4 months ago)
• Language: Python
• Size: 34.2 KB
• Stars: 1
• Watchers: 3
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# plugin to create rdf file for cell segmentation/classification model outputs

# Example

In the following example, we initialize the plugin, add a polygon, add a point,

and save the state to disk.

```python

import sbumed_predictions_to_graph

# Initialize the plugin with metadata.

plugin_state = sbumed_predictions_to_graph.State(

    path="predictions.ttl.gz",

    creator="Jakub Kaczmarzyk",

    name="HoverNet Analysis Pipeline",

    github_url="https://github.com/david-belinsky-sbu/Hovernet_modified/commit/6cd610a32472184d6fbf341cb24902c4180ca3e8",

    slide_path="path/to/slide.svs",

    description="multi-class segmentation using HoverNet",

)

# Add polygon to the state.

plugin_state.add(

    cell_type="lymphocyte",

    probability=0.92,

    polygon_coords=[(24, 50), (10, 10), (20, 4), (24, 50)],

)

# Add point to the state.

plugin.state.add(

    cell_type="lymphocyte",

    probability=0.86,

    point=[(25, 10)],

)

# Write the state to disk. This file can be read by viewing software.

plugin_state.write()

```