Contents

pyluna-pathology.luna.pathology.cli package

Submodules

pyluna-pathology.luna.pathology.cli.collect_tile_segment module

luna.pathology.cli.collect_tile_segment.collect_tile_with_datastore(app_config: str, datastore_id: str, method_data: dict)[source]

Save tiles as a parquet file.

Save tiles as a parquet file, indexed by slide id, address, and optionally patient_id.

Parameters

  • app_config (string) – path to application configuration file.

  • datastore_id (string) – datastore name. usually a slide id.

  • method_data (dict) – method parameters including input, output details.

Returns

None

pyluna-pathology.luna.pathology.cli.extract_slide_texture_features module

pyluna-pathology.luna.pathology.cli.generate_tile_labels module

pyluna-pathology.luna.pathology.cli.infer_tile_labels module

pyluna-pathology.luna.pathology.cli.load_slide module

luna.pathology.cli.load_slide.load_slide_with_datastore(app_config, datastore_id, method_data)[source]

Load a slide to the datastore from the whole slide image table.

Parameters

  • app_config (string) – path to application configuration file.

  • datastore_id (string) – datastore name. usually a slide id.

  • method_data (dict) – method parameters including input, output details.

Returns

None

pyluna-pathology.luna.pathology.cli.visualize_tile_labels module

Module contents

Created on April 27, 2021

@author: pashaa@mskcc.org