scip package

Subpackages

• scip.export package
  • Submodules
  • scip.export.anndata module
    • export()
  • scip.export.parquet module
    • export()
• scip.features package
  • compute_features()
  • extract_features()
  • features_partition()
  • Submodules
  • scip.features.bbox module
    • bbox_features()
  • scip.features.intensity module
    • intensity_features()
  • scip.features.raw_intensity module
    • raw_intensity_features()
  • scip.features.shape module
    • shape_features()
  • scip.features.texture module
    • texture_features()
• scip.filter package
  • Submodules
  • scip.filter.threshold module
    • feature_partition()
    • item()
    • predicate()
• scip.illumination_correction package
  • Submodules
  • scip.illumination_correction.jones_2006 module
    • correct()
• scip.loading package
  • load_meta()
  • load_pixels()
  • Submodules
  • scip.loading.czi module
    • get_group_keys()
    • get_loader_meta()
    • load_pixels()
  • scip.loading.multiframe_tiff module
    • bag_from_directory()
    • load_image()
  • scip.loading.tiff module
    • get_group_keys()
    • get_loader_meta()
    • load_pixels()
  • scip.loading.util module
    • get_images_bag()
  • scip.loading.zarr module
    • get_group_keys()
    • get_loader_meta()
    • load_image_partition()
    • load_pixels()
    • reload_image_partition()
• scip.masking package
  • apply_mask_partition()
  • bounding_box_partition()
  • compute_filters()
  • mask()
  • mask_post_process()
  • remove_regions_touching_border_partition()
  • Subpackages
    • scip.masking.filters package
      • Submodules
      • scip.masking.filters.normaltest module
      • scip.masking.filters.std module
      • scip.masking.filters.value_range module
  • Submodules
  • scip.masking.circle module
    • create_masks_on_bag()
    • get_mask()
  • scip.masking.li module
    • create_masks_on_bag()
  • scip.masking.otsu module
    • create_masks_on_bag()
  • scip.masking.sobel module
    • create_masks_on_bag()
    • get_mask()
  • scip.masking.spot module
    • create_masks_on_bag()
  • scip.masking.watershed module
    • create_masks_on_bag()
    • get_mask()
• scip.normalization package
  • Submodules
  • scip.normalization.quantile_normalization module
    • get_distributed_minmax()
    • quantile_normalization()
• scip.projection package
  • project_block_partition()
  • Submodules
  • scip.projection.op module
    • project_block()
• scip.segmentation package
  • export_labeled_mask()
  • segment()
  • to_events()
  • Submodules
  • scip.segmentation.cellpose module
  • scip.segmentation.watershed_dapi module
    • segment_block()
• scip.utils package
  • Submodules
  • scip.utils.util module
    • ClientClusterContext
      • ClientClusterContext.wait()
    • check()
    • configure_logging()
    • copy_without()
    • load_yaml_config()
    • make_output_dir()
    • prerun()

Submodules

scip.main module

scip.main.main(*, paths: List[str], output: Path, config: str, mode: str, limit: int | None = -1, with_replacement: bool | None = False, n_partitions: int | None = 10, n_workers: int | None = 1, n_nodes: int | None = 1, n_cores: int | None = None, n_threads: int | None = 1, memory: int | None = 1, walltime: str | None = None, job_extra: str | None = '', local_directory: str | None = 'tmp', headless: bool | None = False, port: int | None = 8787, debug: bool | None = False, timing: Any | None = None, gpu: int | None = 0, scheduler_adress: str | None = None)