cellcoloc 0.0.1__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- cellcoloc/__init__.py +111 -0
- cellcoloc/analysis.py +1163 -0
- cellcoloc/config.py +280 -0
- cellcoloc/filtering.py +392 -0
- cellcoloc/io.py +397 -0
- cellcoloc/roi.py +169 -0
- cellcoloc/runtime.py +162 -0
- cellcoloc/schemas.py +143 -0
- cellcoloc/segmentation.py +589 -0
- cellcoloc/visualization.py +440 -0
- cellcoloc-0.0.1.dist-info/METADATA +316 -0
- cellcoloc-0.0.1.dist-info/RECORD +14 -0
- cellcoloc-0.0.1.dist-info/WHEEL +4 -0
- cellcoloc-0.0.1.dist-info/licenses/LICENSE +674 -0
cellcoloc/__init__.py
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"""Reusable core pipeline for interactive segmentation-based colocalization.
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The package is intentionally structured so that project-specific user scripts
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can stay small: they define settings, call the imported pipeline functions cell
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by cell, and write all outputs to a standardized ``results`` directory located
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next to the source dataset.
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author: Fabrizio Musacchio
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date: May/June 2026
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"""
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from __future__ import annotations
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from .runtime import get_runtime_cache_root, prepare_runtime_environment
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prepare_runtime_environment()
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from .analysis import (
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analyze_existing_masks,
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build_positive_cell_mask,
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prepare_loaded_images_for_analysis,
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refine_run_result_from_cellpose_cache,
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run_roi_cellpose_colocalization,
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)
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from .config import (
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CellposeModelConfig,
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ChannelConfig,
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ColocalizationConfig,
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DisplayNames,
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OptionalRegionSegmentationConfig,
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RuntimeConfig,
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)
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from .io import (
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build_results_paths,
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export_analysis_outputs,
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load_analysis_images,
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load_roi_labels,
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save_roi_labels,
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try_load_roi_labels,
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)
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from .roi import (
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create_full_image_roi_labels,
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create_roi_drawing_viewer,
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get_bbox_2d,
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get_roi_label_points,
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rasterize_shapes_to_labelmask,
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save_roi_labels_from_shapes,
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)
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from .schemas import (
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ColocalizationRunResult,
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ColocalizationTables,
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LoadedImageChannels,
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OptionalRegionSegmentationResult,
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ResultsPaths,
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)
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from .segmentation import (
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create_cellpose_model,
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create_cellpose_models_for_channels,
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evaluate_cellpose_model,
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filter_labels_by_size,
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get_cellpose_major_version,
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get_available_cellpose_model_names,
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relabel_with_offset,
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segment_optional_region,
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)
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from .visualization import show_analysis_results, show_optional_region_segmentation
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from .visualization import extract_label_masks_from_viewer
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__all__ = [
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"CellposeModelConfig",
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"ChannelConfig",
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"ColocalizationConfig",
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"DisplayNames",
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"OptionalRegionSegmentationConfig",
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"RuntimeConfig",
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"ResultsPaths",
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"LoadedImageChannels",
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"OptionalRegionSegmentationResult",
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"ColocalizationTables",
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"ColocalizationRunResult",
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"build_results_paths",
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"load_analysis_images",
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"save_roi_labels",
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"load_roi_labels",
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"try_load_roi_labels",
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"export_analysis_outputs",
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"analyze_existing_masks",
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"prepare_loaded_images_for_analysis",
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"prepare_runtime_environment",
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"get_runtime_cache_root",
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"create_full_image_roi_labels",
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"rasterize_shapes_to_labelmask",
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"create_roi_drawing_viewer",
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"save_roi_labels_from_shapes",
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"get_bbox_2d",
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"get_roi_label_points",
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"create_cellpose_model",
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"create_cellpose_models_for_channels",
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"evaluate_cellpose_model",
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"relabel_with_offset",
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"filter_labels_by_size",
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"get_cellpose_major_version",
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"get_available_cellpose_model_names",
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"segment_optional_region",
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"run_roi_cellpose_colocalization",
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"refine_run_result_from_cellpose_cache",
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"build_positive_cell_mask",
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"extract_label_masks_from_viewer",
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"show_optional_region_segmentation",
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"show_analysis_results",
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]
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