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Merge pull request #650 from fractal-analytics-platform/649-cellpose-…
…options Expand cellpose options
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examples/06_cellpose_dev_example/fetch_test_data_from_zenodo.sh
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| @@ -0,0 +1,5 @@ | ||
| #!/bin/bash | ||
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| DOI="10.5281/zenodo.7059515" | ||
| CLEAN_DOI=${DOI/\//_} | ||
| zenodo_get $DOI -o ../images/${CLEAN_DOI} |
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examples/06_cellpose_dev_example/run_example_cellpose_normalization.py
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| """ | ||
| Copyright 2022 (C) Friedrich Miescher Institute for Biomedical Research and | ||
| University of Zurich | ||
| Original authors: | ||
| Marco Franzon <marco.franzon@exact-lab.it> | ||
| Tommaso Comparin <tommaso.comparin@exact-lab.it> | ||
| This file is part of Fractal and was originally developed by eXact lab S.r.l. | ||
| <exact-lab.it> under contract with Liberali Lab from the Friedrich Miescher | ||
| Institute for Biomedical Research and Pelkmans Lab from the University of | ||
| Zurich. | ||
| """ | ||
| import os | ||
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| from devtools import debug | ||
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| from fractal_tasks_core.channels import OmeroChannel | ||
| from fractal_tasks_core.channels import Window | ||
| from fractal_tasks_core.tasks.cellpose_segmentation import ( | ||
| cellpose_segmentation, | ||
| ) | ||
| from fractal_tasks_core.tasks.cellpose_transforms import ( | ||
| CellposeCustomNormalizer, | ||
| ) | ||
| from fractal_tasks_core.tasks.copy_ome_zarr import copy_ome_zarr | ||
| from fractal_tasks_core.tasks.create_ome_zarr import create_ome_zarr | ||
| from fractal_tasks_core.tasks.maximum_intensity_projection import ( | ||
| maximum_intensity_projection, | ||
| ) | ||
| from fractal_tasks_core.tasks.yokogawa_to_ome_zarr import yokogawa_to_ome_zarr | ||
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| allowed_channels = [ | ||
| OmeroChannel( | ||
| label="DAPI", | ||
| wavelength_id="A01_C01", | ||
| color="00FFFF", | ||
| window=Window(start=110, end=700), | ||
| ) | ||
| ] | ||
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| num_levels = 6 | ||
| coarsening_xy = 2 | ||
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| # Init | ||
| img_path = "../images/10.5281_zenodo.7059515/" | ||
| if not os.path.isdir(img_path): | ||
| raise FileNotFoundError( | ||
| f"{img_path} is missing," | ||
| " try running ./fetch_test_data_from_zenodo.sh" | ||
| ) | ||
| zarr_path = "tmp_out_normalize/" | ||
| metadata: dict = {} | ||
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| # Create zarr structure | ||
| metadata_update = create_ome_zarr( | ||
| input_paths=[img_path], | ||
| output_path=zarr_path, | ||
| metadata=metadata, | ||
| image_extension="png", | ||
| allowed_channels=allowed_channels, | ||
| num_levels=num_levels, | ||
| coarsening_xy=coarsening_xy, | ||
| overwrite=True, | ||
| ) | ||
| metadata.update(metadata_update) | ||
| debug(metadata) | ||
|
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| # Yokogawa to zarr | ||
| for component in metadata["image"]: | ||
| yokogawa_to_ome_zarr( | ||
| input_paths=[zarr_path], | ||
| output_path=zarr_path, | ||
| metadata=metadata, | ||
| component=component, | ||
| ) | ||
| debug(metadata) | ||
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| # Copy zarr structure | ||
| metadata_update = copy_ome_zarr( | ||
| input_paths=[zarr_path], | ||
| output_path=zarr_path, | ||
| metadata=metadata, | ||
| suffix="mip", | ||
| overwrite=True, | ||
| ) | ||
| metadata.update(metadata_update) | ||
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| # Make MIP | ||
| for component in metadata["image"]: | ||
| metadata_update = maximum_intensity_projection( | ||
| input_paths=[zarr_path], | ||
| output_path=zarr_path, | ||
| metadata=metadata, | ||
| component=component, | ||
| ) | ||
| metadata.update(metadata_update) | ||
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| normalize = CellposeCustomNormalizer(default_normalize=True) | ||
| normalize = CellposeCustomNormalizer( | ||
| default_normalize=False, lower_percentile=1.0, upper_percentile=99.0 | ||
| ) | ||
| # normalize=CellposeCustomNormalizer( | ||
| # default_normalize=True, | ||
| # lower_percentile=1.0, | ||
| # upper_percentile=99.0 | ||
| # ) # ValueError | ||
| # normalize=CellposeCustomNormalizer( | ||
| # default_normalize=False, | ||
| # lower_percentile=1.0, | ||
| # upper_percentile=99.0, | ||
| # lower_bound=100, | ||
| # upper_bound=500 | ||
| # ) # ValueError | ||
| normalize = CellposeCustomNormalizer( | ||
| default_normalize=False, lower_bound=100, upper_bound=500 | ||
| ) | ||
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| # Per-FOV labeling | ||
| for component in metadata["image"]: | ||
| cellpose_segmentation( | ||
| input_paths=[zarr_path], | ||
| output_path=zarr_path, | ||
| metadata=metadata, | ||
| component=component, | ||
| channel=dict(wavelength_id="A01_C01"), | ||
| level=1, | ||
| relabeling=True, | ||
| diameter_level0=40.0, | ||
| model_type="cyto2", | ||
| normalize=normalize, | ||
| ) | ||
| metadata.update(metadata_update) | ||
| debug(metadata) |
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