First commit for examples/06_secondary_labeling

examples/06_secondary_labeling/.gitignore

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+images
+model
+output
+backup
+tmp*
+slurm-*.out
+slurm-*.err

examples/06_secondary_labeling/01_final_metadata.json

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+{
+    "coarsening_xy": 2,
+    "copy_zarr": {
+        "sources": {
+            "RS220304172545_mip": "/home/tommaso/Fractal/fractal-tasks-core/examples/06_secondary_labeling/output/RS220304172545.zarr"
+        },
+        "suffix": "mip"
+    },
+    "image": [
+        "RS220304172545_mip.zarr/A/06/0/"
+    ],
+    "num_levels": 5,
+    "original_paths": [
+        "images/*.tif"
+    ],
+    "plate": [
+        "RS220304172545_mip.zarr"
+    ],
+    "well": [
+        "RS220304172545_mip.zarr/A/06/"
+    ]
+}

examples/06_secondary_labeling/01_images_to_mip.py

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+import json
+from pathlib import Path
+
+from devtools import debug
+
+from fractal_tasks_core.copy_ome_zarr import copy_ome_zarr
+from fractal_tasks_core.create_ome_zarr import create_ome_zarr
+from fractal_tasks_core.maximum_intensity_projection import (
+    maximum_intensity_projection,
+)
+from fractal_tasks_core.yokogawa_to_ome_zarr import yokogawa_to_ome_zarr
+
+
+allowed_channels = [
+    {
+        "wavelength_id": "A01_C01",
+        "colormap": "00FFFF",
+        "end": 2000,
+        "label": "Channel 1",
+        "start": 110,
+    },
+    {
+        "wavelength_id": "A02_C02",
+        "colormap": "FF00FF",
+        "end": 500,
+        "label": "Channel 2",
+        "start": 110,
+    },
+    {
+        "wavelength_id": "A03_C03",
+        "colormap": "00FF00",
+        "end": 1600,
+        "label": "Channel 3",
+        "start": 110,
+    },
+    {
+        "wavelength_id": "A04_C04",
+        "colormap": "FFFF00",
+        "end": 1600,
+        "label": "Channel 4",
+        "start": 110,
+    },
+]
+
+
+num_levels = 5
+coarsening_xy = 2
+
+
+# Init
+img_path = Path("images/*.tif")
+zarr_path = Path("output/*zarr")
+zarr_path_mip = Path("output/*zarr")
+metadata = {}
+
+# Create zarr structure
+metadata_update = create_ome_zarr(
+    input_paths=[img_path],
+    output_path=zarr_path,
+    metadata=metadata,
+    allowed_channels=allowed_channels,
+    num_levels=num_levels,
+    coarsening_xy=coarsening_xy,
+    metadata_table="mrf_mlf",
+)
+metadata.update(metadata_update)
+debug(metadata)
+
+# 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)
+
+# Replicate
+metadata_update = copy_ome_zarr(
+    input_paths=[zarr_path],
+    output_path=zarr_path_mip,
+    metadata=metadata,
+    project_to_2D=True,
+    suffix="mip",
+)
+metadata.update(metadata_update)
+debug(metadata)
+
+# MIP
+for component in metadata["image"]:
+    maximum_intensity_projection(
+        input_paths=[zarr_path_mip],
+        output_path=zarr_path_mip,
+        metadata=metadata,
+        component=component,
+    )
+debug(metadata)
+with open("01_final_metadata.json", "w") as f:
+    json.dump(metadata, f, indent=4, sort_keys=True)

examples/06_secondary_labeling/02_cellpose_organoids.py

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+import json
+import os
+import shutil
+from pathlib import Path
+
+from devtools import debug
+
+from fractal_tasks_core.cellpose_segmentation import cellpose_segmentation
+
+
+if os.path.exists("tmp"):
+    shutil.rmtree("tmp")
+os.mkdir("tmp")
+shutil.copytree(
+    "output/RS220304172545_mip.zarr", "tmp/RS220304172545_mip.zarr"
+)
+
+# Init
+zarr_path_mip = Path("tmp/*zarr")
+with open("01_final_metadata.json", "r") as f:
+    metadata = json.load(f)
+
+
+# Cellpose for organoids
+for component in metadata["image"]:
+    cellpose_segmentation(
+        input_paths=[zarr_path_mip],
+        output_path=zarr_path_mip,
+        metadata=metadata,
+        component=component,
+        wavelength_id="A01_C01",
+        level=3,
+        relabeling=True,
+        diameter_level0=1000.0,
+        ROI_table_name="well_ROI_table",
+        cellprob_threshold=-3.0,
+        flow_threshold=0.4,
+        pretrained_model="model/Hummingbird.331986",
+        output_label_name="organoids",
+    )
+
+debug(metadata)
+with open("02_final_metadata.json", "w") as f:
+    json.dump(metadata, f, indent=4, sort_keys=True)

examples/06_secondary_labeling/02_final_metadata.json

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+{
+    "coarsening_xy": 2,
+    "copy_zarr": {
+        "sources": {
+            "RS220304172545_mip": "/home/tommaso/Fractal/fractal-tasks-core/examples/06_secondary_labeling/output/RS220304172545.zarr"
+        },
+        "suffix": "mip"
+    },
+    "image": [
+        "RS220304172545_mip.zarr/A/06/0/"
+    ],
+    "num_levels": 5,
+    "original_paths": [
+        "images/*.tif"
+    ],
+    "plate": [
+        "RS220304172545_mip.zarr"
+    ],
+    "well": [
+        "RS220304172545_mip.zarr/A/06/"
+    ]
+}