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Fix blocking for synapse detection
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flamingo_tools/segmentation/synapse_detection.py

Lines changed: 1 addition & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -37,7 +37,7 @@ def map_and_filter_detections(
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points = detections[["z", "y", "x"]].values.astype("int")
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# Set the block shape (this could also be exposed as a parameter; it should not matter much though).
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block_shape = (64, 256, 256)
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block_shape = (128, 128, 128)
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# Determine the halo. We set it to 2 pixels + the max-distance in pixels, to ensure all distances
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# that are smaller than the max distance are measured.
@@ -83,10 +83,6 @@ def run_prediction(
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block_shape: The block-shape for running the prediction.
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halo: The halo (= block overlap) to use for prediction.
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"""
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if block_shape is None:
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block_shape = (64, 256, 256)
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if halo is None:
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halo = (16, 64, 64)
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# Skip existing prediction, which is saved in output_folder/predictions.zarr
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skip_prediction = False

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