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Component labeling with multiple parameter configurations
1 parent 39adf31 commit bc80409

15 files changed

+852
-120
lines changed

‎flamingo_tools/segmentation/postprocessing.py‎

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@@ -524,6 +524,7 @@ def label_components_ihc(
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min_size: int = 1000,
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min_component_length: int = 50,
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max_edge_distance: float = 30,
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min_nn_100_distance: float = None,
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) -> List[int]:
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"""Label components using graph connected components.
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@@ -532,6 +533,7 @@ def label_components_ihc(
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min_size: Minimal number of pixels for filtering small instances.
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min_component_length: Minimal length for filtering out connected components.
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max_edge_distance: Maximal distance in micrometer between points to create edges for connected components.
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min_nn_100_distance: Minimal value for average distance to 100 nearest neighbors.
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Returns:
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List of component label for each point in dataframe. 0 - background, then in descending order of size
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entries_filtered = table[table.n_pixels < min_size]
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table = table[table.n_pixels >= min_size]
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keyword = "distance_nn100"
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if min_nn_100_distance is not None:
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distance_avg = nearest_neighbor_distance(table, n_neighbors=100)
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table.loc[:, keyword] = list(distance_avg)
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entries_filtered_01 = table[table[keyword] < min_nn_100_distance]
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table = table[table[keyword] >= min_nn_100_distance]
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entries_filtered = pd.concat([entries_filtered, entries_filtered_01], ignore_index=True)
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components = components_ihc(table, min_component_length=min_component_length,
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max_edge_distance=max_edge_distance)
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‎reproducibility/label_components/G_EK_000233_L_IHC.json‎

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[
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{
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"cochlea": "G_EK_000233_L",
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"cell_type": "ihc",
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"segmentation_channel": "IHC_v6",
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"component_list": [
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1
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],
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"custom_dic": {
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"min_size_global": 1000,
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"label_dicts": {
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"1": {
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"label_params": [
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{
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"max_edge_distance": 30,
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"min_nn_100_distance": 57
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},
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{
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"max_edge_distance": 25,
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"min_nn_100_distance": 57
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},
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{
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"max_edge_distance": 30,
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"min_nn_100_distance": 60
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}
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],
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"components": [
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[
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],
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[
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],
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[
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]
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]
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}
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}
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}
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}
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]

‎reproducibility/label_components/G_LR_000233_R_IHC.json‎

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[
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{
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"cochlea": "G_LR_000233_R",
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"cell_type": "ihc",
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"segmentation_channel": "IHC_v6",
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"component_list": [
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1
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],
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"custom_dic": {
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"min_size_global": 10000,
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"label_dicts": {
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"1": {
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"label_params": [
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{
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"min_size": 10000,
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"max_edge_distance": 25,
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"min_component_length": 200,
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"min_nn_100_distance": 75
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},
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{
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"min_size": 10000,
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"max_edge_distance": 23,
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"min_component_length": 50,
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"min_nn_100_distance": 70
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},
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{
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"min_size": 12000,
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"max_edge_distance": 23,
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"min_component_length": 20,
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"min_nn_100_distance": 65
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}
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],
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"components": [
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[
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],
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]
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]
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}
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}
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}
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}
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]

‎reproducibility/label_components/LaVision-M02_IHC.json‎

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[
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{
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"cochlea": "LaVision-M02",
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"cell_type": "ihc",
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"segmentation_channel": "IHC_LOWRES-v3",
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"component_list": [
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1
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],
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"custom_dic": {
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"min_size_global": 500,
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"label_dicts": {
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"1": {
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"label_params": [
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{
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"min_size": 100,
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"max_edge_distance": 39,
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"min_component_length": 2
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}
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],
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"components": [
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]
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]
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}
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}
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}
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}
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]

‎reproducibility/label_components/LaVision-M04_IHC.json‎

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[
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{
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"cochlea": "LaVision-M04",
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"cell_type": "ihc",
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"segmentation_channel": "IHC_LOWRES-v3",
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"component_list": [
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"custom_dic": {
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"min_size_global": 500,
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"missing_ids": [
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],
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"label_dicts": {
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"label_params": [
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{
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"min_size": 500,
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"max_edge_distance": 55,
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"min_component_length": 10
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}
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],
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"components": [
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}
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}
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}
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}
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]

‎reproducibility/label_components/LaVision-Mar05_IHC.json‎

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[
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{
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"cochlea": "LaVision-Mar05",
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"cell_type": "ihc",
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"segmentation_channel": "IHC_LOWRES-v3",
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"component_list": [
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"min_size": 20,
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"max_edge_distance": 50,
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"min_component_length": 20
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}
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]

‎reproducibility/label_components/LaVision-OTOF23R_IHC.json‎

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[
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{
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"cochlea": "LaVision-OTOF23R",
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"cell_type": "ihc",
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"segmentation_channel": "IHC_LOWRES-v3",
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"component_list": [
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],
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"min_size": 20,
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"max_edge_distance": 50,
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"min_component_length": 20
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}
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]

‎reproducibility/label_components/LaVision-OTOF25R_IHC.json‎

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[
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{
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"cochlea": "LaVision-OTOF25R",
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"cell_type": "ihc",
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"segmentation_channel": "IHC_LOWRES-v3",
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"component_list": [
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],
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"custom_dic": {
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"min_size_global": 500,
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"missing_ids": [
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],
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"label_dicts": {
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"label_params": [
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"min_size": 500,
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"max_edge_distance": 65,
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"min_component_length": 5
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},
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{
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"min_size": 400,
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"max_edge_distance": 45,
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"min_component_length": 5
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{
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"min_size": 400,
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"min_size": 400,
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"max_edge_distance": 50,
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"components": [
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"2": {
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"label_params": [
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"min_size": 500,
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"max_edge_distance": 65,
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"min_component_length": 5
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}
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"components": [
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[
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}
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}
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}
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}
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]

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