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20230412_MCZ-masks.json
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20230412_MCZ-masks.json
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{
"1": {
"category": "extraction",
"function": "infer_nuclei_fromlabel",
"parameter_values": {
"gauss_sig": 5.0,
"max_hole_w": 35,
"median_sz": 3,
"nuc_ch": 0,
"small_obj_w": 15,
"thresh_factor": 0.8,
"thresh_max": 1.0,
"thresh_min": 0.1
},
"parent": 0
},
"2": {
"category": "extraction",
"function": "raw_cellmask_fromaggr",
"parameter_values": {
"scale_min_max": true
},
"parent": 0
},
"3": {
"category": "preprocessing",
"function": "scale_and_smooth",
"parameter_values": {
"gauss_sig": 4.5,
"median_sz": 4
},
"parent": 2
},
"4": {
"category": "preprocessing",
"function": "non_linear_cellmask_transform_MCZ",
"parent": 3
},
"5": {
"category": "core",
"function": "masked_object_thresh",
"parameter_values": {
"cutoff_size": 647,
"th_adjust": 0.94,
"th_method": "ave_tri_med"
},
"parent": 4
},
"6": {
"category": "postprocessing",
"function": "fill_and_filter_linear_size",
"parameter_values": {
"hole_max": 62,
"hole_min": 0,
"method": "slice_by_slice",
"min_size": 42
},
"parent": 5
},
"7": {
"category": "postpostprocessing",
"function": "choose_max_label_cellmask_union_nucleus",
"parameter_values": {
"interior_labels": true
},
"parent": [
3,
6,
1
]
},
"8": {
"category": "postpostprocessing",
"function": "infer_cytoplasm",
"parameter_values": {
"erode_nuclei": true
},
"parent": [
1,
7
]
},
"9": {
"category": "export",
"function": "stack_masks",
"parent": [
1,
7,
8
]
}
}