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config/config.yaml

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+data:
+  # TODO: Update this path for your HPC cluster, e.g.:
+  # root: "/scratch/$USER/immunogold_data/Gold Particle Labelling"
+  root: "/Users/mpcr/Downloads/Max Planck Data/Gold Particle Labelling"
+  analyzed_dir: "analyzed synapses"
+  test_dir: "labeled replica - Test Data from Synapses"
+  synapse_ids: ["S1", "S4", "S7", "S8", "S13", "S15", "S22", "S25", "S27", "S29"]
+  # S7 and S15 have no 6nm annotations — exclude from 6nm evaluation
+  incomplete_6nm: ["S7", "S15"]
+  raw_dir: "data/raw"
+  annotation_dir: "data/annotations"
+  weights_dir: "weights"
+  patch_size: 512
+  stride: 2
+  bead_classes: ["6nm", "12nm"]
+
+heatmap:
+  sigmas:
+    6nm: 1.0
+    12nm: 1.5
+
+model:
+  backbone: "resnet50"
+  pretrained_weights: "weights/cem500k_mocov2_resnet50.pth.tar"
+  cem500k_url: "https://zenodo.org/records/6453140/files/cem500k_mocov2_resnet50_200ep.pth.tar?download=1"
+  bifpn_channels: 128
+  bifpn_rounds: 2
+  num_classes: 2
+
+training:
+  batch_size: 8
+  n_seeds: 5
+  n_snapshot_epochs: [150, 170, 190]
+  hard_mining_fraction: 0.7
+  copy_paste_per_class: 5
+
+  phases:
+    phase1:
+      epochs: 60
+      lr: 1.0e-3
+      weight_decay: 1.0e-4
+      freeze_encoder: true
+    phase2:
+      epochs: 60
+      lr_layer3: 1.0e-5
+      lr_layer4: 5.0e-5
+      lr_decoder: 5.0e-4
+      weight_decay: 1.0e-4
+    phase3:
+      epochs: 80
+      lr_stem: 1.0e-6
+      lr_layer1: 5.0e-6
+      lr_layer2: 1.0e-5
+      lr_layer3: 5.0e-5
+      lr_layer4: 1.0e-4
+      lr_decoder: 2.0e-4
+      weight_decay: 1.0e-4
+      eta_min: 1.0e-7
+
+  loss:
+    focal_alpha: 2
+    focal_beta: 4
+    lambda_offset: 1.0
+
+  early_stopping:
+    patience: 20
+    monitor: "val_f1_mean"
+
+postprocessing:
+  nms_kernel_size:
+    6nm: 3
+    12nm: 5
+  confidence_threshold_sweep:
+    start: 0.05
+    stop: 0.95
+    step: 0.01
+  mask_filter_margin_px: 5
+  cross_class_nms_distance_px: 8
+
+evaluation:
+  match_radii_px:
+    6nm: 9
+    12nm: 15
+  loocv_val_offset: 1
+
+tta:
+  enabled: true
+  n_geometric: 8      # D4 group: 4 rotations x 2 reflections
+  intensity_factors: [0.9, 1.1]
+
+ensemble:
+  n_seeds: 5
+  snapshot_epochs: [150, 170, 190]
+  # Total ensemble members per fold: 5 seeds x 3 snapshots = 15