| data: |
| |
| |
| 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"] |
| |
| 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 |
| intensity_factors: [0.9, 1.1] |
|
|
| ensemble: |
| n_seeds: 5 |
| snapshot_epochs: [150, 170, 190] |
| |
|
|
