| { | |
| "model": { | |
| "hf_path": "anforsm/3DEM_TACC_LSD_AFF", | |
| "hyperparameters": { | |
| "downsample_factors": [ | |
| [ | |
| 1, | |
| 2, | |
| 2 | |
| ], | |
| [ | |
| 1, | |
| 2, | |
| 2 | |
| ], | |
| [ | |
| 2, | |
| 2, | |
| 2 | |
| ] | |
| ], | |
| "fmap_inc_factor": 5, | |
| "in_channels": 1, | |
| "kernel_size_down": [ | |
| [ | |
| [ | |
| 3, | |
| 3, | |
| 3 | |
| ], | |
| [ | |
| 3, | |
| 3, | |
| 3 | |
| ] | |
| ], | |
| [ | |
| [ | |
| 3, | |
| 3, | |
| 3 | |
| ], | |
| [ | |
| 3, | |
| 3, | |
| 3 | |
| ] | |
| ], | |
| [ | |
| [ | |
| 3, | |
| 3, | |
| 3 | |
| ], | |
| [ | |
| 3, | |
| 3, | |
| 3 | |
| ] | |
| ], | |
| [ | |
| [ | |
| 1, | |
| 3, | |
| 3 | |
| ], | |
| [ | |
| 1, | |
| 3, | |
| 3 | |
| ] | |
| ] | |
| ], | |
| "kernel_size_up": [ | |
| [ | |
| [ | |
| 3, | |
| 3, | |
| 3 | |
| ], | |
| [ | |
| 3, | |
| 3, | |
| 3 | |
| ] | |
| ], | |
| [ | |
| [ | |
| 3, | |
| 3, | |
| 3 | |
| ], | |
| [ | |
| 3, | |
| 3, | |
| 3 | |
| ] | |
| ], | |
| [ | |
| [ | |
| 3, | |
| 3, | |
| 3 | |
| ], | |
| [ | |
| 3, | |
| 3, | |
| 3 | |
| ] | |
| ] | |
| ], | |
| "output_shapes": [ | |
| 10, | |
| 3 | |
| ] | |
| }, | |
| "name": "3D Model With LSD", | |
| "path": "out" | |
| }, | |
| "pipeline": { | |
| "_order": [ | |
| "source", | |
| "normalize", | |
| "augment", | |
| "lsd_target", | |
| "target" | |
| ], | |
| "_outputs": [ | |
| "RAW", | |
| "LABELS", | |
| "GT_AFFS", | |
| "AFFS_WEIGHTS", | |
| "GT_LSDS", | |
| "LSDS_WEIGHTS", | |
| "GT_AFFS_MASK", | |
| "LABELS_MASK" | |
| ], | |
| "augment": [ | |
| { | |
| "elastic_augment": { | |
| "control_point_spacing": [ | |
| 1, | |
| 50, | |
| 50 | |
| ], | |
| "jitter_sigma": [ | |
| 0, | |
| 5, | |
| 5 | |
| ], | |
| "rotation_interval": [ | |
| 0, | |
| 1.570796 | |
| ], | |
| "scale_interval": [ | |
| 0.5, | |
| 2 | |
| ], | |
| "subsample": 4 | |
| } | |
| }, | |
| { | |
| "simple_augment": { | |
| "transpose_only": [ | |
| 1, | |
| 2 | |
| ] | |
| } | |
| }, | |
| { | |
| "noise_augment": { | |
| "array": "RAW" | |
| } | |
| }, | |
| { | |
| "intensity_augment": { | |
| "array": "RAW", | |
| "scale_max": 1.1, | |
| "scale_min": 0.9, | |
| "shift_max": 0.1, | |
| "shift_min": -0.1 | |
| } | |
| }, | |
| { | |
| "smooth_array": { | |
| "array": "RAW" | |
| } | |
| }, | |
| { | |
| "grow_boundary": { | |
| "labels": "LABELS", | |
| "only_xy": true | |
| } | |
| } | |
| ], | |
| "lsd_target": [ | |
| { | |
| "add_local_shape_descriptor": { | |
| "descriptor": "GT_LSDS", | |
| "downsample": 2, | |
| "labels_mask": "LABELS_MASK", | |
| "lsds_mask": "LSDS_WEIGHTS", | |
| "segmentation": "LABELS", | |
| "sigma": 40 | |
| } | |
| } | |
| ], | |
| "normalize": [ | |
| { | |
| "normalize": { | |
| "array": "RAW" | |
| } | |
| } | |
| ], | |
| "source": [ | |
| [ | |
| [ | |
| { | |
| "zarr_source": { | |
| "array_specs": { | |
| "_labels": { | |
| "array_spec": { | |
| "interpolatable": false | |
| } | |
| }, | |
| "_labels_mask": { | |
| "array_spec": { | |
| "interpolatable": false | |
| } | |
| }, | |
| "_raw": { | |
| "array_spec": { | |
| "interpolatable": true | |
| } | |
| } | |
| }, | |
| "datasets": { | |
| "_labels": "labels/s0", | |
| "_labels_mask": "labels_mask/s0", | |
| "_raw": "raw/s0" | |
| }, | |
| "store": "SynapseWeb/kh2015/oblique" | |
| } | |
| }, | |
| { | |
| "pad": { | |
| "key": "RAW", | |
| "size": null | |
| } | |
| }, | |
| { | |
| "pad": { | |
| "key": "LABELS", | |
| "size": { | |
| "coordinate": { | |
| "_positional": [ | |
| 450, | |
| 290, | |
| 290 | |
| ] | |
| } | |
| } | |
| } | |
| }, | |
| { | |
| "pad": { | |
| "key": "LABELS_MASK", | |
| "size": { | |
| "coordinate": { | |
| "_positional": [ | |
| 450, | |
| 290, | |
| 290 | |
| ] | |
| } | |
| } | |
| } | |
| }, | |
| { | |
| "random_location": { | |
| "mask": "LABELS_MASK", | |
| "min_masked": 0.1 | |
| } | |
| } | |
| ], | |
| [ | |
| { | |
| "zarr_source": { | |
| "array_specs": { | |
| "_labels": { | |
| "array_spec": { | |
| "interpolatable": false | |
| } | |
| }, | |
| "_labels_mask": { | |
| "array_spec": { | |
| "interpolatable": false | |
| } | |
| }, | |
| "_raw": { | |
| "array_spec": { | |
| "interpolatable": true | |
| } | |
| } | |
| }, | |
| "datasets": { | |
| "_labels": "labels/s0", | |
| "_labels_mask": "labels_mask/s0", | |
| "_raw": "raw/s0" | |
| }, | |
| "store": "SynapseWeb/kh2015/spine" | |
| } | |
| }, | |
| { | |
| "pad": { | |
| "key": "RAW", | |
| "size": null | |
| } | |
| }, | |
| { | |
| "pad": { | |
| "key": "LABELS", | |
| "size": { | |
| "coordinate": { | |
| "_positional": [ | |
| 450, | |
| 290, | |
| 290 | |
| ] | |
| } | |
| } | |
| } | |
| }, | |
| { | |
| "pad": { | |
| "key": "LABELS_MASK", | |
| "size": { | |
| "coordinate": { | |
| "_positional": [ | |
| 450, | |
| 290, | |
| 290 | |
| ] | |
| } | |
| } | |
| } | |
| }, | |
| { | |
| "random_location": { | |
| "mask": "LABELS_MASK", | |
| "min_masked": 0.1 | |
| } | |
| } | |
| ] | |
| ], | |
| { | |
| "random_provider": {} | |
| } | |
| ], | |
| "target": [ | |
| { | |
| "add_affinities": { | |
| "affinities": "GT_AFFS", | |
| "affinities_mask": "GT_AFFS_MASK", | |
| "affinity_neighborhood": [ | |
| [ | |
| -1, | |
| 0, | |
| 0 | |
| ], | |
| [ | |
| 0, | |
| -1, | |
| 0 | |
| ], | |
| [ | |
| 0, | |
| 0, | |
| -1 | |
| ] | |
| ], | |
| "labels": "LABELS", | |
| "labels_mask": "LABELS_MASK" | |
| } | |
| }, | |
| { | |
| "balance_labels": { | |
| "labels": "GT_AFFS", | |
| "mask": "GT_AFFS_MASK", | |
| "scales": "AFFS_WEIGHTS" | |
| } | |
| }, | |
| { | |
| "intensity_scale_shift": { | |
| "array": "RAW", | |
| "scale": 2, | |
| "shift": -1 | |
| } | |
| }, | |
| { | |
| "unsqueeze": { | |
| "arrays": [ | |
| "RAW" | |
| ], | |
| "axis": 0 | |
| } | |
| } | |
| ] | |
| }, | |
| "predict": { | |
| "model": { | |
| "path": "out/latest_model3.pt" | |
| }, | |
| "output": [ | |
| { | |
| "dataset": "pred_affs", | |
| "path": "out_zarr.zarr", | |
| "stacked": true | |
| } | |
| ], | |
| "source": [ | |
| { | |
| "dataset": "raw/s0", | |
| "path": "SynapseWeb/kh2015/oblique" | |
| } | |
| ] | |
| }, | |
| "training": { | |
| "batch_outputs": [ | |
| "raw", | |
| "labels", | |
| "gt_affs", | |
| "affs_weights", | |
| "gt_lsds", | |
| "lsds_weights" | |
| ], | |
| "logging": { | |
| "wandb": false | |
| }, | |
| "loss": { | |
| "_inputs": [ | |
| "lsds", | |
| "gt_lsds", | |
| "lsds_weights", | |
| "affs", | |
| "gt_affs", | |
| "affs_weights" | |
| ], | |
| "weighted_m_s_e_loss_double": {} | |
| }, | |
| "model_inputs": [ | |
| "raw" | |
| ], | |
| "model_outputs": [ | |
| "lsds", | |
| "affs" | |
| ], | |
| "multi_gpu": true, | |
| "save_every": 1000, | |
| "train_dataloader": { | |
| "batch_size": 2, | |
| "input_image_shape": [ | |
| 36, | |
| 212, | |
| 212 | |
| ], | |
| "num_workers": 4, | |
| "output_image_shape": [ | |
| 12, | |
| 120, | |
| 120 | |
| ], | |
| "parallel": true, | |
| "precache_per_worker": 4 | |
| } | |
| } | |
| } |