{ "area_vx2": 485000.0, "base_shape_zyx": [ 18946, 8174, 8174 ], "bbox": [ [ 4064.110107421875, 3231.386474609375, 8660.625 ], [ 4494.90625, 3732.836181640625, 9575.609375 ] ], "extra_channels": [ { "dtype": "float32", "file": "flow_gate_local_contrast.tif", "name": "flow_gate_local_contrast", "range": [ 0.0, 1.0 ], "source": "pred_dt_flow_gate.local_contrast", "source_config": { "backtrack_distance": 50.0, "gate_factor": 1.0, "grid_step": 4, "local_boost": 0.5 } }, { "dtype": "float32", "file": "flow_gate_component_normalized.tif", "name": "flow_gate_component_normalized", "range": [ 0.0, 1.0 ], "source": "pred_dt_flow_gate.component_normalized", "source_config": { "backtrack_distance": 50.0, "gate_factor": 1.0, "grid_step": 4, "local_boost": 0.5 } } ], "fit_config": { "_corr_point_roi_init_": { "effective_seed": [ 17056.57421875, 14229.2587890625, 36661.9375 ], "final_anchor_h": 203.59357325732708, "final_anchor_w": 50.21472416818142, "final_shell_id": "shell_0007.tifxyz", "final_trim_bottom": 21, "final_trim_top": 20, "init_margin_grid_points": 80, "initial_seed": [ 17056.57421875, 14229.2587890625, 36661.9375 ], "initial_shell_id": "shell_0007.tifxyz", "initial_skipped_point_count": 0, "initial_skipped_reasons": {}, "initial_trim_bottom": 21, "initial_trim_top": 20, "initial_usable_point_count": 15, "mode": "corr-point-roi", "model_h": 8336.47232055664, "model_w": 8067.605018615723, "model_w_unit": "voxels", "output_radius_grid_points": 20, "parsed_point_count": 15, "projected_h_span_grid": 6.7294464111328125, "projected_h_span_vx": 336.4723205566406, "projected_points": [ { "collection_id": 2818, "direction_sign": -1, "grid_distance_to_anchor": 3.6359841838688833, "h": 199.97409057617188, "point_id": 112879, "row_index": 0, "w": 49.868709564208984 }, { "collection_id": 2818, "direction_sign": 1, "grid_distance_to_anchor": 2.766599074788507, "h": 200.83470153808594, "point_id": 112880, "row_index": 1, "w": 50.00809097290039 }, { "collection_id": 2818, "direction_sign": 1, "grid_distance_to_anchor": 2.1794631867968315, "h": 201.42185974121094, "point_id": 112881, "row_index": 2, "w": 50.03109359741211 }, { "collection_id": 2818, "direction_sign": 1, "grid_distance_to_anchor": 1.680438077029144, "h": 201.92385864257813, "point_id": 112882, "row_index": 3, "w": 50.025184631347656 }, { "collection_id": 2818, "direction_sign": 1, "grid_distance_to_anchor": 1.0638291439994514, "h": 202.53070068359375, "point_id": 112883, "row_index": 4, "w": 50.169620513916016 }, { "collection_id": 2818, "direction_sign": 1, "grid_distance_to_anchor": 0.49502326174928013, "h": 203.11167907714844, "point_id": 112884, "row_index": 5, "w": 50.32797622680664 }, { "collection_id": 2818, "direction_sign": -1, "grid_distance_to_anchor": 0.4824957071211627, "h": 203.28285217285156, "point_id": 112885, "row_index": 6, "w": 50.5838508605957 }, { "collection_id": 2818, "direction_sign": -1, "grid_distance_to_anchor": 0.6107336483551631, "h": 203.87913513183594, "point_id": 112886, "row_index": 7, "w": 50.75458526611328 }, { "collection_id": 2818, "direction_sign": -1, "grid_distance_to_anchor": 0.7384069140594494, "h": 204.21949768066406, "point_id": 112887, "row_index": 8, "w": 50.606468200683594 }, { "collection_id": 2818, "direction_sign": -1, "grid_distance_to_anchor": 1.1081464971562849, "h": 204.63018798828125, "point_id": 112888, "row_index": 9, "w": 50.60641098022461 }, { "collection_id": 2818, "direction_sign": -1, "grid_distance_to_anchor": 1.6264402137923242, "h": 205.15567016601563, "point_id": 112889, "row_index": 10, "w": 50.66767120361328 }, { "collection_id": 2818, "direction_sign": -1, "grid_distance_to_anchor": 2.1749078083231987, "h": 205.700439453125, "point_id": 112890, "row_index": 11, "w": 50.75448226928711 }, { "collection_id": 2818, "direction_sign": -1, "grid_distance_to_anchor": 2.7374074189387527, "h": 206.2458038330078, "point_id": 112891, "row_index": 12, "w": 50.89227294921875 }, { "collection_id": 2818, "direction_sign": -1, "grid_distance_to_anchor": 3.218770639771683, "h": 206.669189453125, "point_id": 112892, "row_index": 13, "w": 51.163970947265625 }, { "collection_id": 2818, "direction_sign": -1, "grid_distance_to_anchor": 3.2686515530164093, "h": 206.7035369873047, "point_id": 112893, "row_index": 14, "w": 51.22080993652344 } ], "projected_w_span_grid": 1.3521003723144531, "projected_w_span_vx": 67.60501861572266, "projection_mode": "normal-line", "skipped_point_count": 0, "skipped_points": [], "skipped_reasons": {}, "usable_point_count": 15, "windings": 1 }, "args": { "approval-inpaint": false, "approval-inpaint-corr-spacing": null, "approval-inpaint-output-mask": false, "approval-inpaint-output-mask-dilate": 3, "approval-inpaint-padding-frac": 0.25, "approval-inpaint-tifxyz": null, "corr-point-roi": true, "corr-point-roi-init-margin": 80, "corr-point-roi-output-radius": 20, "crop": null, "cuda-gridsample": 1, "depth": 1, "device": "cuda", "downscale": 4.0, "erode-valid-mask": 0, "flatten-solver": "torch", "init-mode": "shell-dir-crop", "input": "/ephemeral/lasag_strip_outputs/.lasagna_point_strip_work/collection_2818/point_strip.lasagna.json", "mesh-h": 32, "mesh-step": 50, "mesh-w": 32, "model-h": 8336.47232055664, "model-init": "seed", "model-input": null, "model-output": "/tmp/fit_reopt_2haszm8b/model_reopt.pt", "model-w": 8067.605018615723, "model-w-unit": "voxels", "normal-mask-zero": 0, "out-dir": null, "progress": true, "pyramid-d": false, "seed": [ 17056.57421875, 14229.2587890625, 36661.9375 ], "snapshot-interval": 1000, "sparse-prefetch-backend": "tensorstore", "subsample-mesh": 4, "subsample-winding": 4, "tifxyz-flow-gate-channels": true, "tifxyz-init": null, "winding-step": 25, "winding-volume": null, "windings": 1, "z-center": 0.0 }, "base": { "bend": 100.0, "corr": 0.0001, "data": 0.0, "data_plain": 0.0, "ext_offset": 0.0, "normal": 1.0, "pred_dt": 0.001, "smooth": 10.0, "station_n": 0.1, "station_t": 0.1, "step": 10.0, "winding_density": 0.01 }, "corr_points": { "collections": { "2818": { "color": [ 1.0, 0.0, 0.7058823704719543 ], "metadata": { "winding_is_absolute": true }, "name": "same_wrap2588", "points": { "112879": { "creation_time": 1779685856911, "p": [ 17069.962890625, 14147.0498046875, 35865.640625 ], "wind_a": 0.0 }, "112880": { "creation_time": 1779685856911, "p": [ 17067.685546875, 14161.0419921875, 35979.765625 ], "wind_a": 0.0 }, "112881": { "creation_time": 1779685856911, "p": [ 17064.775390625, 14178.91015625, 36092.26953125 ], "wind_a": 0.0 }, "112882": { "creation_time": 1779685856911, "p": [ 17061.037109375, 14201.85546875, 36202.63671875 ], "wind_a": 0.0 }, "112883": { "creation_time": 1779685856911, "p": [ 17059.251953125, 14212.8173828125, 36318.0390625 ], "wind_a": 0.0 }, "112884": { "creation_time": 1779685856911, "p": [ 17055.681640625, 14234.7392578125, 36428.8359375 ], "wind_a": 0.0 }, "112885": { "creation_time": 1779685856911, "p": [ 17055.681640625, 14234.7392578125, 36544.23828125 ], "wind_a": 0.0 }, "112886": { "creation_time": 1779685856911, "p": [ 17056.57421875, 14229.2587890625, 36661.9375 ], "wind_a": 0.0 }, "112887": { "creation_time": 1779685856911, "p": [ 17058.359375, 14218.2978515625, 36777.3359375 ], "wind_a": 0.0 }, "112888": { "creation_time": 1779685856911, "p": [ 17062.01953125, 14195.8330078125, 36887.91015625 ], "wind_a": 0.0 }, "112889": { "creation_time": 1779685856911, "p": [ 17068.083984375, 14158.5888671875, 36992.27734375 ], "wind_a": 0.0 }, "112890": { "creation_time": 1779685856911, "p": [ 17072.888671875, 14129.0947265625, 37099.90234375 ], "wind_a": 0.0 }, "112891": { "creation_time": 1779685856911, "p": [ 17080.84765625, 14080.2236328125, 37199.390625 ], "wind_a": 0.0 }, "112892": { "creation_time": 1779685856911, "p": [ 17090.69921875, 14019.7265625, 37294.00390625 ], "wind_a": 0.0 }, "112893": { "creation_time": 1779685856911, "p": [ 17092.27734375, 14010.0341796875, 37309.375 ], "wind_a": 0.0 } } } } }, "lasagna_base_shape_zyx": [ 75784, 32693, 32693 ], "stages": [ { "lr": 0.1, "min_scaledown": 0, "name": "stage0", "params": [ "mesh_ms" ], "steps": 1000, "w_fac": { "corr": 0.0, "pred_dt": 0.0, "station_n": 10.0, "station_t": 10.0 } }, { "lr": 0.1, "min_scaledown": 0, "name": "stage1", "params": [ "mesh_ms" ], "steps": 1000, "w_fac": { "pred_dt": 0.0, "station_n": 10.0, "station_t": 10.0 } }, { "lr": 0.01, "min_scaledown": 0, "name": "stage2", "params": [ "mesh_ms" ], "steps": 500, "w_fac": { "pred_dt": 0.0, "station_n": 10.0, "station_t": 10.0 } }, { "_lr": [ 10.0, 1.0, 0.1, 0.01, 0.001 ], "args": { "pred_dt_flow_gate": { "anticipatory_pull": { "_debug_roi_center_xyz": [ 17499, 13412, 51144 ], "debug_roi_k": 8, "debug_roi_root_min": 0.5, "debug_roi_tip_max": 0.5, "debug_slice_upsample": 8, "enabled": true, "inlier_one": 120.0, "inlier_zero": 80.0, "loss_weight": 2.0, "samples": 8 }, "backtrack_distance": 50.0, "debug": false, "debug_out_dir": "/home/ubuntu/villa/lasagna", "debug_vis_interval": 0, "enabled": true, "gate_factor": 1.0, "local_boost": 0.5 }, "status_interval": 10 }, "dlr": [ 1.0, 0.1, 0.01, 0.001, 0.0001 ], "lr": 1.0, "min_scaledown": 0, "name": "snap", "params": [ "mesh_ms" ], "steps": 500 } ], "vc3d_volume_shape_zyx": [ 18946, 8174, 8174 ] }, "format": "tifxyz", "lasagna_base_shape_zyx": [ 75784, 32693, 32693 ], "lasagna_job": { "config": { "args": { "corr-point-roi": true, "corr-point-roi-init-margin": 80, "corr-point-roi-output-radius": 20, "init-mode": "shell-dir-crop", "mesh-step": 50.0, "model-h": 5000.0, "model-init": "seed", "model-w": 5000.0, "model-w-unit": "voxels", "seed": [ 4264.1435546875, 3557.314697265625, 9165.484375 ], "tifxyz-flow-gate-channels": true, "windings": 1 }, "base": { "bend": 100.0, "corr": 0.0001, "data": 0.0, "data_plain": 0.0, "ext_offset": 0.0, "normal": 1.0, "pred_dt": 0.001, "smooth": 10.0, "station_n": 0.1, "station_t": 0.1, "step": 10.0, "winding_density": 0.01 }, "corr_points": { "collections": { "2818": { "color": [ 1.0, 0.0, 0.7058823704719543 ], "metadata": { "winding_is_absolute": true }, "name": "same_wrap2588", "points": { "112879": { "creation_time": 1779685856911, "p": [ 4267.49072265625, 3536.762451171875, 8966.41015625 ], "wind_a": 0.0 }, "112880": { "creation_time": 1779685856911, "p": [ 4266.92138671875, 3540.260498046875, 8994.94140625 ], "wind_a": 0.0 }, "112881": { "creation_time": 1779685856911, "p": [ 4266.19384765625, 3544.7275390625, 9023.0673828125 ], "wind_a": 0.0 }, "112882": { "creation_time": 1779685856911, "p": [ 4265.25927734375, 3550.4638671875, 9050.6591796875 ], "wind_a": 0.0 }, "112883": { "creation_time": 1779685856911, "p": [ 4264.81298828125, 3553.204345703125, 9079.509765625 ], "wind_a": 0.0 }, "112884": { "creation_time": 1779685856911, "p": [ 4263.92041015625, 3558.684814453125, 9107.208984375 ], "wind_a": 0.0 }, "112885": { "creation_time": 1779685856911, "p": [ 4263.92041015625, 3558.684814453125, 9136.0595703125 ], "wind_a": 0.0 }, "112886": { "creation_time": 1779685856911, "p": [ 4264.1435546875, 3557.314697265625, 9165.484375 ], "wind_a": 0.0 }, "112887": { "creation_time": 1779685856911, "p": [ 4264.58984375, 3554.574462890625, 9194.333984375 ], "wind_a": 0.0 }, "112888": { "creation_time": 1779685856911, "p": [ 4265.5048828125, 3548.958251953125, 9221.9775390625 ], "wind_a": 0.0 }, "112889": { "creation_time": 1779685856911, "p": [ 4267.02099609375, 3539.647216796875, 9248.0693359375 ], "wind_a": 0.0 }, "112890": { "creation_time": 1779685856911, "p": [ 4268.22216796875, 3532.273681640625, 9274.9755859375 ], "wind_a": 0.0 }, "112891": { "creation_time": 1779685856911, "p": [ 4270.2119140625, 3520.055908203125, 9299.84765625 ], "wind_a": 0.0 }, "112892": { "creation_time": 1779685856911, "p": [ 4272.6748046875, 3504.931640625, 9323.5009765625 ], "wind_a": 0.0 }, "112893": { "creation_time": 1779685856911, "p": [ 4273.0693359375, 3502.508544921875, 9327.34375 ], "wind_a": 0.0 } } } } }, "stages": [ { "lr": 0.1, "min_scaledown": 0, "name": "stage0", "params": [ "mesh_ms" ], "steps": 1000, "w_fac": { "corr": 0.0, "pred_dt": 0.0, "station_n": 10.0, "station_t": 10.0 } }, { "lr": 0.1, "min_scaledown": 0, "name": "stage1", "params": [ "mesh_ms" ], "steps": 1000, "w_fac": { "pred_dt": 0.0, "station_n": 10.0, "station_t": 10.0 } }, { "lr": 0.01, "min_scaledown": 0, "name": "stage2", "params": [ "mesh_ms" ], "steps": 500, "w_fac": { "pred_dt": 0.0, "station_n": 10.0, "station_t": 10.0 } }, { "_lr": [ 10.0, 1.0, 0.1, 0.01, 0.001 ], "args": { "pred_dt_flow_gate": { "anticipatory_pull": { "_debug_roi_center_xyz": [ 17499, 13412, 51144 ], "debug_roi_k": 8, "debug_roi_root_min": 0.5, "debug_roi_tip_max": 0.5, "debug_slice_upsample": 8, "enabled": true, "inlier_one": 120.0, "inlier_zero": 80.0, "loss_weight": 2.0, "samples": 8 }, "backtrack_distance": 50.0, "debug": false, "debug_out_dir": "/home/ubuntu/villa/lasagna", "debug_vis_interval": 0, "enabled": true, "gate_factor": 1.0, "local_boost": 0.5 }, "status_interval": 10 }, "dlr": [ 1.0, 0.1, 0.01, 0.001, 0.0001 ], "lr": 1.0, "min_scaledown": 0, "name": "snap", "params": [ "mesh_ms" ], "steps": 500 } ] }, "linked_surfaces": [], "model": null, "volume_shape_zyx": [ 18946, 8174, 8174 ] }, "model_source": "/tmp/fit_reopt_2haszm8b/model_reopt.pt", "scale": [ 0.07999999821186066, 0.07999999821186066 ], "tags": { "date_last_modified": "20260614185644578", "reviewed": { "date": "20260604080934281" } }, "type": "seg", "uuid": "same_wrap002588_lasagna" }