{ "area_vx2": 669375.0, "base_shape_zyx": [ 18946, 8174, 8174 ], "bbox": [ [ 4214.07421875, 3659.960693359375, 10746.669921875 ], [ 4940.326171875, 4244.58740234375, 11719.0068359375 ] ], "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": [ 18116.890625, 16428.287109375, 44895.30859375 ], "final_anchor_h": 251.81783652305603, "final_anchor_w": 48.51303958892822, "final_shell_id": "shell_0007.tifxyz", "final_trim_bottom": 21, "final_trim_top": 20, "init_margin_grid_points": 80, "initial_seed": [ 18058.818359375, 16486.958984375, 44812.7578125 ], "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": 26, "mode": "corr-point-roi", "model_h": 8564.961242675781, "model_w": 8111.607360839844, "model_w_unit": "voxels", "output_radius_grid_points": 20, "parsed_point_count": 26, "projected_h_span_grid": 11.299224853515625, "projected_h_span_vx": 564.9612426757813, "projected_points": [ { "collection_id": 2246, "direction_sign": 1, "grid_distance_to_anchor": 6.375012927557071, "h": 245.47140502929688, "point_id": 83453, "row_index": 0, "w": 47.91004943847656 }, { "collection_id": 2246, "direction_sign": 1, "grid_distance_to_anchor": 5.775516502841782, "h": 246.0633544921875, "point_id": 83454, "row_index": 1, "w": 48.02056884765625 }, { "collection_id": 2246, "direction_sign": 1, "grid_distance_to_anchor": 5.1526524883589655, "h": 246.68057250976563, "point_id": 83455, "row_index": 2, "w": 48.1151123046875 }, { "collection_id": 2246, "direction_sign": 1, "grid_distance_to_anchor": 4.651804605821171, "h": 247.17477416992188, "point_id": 83456, "row_index": 3, "w": 48.22798156738281 }, { "collection_id": 2246, "direction_sign": 1, "grid_distance_to_anchor": 4.514390323987045, "h": 247.3074951171875, "point_id": 83457, "row_index": 4, "w": 48.32188415527344 }, { "collection_id": 2246, "direction_sign": 1, "grid_distance_to_anchor": 4.60976827379386, "h": 247.2143096923828, "point_id": 83458, "row_index": 5, "w": 48.27323913574219 }, { "collection_id": 2246, "direction_sign": 1, "grid_distance_to_anchor": 3.1913946352229274, "h": 248.62722778320313, "point_id": 83459, "row_index": 6, "w": 48.44221878051758 }, { "collection_id": 2246, "direction_sign": 1, "grid_distance_to_anchor": 2.4011836790516123, "h": 249.4183807373047, "point_id": 83460, "row_index": 7, "w": 48.42196273803711 }, { "collection_id": 2246, "direction_sign": 1, "grid_distance_to_anchor": 1.733905602936547, "h": 250.08584594726563, "point_id": 83461, "row_index": 8, "w": 48.59450912475586 }, { "collection_id": 2246, "direction_sign": 1, "grid_distance_to_anchor": 1.8790095774669975, "h": 249.97647094726563, "point_id": 83462, "row_index": 9, "w": 48.887271881103516 }, { "collection_id": 2246, "direction_sign": 1, "grid_distance_to_anchor": 1.8235488983209194, "h": 250.06301879882813, "point_id": 83463, "row_index": 10, "w": 49.008968353271484 }, { "collection_id": 2246, "direction_sign": -1, "grid_distance_to_anchor": 2.1307552070276445, "h": 249.79415893554688, "point_id": 83464, "row_index": 11, "w": 49.18000793457031 }, { "collection_id": 2246, "direction_sign": -1, "grid_distance_to_anchor": 1.3575252731230172, "h": 250.64198303222656, "point_id": 83465, "row_index": 12, "w": 49.19145202636719 }, { "collection_id": 2246, "direction_sign": -1, "grid_distance_to_anchor": 1.2707100743385655, "h": 250.72299194335938, "point_id": 83466, "row_index": 13, "w": 49.15803527832031 }, { "collection_id": 2246, "direction_sign": -1, "grid_distance_to_anchor": 0.7714013079536659, "h": 251.129150390625, "point_id": 83467, "row_index": 14, "w": 48.86056137084961 }, { "collection_id": 2246, "direction_sign": -1, "grid_distance_to_anchor": 0.29810011146099696, "h": 251.52662658691406, "point_id": 83468, "row_index": 15, "w": 48.449317932128906 }, { "collection_id": 2246, "direction_sign": -1, "grid_distance_to_anchor": 0.4961470061456719, "h": 252.19281005859375, "point_id": 83469, "row_index": 16, "w": 48.18814468383789 }, { "collection_id": 2246, "direction_sign": -1, "grid_distance_to_anchor": 1.1246895240843375, "h": 252.7877197265625, "point_id": 83470, "row_index": 17, "w": 47.943607330322266 }, { "collection_id": 2246, "direction_sign": -1, "grid_distance_to_anchor": 1.6733406320403361, "h": 253.30535888671875, "point_id": 83471, "row_index": 18, "w": 47.74665451049805 }, { "collection_id": 2246, "direction_sign": -1, "grid_distance_to_anchor": 2.2671874427086784, "h": 253.87892150878906, "point_id": 83472, "row_index": 19, "w": 47.568546295166016 }, { "collection_id": 2246, "direction_sign": -1, "grid_distance_to_anchor": 2.85314647491852, "h": 254.4505157470703, "point_id": 83473, "row_index": 20, "w": 47.413291931152344 }, { "collection_id": 2246, "direction_sign": -1, "grid_distance_to_anchor": 3.442255411066267, "h": 255.03257751464844, "point_id": 83474, "row_index": 21, "w": 47.28236389160156 }, { "collection_id": 2246, "direction_sign": -1, "grid_distance_to_anchor": 3.991208240724693, "h": 255.58438110351563, "point_id": 83475, "row_index": 22, "w": 47.19285583496094 }, { "collection_id": 2246, "direction_sign": -1, "grid_distance_to_anchor": 4.567263881718611, "h": 256.1627197265625, "point_id": 83476, "row_index": 23, "w": 47.10524368286133 }, { "collection_id": 2246, "direction_sign": -1, "grid_distance_to_anchor": 5.091291764658691, "h": 256.66973876953125, "point_id": 83477, "row_index": 24, "w": 46.970218658447266 }, { "collection_id": 2246, "direction_sign": -1, "grid_distance_to_anchor": 5.190785473224081, "h": 256.7706298828125, "point_id": 83478, "row_index": 25, "w": 46.95930480957031 } ], "projected_w_span_grid": 2.232147216796875, "projected_w_span_vx": 111.60736083984375, "projection_mode": "normal-line", "skipped_point_count": 0, "skipped_points": [], "skipped_reasons": {}, "usable_point_count": 26, "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_2246/point_strip.lasagna.json", "mesh-h": 32, "mesh-step": 50, "mesh-w": 32, "model-h": 8564.961242675781, "model-init": "seed", "model-input": null, "model-output": "/tmp/fit_reopt_ni61n1ax/model_reopt.pt", "model-w": 8111.607360839844, "model-w-unit": "voxels", "normal-mask-zero": 0, "out-dir": null, "progress": true, "pyramid-d": false, "seed": [ 18116.890625, 16428.287109375, 44895.30859375 ], "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": { "2246": { "color": [ 0.7058823704719543, 1.0, 0.3137255012989044 ], "metadata": { "winding_is_absolute": true }, "name": "same_wrap1892", "points": { "83453": { "creation_time": 1779569317039, "p": [ 18474.666015625, 16066.830078125, 43599.2109375 ], "wind_a": 0.0 }, "83454": { "creation_time": 1779569317039, "p": [ 18408.046875, 16134.134765625, 43660.29296875 ], "wind_a": 0.0 }, "83455": { "creation_time": 1779569317039, "p": [ 18336.974609375, 16205.9375, 43706.09375 ], "wind_a": 0.0 }, "83456": { "creation_time": 1779569317039, "p": [ 18269.955078125, 16273.6474609375, 43765.796875 ], "wind_a": 0.0 }, "83457": { "creation_time": 1779569317039, "p": [ 18210.056640625, 16334.1630859375, 43842.0859375 ], "wind_a": 0.0 }, "83458": { "creation_time": 1779569317039, "p": [ 18181.693359375, 16362.8193359375, 43945.38671875 ], "wind_a": 0.0 }, "83459": { "creation_time": 1779569317039, "p": [ 18168.013671875, 16376.6396484375, 44057.33203125 ], "wind_a": 0.0 }, "83460": { "creation_time": 1779569317039, "p": [ 18120.98828125, 16424.1484375, 44146.390625 ], "wind_a": 0.0 }, "83461": { "creation_time": 1779569317039, "p": [ 18054.431640625, 16491.390625, 44207.68359375 ], "wind_a": 0.0 }, "83462": { "creation_time": 1779569317039, "p": [ 17997.501953125, 16548.90625, 44294.1640625 ], "wind_a": 0.0 }, "83463": { "creation_time": 1779569317039, "p": [ 17966.845703125, 16579.87890625, 44396.11328125 ], "wind_a": 0.0 }, "83464": { "creation_time": 1779569317039, "p": [ 17959.033203125, 16587.771484375, 44511.51171875 ], "wind_a": 0.0 }, "83465": { "creation_time": 1779569317039, "p": [ 17967.0546875, 16579.666015625, 44626.7890625 ], "wind_a": 0.0 }, "83466": { "creation_time": 1779569317039, "p": [ 18004.650390625, 16541.685546875, 44724.65234375 ], "wind_a": 0.0 }, "83467": { "creation_time": 1779569317039, "p": [ 18058.818359375, 16486.958984375, 44812.7578125 ], "wind_a": 0.0 }, "83468": { "creation_time": 1779569317039, "p": [ 18116.890625, 16428.287109375, 44895.30859375 ], "wind_a": 0.0 }, "83469": { "creation_time": 1779569317039, "p": [ 18171.05859375, 16373.5625, 44983.4140625 ], "wind_a": 0.0 }, "83470": { "creation_time": 1779569317039, "p": [ 18214.177734375, 16330.0, 45078.02734375 ], "wind_a": 0.0 }, "83471": { "creation_time": 1779569317039, "p": [ 18249.009765625, 16294.80859375, 45177.515625 ], "wind_a": 0.0 }, "83472": { "creation_time": 1779569317039, "p": [ 18279.349609375, 16264.15625, 45279.65234375 ], "wind_a": 0.0 }, "83473": { "creation_time": 1779569317039, "p": [ 18302.7890625, 16240.4775390625, 45385.8515625 ], "wind_a": 0.0 }, "83474": { "creation_time": 1779569317039, "p": [ 18318.4140625, 16224.69140625, 45496.65234375 ], "wind_a": 0.0 }, "83475": { "creation_time": 1779569317039, "p": [ 18326.2265625, 16216.7978515625, 45612.05078125 ], "wind_a": 0.0 }, "83476": { "creation_time": 1779569317039, "p": [ 18334.783203125, 16208.1533203125, 45727.015625 ], "wind_a": 0.0 }, "83477": { "creation_time": 1779569317039, "p": [ 18349.6640625, 16193.119140625, 45838.25 ], "wind_a": 0.0 }, "83478": { "creation_time": 1779569317039, "p": [ 18349.6640625, 16193.119140625, 45859.2265625 ], "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": [ 4501.16259765625, 4135.42138671875, 11181.1630859375 ], "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": { "2246": { "color": [ 0.7058823704719543, 1.0, 0.3137255012989044 ], "metadata": { "winding_is_absolute": true }, "name": "same_wrap1892", "points": { "83453": { "creation_time": 1779569317039, "p": [ 4618.66650390625, 4016.70751953125, 10899.802734375 ], "wind_a": 0.0 }, "83454": { "creation_time": 1779569317039, "p": [ 4602.01171875, 4033.53369140625, 10915.0732421875 ], "wind_a": 0.0 }, "83455": { "creation_time": 1779569317039, "p": [ 4584.24365234375, 4051.484375, 10926.5234375 ], "wind_a": 0.0 }, "83456": { "creation_time": 1779569317039, "p": [ 4567.48876953125, 4068.411865234375, 10941.44921875 ], "wind_a": 0.0 }, "83457": { "creation_time": 1779569317039, "p": [ 4552.51416015625, 4083.540771484375, 10960.521484375 ], "wind_a": 0.0 }, "83458": { "creation_time": 1779569317039, "p": [ 4545.42333984375, 4090.704833984375, 10986.3466796875 ], "wind_a": 0.0 }, "83459": { "creation_time": 1779569317039, "p": [ 4542.00341796875, 4094.159912109375, 11014.3330078125 ], "wind_a": 0.0 }, "83460": { "creation_time": 1779569317039, "p": [ 4530.2470703125, 4106.037109375, 11036.59765625 ], "wind_a": 0.0 }, "83461": { "creation_time": 1779569317039, "p": [ 4513.60791015625, 4122.84765625, 11051.9208984375 ], "wind_a": 0.0 }, "83462": { "creation_time": 1779569317039, "p": [ 4499.37548828125, 4137.2265625, 11073.541015625 ], "wind_a": 0.0 }, "83463": { "creation_time": 1779569317039, "p": [ 4491.71142578125, 4144.9697265625, 11099.0283203125 ], "wind_a": 0.0 }, "83464": { "creation_time": 1779569317039, "p": [ 4489.75830078125, 4146.94287109375, 11127.8779296875 ], "wind_a": 0.0 }, "83465": { "creation_time": 1779569317039, "p": [ 4491.763671875, 4144.91650390625, 11156.697265625 ], "wind_a": 0.0 }, "83466": { "creation_time": 1779569317039, "p": [ 4501.16259765625, 4135.42138671875, 11181.1630859375 ], "wind_a": 0.0 }, "83467": { "creation_time": 1779569317039, "p": [ 4514.70458984375, 4121.73974609375, 11203.189453125 ], "wind_a": 0.0 }, "83468": { "creation_time": 1779569317039, "p": [ 4529.22265625, 4107.07177734375, 11223.8271484375 ], "wind_a": 0.0 }, "83469": { "creation_time": 1779569317039, "p": [ 4542.7646484375, 4093.390625, 11245.853515625 ], "wind_a": 0.0 }, "83470": { "creation_time": 1779569317039, "p": [ 4553.54443359375, 4082.5, 11269.5068359375 ], "wind_a": 0.0 }, "83471": { "creation_time": 1779569317039, "p": [ 4562.25244140625, 4073.7021484375, 11294.37890625 ], "wind_a": 0.0 }, "83472": { "creation_time": 1779569317039, "p": [ 4569.83740234375, 4066.0390625, 11319.9130859375 ], "wind_a": 0.0 }, "83473": { "creation_time": 1779569317039, "p": [ 4575.697265625, 4060.119384765625, 11346.462890625 ], "wind_a": 0.0 }, "83474": { "creation_time": 1779569317039, "p": [ 4579.603515625, 4056.1728515625, 11374.1630859375 ], "wind_a": 0.0 }, "83475": { "creation_time": 1779569317039, "p": [ 4581.556640625, 4054.199462890625, 11403.0126953125 ], "wind_a": 0.0 }, "83476": { "creation_time": 1779569317039, "p": [ 4583.69580078125, 4052.038330078125, 11431.75390625 ], "wind_a": 0.0 }, "83477": { "creation_time": 1779569317039, "p": [ 4587.416015625, 4048.27978515625, 11459.5625 ], "wind_a": 0.0 }, "83478": { "creation_time": 1779569317039, "p": [ 4587.416015625, 4048.27978515625, 11464.806640625 ], "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_ni61n1ax/model_reopt.pt", "scale": [ 0.07999999821186066, 0.07999999821186066 ], "tags": { "date_last_modified": "20260614185644417", "reviewed": { "date": "20260604080934247" } }, "type": "seg", "uuid": "same_wrap001892_lasagna" }