{ "area_vx2": 547968.75, "base_shape_zyx": [ 18946, 8174, 8174 ], "bbox": [ [ 4210.837890625, 3122.823486328125, 6706.68798828125 ], [ 4661.2451171875, 3230.762451171875, 7646.54296875 ] ], "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": [ 17296.7421875, 12778.556640625, 28916.935546875 ], "final_anchor_h": 157.00000000745058, "final_anchor_w": 45.01816523820162, "final_shell_id": "shell_0000.tifxyz", "final_trim_bottom": 28, "final_trim_top": 27, "init_margin_grid_points": 80, "initial_seed": [ 17259.068359375, 12755.015625, 29230.93359375 ], "initial_shell_id": "shell_0000.tifxyz", "initial_skipped_point_count": 0, "initial_skipped_reasons": {}, "initial_trim_bottom": 28, "initial_trim_top": 27, "initial_usable_point_count": 26, "mode": "corr-point-roi", "model_h": 9555.401611328125, "model_w": 8713.677787780762, "model_w_unit": "voxels", "output_radius_grid_points": 20, "parsed_point_count": 26, "projected_h_span_grid": 31.1080322265625, "projected_h_span_vx": 1555.401611328125, "projected_points": [ { "collection_id": 3085, "direction_sign": 1, "grid_distance_to_anchor": 12.592898064492465, "h": 165.7474365234375, "point_id": 133338, "row_index": 0, "w": 35.95927810668945 }, { "collection_id": 3085, "direction_sign": 1, "grid_distance_to_anchor": 11.879236978286729, "h": 165.11212158203125, "point_id": 133339, "row_index": 1, "w": 36.34004592895508 }, { "collection_id": 3085, "direction_sign": -1, "grid_distance_to_anchor": 7.650251568968608, "h": 164.6241455078125, "point_id": 133340, "row_index": 2, "w": 45.649635314941406 }, { "collection_id": 3085, "direction_sign": 1, "grid_distance_to_anchor": 10.034115310782017, "h": 163.90377807617188, "point_id": 133341, "row_index": 3, "w": 37.73659133911133 }, { "collection_id": 3085, "direction_sign": 1, "grid_distance_to_anchor": 9.597970183041355, "h": 164.0035400390625, "point_id": 133342, "row_index": 4, "w": 38.45528030395508 }, { "collection_id": 3085, "direction_sign": 1, "grid_distance_to_anchor": 8.752743573601633, "h": 163.72218322753906, "point_id": 133343, "row_index": 5, "w": 39.41256332397461 }, { "collection_id": 3085, "direction_sign": -1, "grid_distance_to_anchor": 8.969587076512573, "h": 156.31431579589844, "point_id": 133344, "row_index": 6, "w": 36.074825286865234 }, { "collection_id": 3085, "direction_sign": -1, "grid_distance_to_anchor": 4.782764161341509, "h": 160.50332641601563, "point_id": 133345, "row_index": 7, "w": 41.76216506958008 }, { "collection_id": 3085, "direction_sign": -1, "grid_distance_to_anchor": 22.960596886645085, "h": 134.639404296875, "point_id": 133346, "row_index": 8, "w": 50.23283386230469 }, { "collection_id": 3085, "direction_sign": 1, "grid_distance_to_anchor": 9.823523955431762, "h": 165.68162536621094, "point_id": 133347, "row_index": 9, "w": 40.42131805419922 }, { "collection_id": 3085, "direction_sign": 1, "grid_distance_to_anchor": 5.015246109724567, "h": 160.2492218017578, "point_id": 133348, "row_index": 10, "w": 41.197792053222656 }, { "collection_id": 3085, "direction_sign": 1, "grid_distance_to_anchor": 4.783610327120521, "h": 160.02029418945313, "point_id": 133349, "row_index": 11, "w": 41.308616638183594 }, { "collection_id": 3085, "direction_sign": -1, "grid_distance_to_anchor": 3.5969781151313507, "h": 158.31739807128906, "point_id": 133350, "row_index": 12, "w": 41.671119689941406 }, { "collection_id": 3085, "direction_sign": -1, "grid_distance_to_anchor": 2.9739575739908255, "h": 155.71774291992188, "point_id": 133351, "row_index": 13, "w": 42.3348388671875 }, { "collection_id": 3085, "direction_sign": 1, "grid_distance_to_anchor": 2.9226139782307756, "h": 159.5187225341797, "point_id": 133352, "row_index": 14, "w": 43.53569793701172 }, { "collection_id": 3085, "direction_sign": -1, "grid_distance_to_anchor": 1.067615552472267, "h": 156.98460388183594, "point_id": 133353, "row_index": 15, "w": 43.950660705566406 }, { "collection_id": 3085, "direction_sign": -1, "grid_distance_to_anchor": 18.13770915616334, "h": 139.16505432128906, "point_id": 133354, "row_index": 16, "w": 48.3183479309082 }, { "collection_id": 3085, "direction_sign": -1, "grid_distance_to_anchor": 1.8361502762272008, "h": 155.16415405273438, "point_id": 133355, "row_index": 17, "w": 45.05159378051758 }, { "collection_id": 3085, "direction_sign": -1, "grid_distance_to_anchor": 3.3270420344459892, "h": 153.72181701660156, "point_id": 133356, "row_index": 18, "w": 45.58625411987305 }, { "collection_id": 3085, "direction_sign": -1, "grid_distance_to_anchor": 3.1231782248129965, "h": 154.08096313476563, "point_id": 133357, "row_index": 19, "w": 46.128780364990234 }, { "collection_id": 3085, "direction_sign": 1, "grid_distance_to_anchor": 1.5543116467167972, "h": 155.9064178466797, "point_id": 133358, "row_index": 20, "w": 46.122684478759766 }, { "collection_id": 3085, "direction_sign": 1, "grid_distance_to_anchor": 0.7608954423199481, "h": 157.32151794433594, "point_id": 133359, "row_index": 21, "w": 45.707794189453125 }, { "collection_id": 3085, "direction_sign": 1, "grid_distance_to_anchor": 1.4358260351872654, "h": 155.6269073486328, "point_id": 133360, "row_index": 22, "w": 45.43794250488281 }, { "collection_id": 3085, "direction_sign": 1, "grid_distance_to_anchor": 1.4632527616302426, "h": 155.53976440429688, "point_id": 133361, "row_index": 23, "w": 45.112083435058594 }, { "collection_id": 3085, "direction_sign": 1, "grid_distance_to_anchor": 1.894896639502414, "h": 155.1117401123047, "point_id": 133362, "row_index": 24, "w": 44.859710693359375 }, { "collection_id": 3085, "direction_sign": 1, "grid_distance_to_anchor": 2.8379025049696733, "h": 154.1858673095703, "point_id": 133363, "row_index": 25, "w": 44.65163040161133 } ], "projected_w_span_grid": 14.273555755615234, "projected_w_span_vx": 713.6777877807617, "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_3085/point_strip.lasagna.json", "mesh-h": 32, "mesh-step": 50, "mesh-w": 32, "model-h": 9555.401611328125, "model-init": "seed", "model-input": null, "model-output": "/tmp/fit_reopt__8fwhzw7/model_reopt.pt", "model-w": 8713.677787780762, "model-w-unit": "voxels", "normal-mask-zero": 0, "out-dir": null, "progress": true, "pyramid-d": false, "seed": [ 17296.7421875, 12778.556640625, 28916.935546875 ], "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": { "3085": { "color": [ 0.7058823704719543, 1.0, 0.3137255012989044 ], "metadata": { "winding_is_absolute": true }, "name": "same_wrap3025", "points": { "133338": { "creation_time": 1779734538303, "p": [ 17428.595703125, 12860.9482421875, 30560.53125 ], "wind_a": 0.0 }, "133339": { "creation_time": 1779734538303, "p": [ 17409.759765625, 12849.177734375, 30449.73046875 ], "wind_a": 0.0 }, "133340": { "creation_time": 1779734538303, "p": [ 17386.21484375, 12834.4658203125, 30341.23046875 ], "wind_a": 0.0 }, "133341": { "creation_time": 1779734538303, "p": [ 17369.220703125, 12823.8466796875, 30229.53125 ], "wind_a": 0.0 }, "133342": { "creation_time": 1779734538303, "p": [ 17353.25, 12813.8671875, 30117.33203125 ], "wind_a": 0.0 }, "133343": { "creation_time": 1779734538303, "p": [ 17329.705078125, 12799.154296875, 30008.83203125 ], "wind_a": 0.0 }, "133344": { "creation_time": 1779734538303, "p": [ 17320.287109375, 12793.26953125, 29893.431640625 ], "wind_a": 0.0 }, "133345": { "creation_time": 1779734538303, "p": [ 17334.4140625, 12802.0966796875, 29780.33203125 ], "wind_a": 0.0 }, "133346": { "creation_time": 1779734538303, "p": [ 17343.83203125, 12807.982421875, 29664.931640625 ], "wind_a": 0.0 }, "133347": { "creation_time": 1779734538303, "p": [ 17317.5390625, 12791.5517578125, 29557.775390625 ], "wind_a": 0.0 }, "133348": { "creation_time": 1779734538303, "p": [ 17277.904296875, 12766.7861328125, 29457.1328125 ], "wind_a": 0.0 }, "133349": { "creation_time": 1779734538303, "p": [ 17254.359375, 12752.0732421875, 29348.6328125 ], "wind_a": 0.0 }, "133350": { "creation_time": 1779734538303, "p": [ 17259.068359375, 12755.015625, 29230.93359375 ], "wind_a": 0.0 }, "133351": { "creation_time": 1779734538303, "p": [ 17295.876953125, 12778.0166015625, 29128.912109375 ], "wind_a": 0.0 }, "133352": { "creation_time": 1779734538303, "p": [ 17288.341796875, 12773.3076171875, 29018.037109375 ], "wind_a": 0.0 }, "133353": { "creation_time": 1779734538303, "p": [ 17296.7421875, 12778.556640625, 28916.935546875 ], "wind_a": 0.0 }, "133354": { "creation_time": 1779734538303, "p": [ 17306.16015625, 12784.44140625, 28801.53515625 ], "wind_a": 0.0 }, "133355": { "creation_time": 1779734538303, "p": [ 17330.74609375, 12799.8046875, 28693.54296875 ], "wind_a": 0.0 }, "133356": { "creation_time": 1779734538303, "p": [ 17396.044921875, 12840.6083984375, 28605.4375 ], "wind_a": 0.0 }, "133357": { "creation_time": 1779734538303, "p": [ 17464.673828125, 12883.4931640625, 28518.958984375 ], "wind_a": 0.0 }, "133358": { "creation_time": 1779734538303, "p": [ 17494.5234375, 12902.14453125, 28413.537109375 ], "wind_a": 0.0 }, "133359": { "creation_time": 1779734538303, "p": [ 17440.390625, 12868.318359375, 28319.978515625 ], "wind_a": 0.0 }, "133360": { "creation_time": 1779734538303, "p": [ 17370.380859375, 12824.572265625, 28237.42578125 ], "wind_a": 0.0 }, "133361": { "creation_time": 1779734538303, "p": [ 17303.703125, 12782.90625, 28153.24609375 ], "wind_a": 0.0 }, "133362": { "creation_time": 1779734538303, "p": [ 17230.365234375, 12737.0791015625, 28072.3203125 ], "wind_a": 0.0 }, "133363": { "creation_time": 1779734538303, "p": [ 17193.142578125, 12713.8203125, 28028.427734375 ], "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": [ 4323.96923828125, 3194.504150390625, 7282.22802734375 ], "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": { "3085": { "color": [ 0.7058823704719543, 1.0, 0.3137255012989044 ], "metadata": { "winding_is_absolute": true }, "name": "same_wrap3025", "points": { "133338": { "creation_time": 1779734538303, "p": [ 4357.14892578125, 3215.237060546875, 7640.1328125 ], "wind_a": 0.0 }, "133339": { "creation_time": 1779734538303, "p": [ 4352.43994140625, 3212.29443359375, 7612.4326171875 ], "wind_a": 0.0 }, "133340": { "creation_time": 1779734538303, "p": [ 4346.5537109375, 3208.616455078125, 7585.3076171875 ], "wind_a": 0.0 }, "133341": { "creation_time": 1779734538303, "p": [ 4342.30517578125, 3205.961669921875, 7557.3828125 ], "wind_a": 0.0 }, "133342": { "creation_time": 1779734538303, "p": [ 4338.3125, 3203.466796875, 7529.3330078125 ], "wind_a": 0.0 }, "133343": { "creation_time": 1779734538303, "p": [ 4332.42626953125, 3199.78857421875, 7502.2080078125 ], "wind_a": 0.0 }, "133344": { "creation_time": 1779734538303, "p": [ 4330.07177734375, 3198.3173828125, 7473.35791015625 ], "wind_a": 0.0 }, "133345": { "creation_time": 1779734538303, "p": [ 4333.603515625, 3200.524169921875, 7445.0830078125 ], "wind_a": 0.0 }, "133346": { "creation_time": 1779734538303, "p": [ 4335.9580078125, 3201.99560546875, 7416.23291015625 ], "wind_a": 0.0 }, "133347": { "creation_time": 1779734538303, "p": [ 4329.384765625, 3197.887939453125, 7389.44384765625 ], "wind_a": 0.0 }, "133348": { "creation_time": 1779734538303, "p": [ 4319.47607421875, 3191.696533203125, 7364.283203125 ], "wind_a": 0.0 }, "133349": { "creation_time": 1779734538303, "p": [ 4313.58984375, 3188.018310546875, 7337.158203125 ], "wind_a": 0.0 }, "133350": { "creation_time": 1779734538303, "p": [ 4314.76708984375, 3188.75390625, 7307.7333984375 ], "wind_a": 0.0 }, "133351": { "creation_time": 1779734538303, "p": [ 4323.96923828125, 3194.504150390625, 7282.22802734375 ], "wind_a": 0.0 }, "133352": { "creation_time": 1779734538303, "p": [ 4322.08544921875, 3193.326904296875, 7254.50927734375 ], "wind_a": 0.0 }, "133353": { "creation_time": 1779734538303, "p": [ 4324.185546875, 3194.63916015625, 7229.23388671875 ], "wind_a": 0.0 }, "133354": { "creation_time": 1779734538303, "p": [ 4326.5400390625, 3196.1103515625, 7200.3837890625 ], "wind_a": 0.0 }, "133355": { "creation_time": 1779734538303, "p": [ 4332.6865234375, 3199.951171875, 7173.3857421875 ], "wind_a": 0.0 }, "133356": { "creation_time": 1779734538303, "p": [ 4349.01123046875, 3210.152099609375, 7151.359375 ], "wind_a": 0.0 }, "133357": { "creation_time": 1779734538303, "p": [ 4366.16845703125, 3220.873291015625, 7129.73974609375 ], "wind_a": 0.0 }, "133358": { "creation_time": 1779734538303, "p": [ 4373.630859375, 3225.5361328125, 7103.38427734375 ], "wind_a": 0.0 }, "133359": { "creation_time": 1779734538303, "p": [ 4360.09765625, 3217.07958984375, 7079.99462890625 ], "wind_a": 0.0 }, "133360": { "creation_time": 1779734538303, "p": [ 4342.59521484375, 3206.14306640625, 7059.3564453125 ], "wind_a": 0.0 }, "133361": { "creation_time": 1779734538303, "p": [ 4325.92578125, 3195.7265625, 7038.3115234375 ], "wind_a": 0.0 }, "133362": { "creation_time": 1779734538303, "p": [ 4307.59130859375, 3184.269775390625, 7018.080078125 ], "wind_a": 0.0 }, "133363": { "creation_time": 1779734538303, "p": [ 4298.28564453125, 3178.455078125, 7007.10693359375 ], "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__8fwhzw7/model_reopt.pt", "scale": [ 0.07999999821186066, 0.07999999821186066 ], "tags": { "date_last_modified": "20260614185644675", "reviewed": { "date": "20260604080934303" } }, "type": "seg", "uuid": "same_wrap003025_lasagna" }