{ "area_vx2": 684687.5, "base_shape_zyx": [ 18946, 8174, 8174 ], "bbox": [ [ 4161.37646484375, 3282.796875, 9931.0751953125 ], [ 4652.58154296875, 3966.503662109375, 10951.8349609375 ] ], "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": [ 17252.38671875, 14490.05078125, 42234.6953125 ], "final_anchor_h": 234.95734059810638, "final_anchor_w": 56.6301047205925, "final_shell_id": "shell_0007.tifxyz", "final_trim_bottom": 21, "final_trim_top": 20, "init_margin_grid_points": 80, "initial_seed": [ 17142.74609375, 14490.05078125, 41920.109375 ], "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": 28, "mode": "corr-point-roi", "model_h": 8683.219909667969, "model_w": 8308.375358581543, "model_w_unit": "voxels", "output_radius_grid_points": 20, "parsed_point_count": 28, "projected_h_span_grid": 13.664398193359375, "projected_h_span_vx": 683.2199096679688, "projected_points": [ { "collection_id": 737, "direction_sign": 1, "grid_distance_to_anchor": 6.547449101324539, "h": 228.90135192871094, "point_id": 80088, "row_index": 0, "w": 54.14131164550781 }, { "collection_id": 737, "direction_sign": 1, "grid_distance_to_anchor": 7.1339215433092695, "h": 228.43069458007813, "point_id": 80089, "row_index": 1, "w": 53.749874114990234 }, { "collection_id": 737, "direction_sign": 1, "grid_distance_to_anchor": 6.947433310593646, "h": 228.83810424804688, "point_id": 80090, "row_index": 2, "w": 53.340457916259766 }, { "collection_id": 737, "direction_sign": 1, "grid_distance_to_anchor": 7.301318035057249, "h": 228.9264373779297, "point_id": 80091, "row_index": 3, "w": 52.514591217041016 }, { "collection_id": 737, "direction_sign": 1, "grid_distance_to_anchor": 7.481474063705314, "h": 229.35861206054688, "point_id": 80092, "row_index": 4, "w": 51.66757583618164 }, { "collection_id": 737, "direction_sign": 1, "grid_distance_to_anchor": 6.47554080221917, "h": 230.00543212890625, "point_id": 80093, "row_index": 5, "w": 52.457427978515625 }, { "collection_id": 737, "direction_sign": 1, "grid_distance_to_anchor": 5.442720999128704, "h": 230.7392120361328, "point_id": 80094, "row_index": 6, "w": 53.1905403137207 }, { "collection_id": 737, "direction_sign": 1, "grid_distance_to_anchor": 4.448735942521938, "h": 231.3816375732422, "point_id": 80095, "row_index": 7, "w": 53.98329544067383 }, { "collection_id": 737, "direction_sign": 1, "grid_distance_to_anchor": 3.9123994201612584, "h": 231.42825317382813, "point_id": 80096, "row_index": 8, "w": 54.94119644165039 }, { "collection_id": 737, "direction_sign": 1, "grid_distance_to_anchor": 4.137804255256515, "h": 230.8990936279297, "point_id": 80097, "row_index": 9, "w": 55.82260513305664 }, { "collection_id": 737, "direction_sign": -1, "grid_distance_to_anchor": 4.782541941502429, "h": 230.21395874023438, "point_id": 80098, "row_index": 10, "w": 57.24087142944336 }, { "collection_id": 737, "direction_sign": -1, "grid_distance_to_anchor": 3.880606420873593, "h": 231.243408203125, "point_id": 80099, "row_index": 11, "w": 57.75518798828125 }, { "collection_id": 737, "direction_sign": -1, "grid_distance_to_anchor": 3.8695276766996014, "h": 231.28021240234375, "point_id": 80100, "row_index": 12, "w": 57.8350830078125 }, { "collection_id": 737, "direction_sign": -1, "grid_distance_to_anchor": 3.811831696184198, "h": 231.33375549316406, "point_id": 80101, "row_index": 13, "w": 57.81319046020508 }, { "collection_id": 737, "direction_sign": -1, "grid_distance_to_anchor": 2.4756830026682, "h": 232.7153778076172, "point_id": 80102, "row_index": 14, "w": 57.68015670776367 }, { "collection_id": 737, "direction_sign": -1, "grid_distance_to_anchor": 1.9345325581188006, "h": 233.24398803710938, "point_id": 80103, "row_index": 15, "w": 57.52834701538086 }, { "collection_id": 737, "direction_sign": -1, "grid_distance_to_anchor": 1.860523764704072, "h": 233.167236328125, "point_id": 80104, "row_index": 16, "w": 57.13713073730469 }, { "collection_id": 737, "direction_sign": -1, "grid_distance_to_anchor": 1.2057433217345206, "h": 233.7924041748047, "point_id": 80105, "row_index": 17, "w": 56.94113540649414 }, { "collection_id": 737, "direction_sign": -1, "grid_distance_to_anchor": 0.5363782540476246, "h": 234.4938201904297, "point_id": 80106, "row_index": 18, "w": 56.9000129699707 }, { "collection_id": 737, "direction_sign": -1, "grid_distance_to_anchor": 0.1682458662513476, "h": 234.86204528808594, "point_id": 80107, "row_index": 19, "w": 56.768760681152344 }, { "collection_id": 737, "direction_sign": -1, "grid_distance_to_anchor": 0.8790473189788713, "h": 235.82260131835938, "point_id": 80108, "row_index": 20, "w": 56.785179138183594 }, { "collection_id": 737, "direction_sign": -1, "grid_distance_to_anchor": 1.6851049199662658, "h": 236.634521484375, "point_id": 80109, "row_index": 21, "w": 56.793331146240234 }, { "collection_id": 737, "direction_sign": -1, "grid_distance_to_anchor": 2.096086034499308, "h": 237.03961181640625, "point_id": 80110, "row_index": 22, "w": 56.870361328125 }, { "collection_id": 737, "direction_sign": 1, "grid_distance_to_anchor": 6.110054008689809, "h": 241.00559997558594, "point_id": 80111, "row_index": 23, "w": 57.496891021728516 }, { "collection_id": 737, "direction_sign": 1, "grid_distance_to_anchor": 4.559359677339193, "h": 239.49063110351563, "point_id": 80112, "row_index": 24, "w": 57.11697006225586 }, { "collection_id": 737, "direction_sign": 1, "grid_distance_to_anchor": 5.0641241631882945, "h": 239.97183227539063, "point_id": 80113, "row_index": 25, "w": 57.337371826171875 }, { "collection_id": 737, "direction_sign": 1, "grid_distance_to_anchor": 6.08975725060813, "h": 240.96958923339844, "point_id": 80114, "row_index": 26, "w": 57.59861373901367 }, { "collection_id": 737, "direction_sign": 1, "grid_distance_to_anchor": 7.2166646363880895, "h": 242.0950927734375, "point_id": 80115, "row_index": 27, "w": 57.69440841674805 } ], "projected_w_span_grid": 6.167507171630859, "projected_w_span_vx": 308.37535858154297, "projection_mode": "normal-line", "skipped_point_count": 0, "skipped_points": [], "skipped_reasons": {}, "usable_point_count": 28, "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_737/point_strip.lasagna.json", "mesh-h": 32, "mesh-step": 50, "mesh-w": 32, "model-h": 8683.219909667969, "model-init": "seed", "model-input": null, "model-output": "/tmp/fit_reopt_zq5cfx2i/model_reopt.pt", "model-w": 8308.375358581543, "model-w-unit": "voxels", "normal-mask-zero": 0, "out-dir": null, "progress": true, "pyramid-d": false, "seed": [ 17252.38671875, 14490.05078125, 42234.6953125 ], "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": { "737": { "color": [ 0.250980406999588, 1.0, 0.6274510025978088 ], "metadata": { "winding_is_absolute": true }, "name": "same_wrap1807", "points": { "80088": { "creation_time": 1779568077273, "p": [ 17503.6484375, 14490.05078125, 40466.85546875 ], "wind_a": 0.0 }, "80089": { "creation_time": 1779568077273, "p": [ 17421.41796875, 14490.05078125, 40547.4453125 ], "wind_a": 0.0 }, "80090": { "creation_time": 1779568077273, "p": [ 17362.029296875, 14490.05078125, 40642.84375 ], "wind_a": 0.0 }, "80091": { "creation_time": 1779568077273, "p": [ 17311.77734375, 14490.05078125, 40742.02734375 ], "wind_a": 0.0 }, "80092": { "creation_time": 1779568077273, "p": [ 17271.390625, 14490.05078125, 40845.30078125 ], "wind_a": 0.0 }, "80093": { "creation_time": 1779568077273, "p": [ 17228.533203125, 14490.05078125, 40947.546875 ], "wind_a": 0.0 }, "80094": { "creation_time": 1779568077273, "p": [ 17188.904296875, 14490.05078125, 41051.1328125 ], "wind_a": 0.0 }, "80095": { "creation_time": 1779568077273, "p": [ 17139.5859375, 14490.05078125, 41150.703125 ], "wind_a": 0.0 }, "80096": { "creation_time": 1779568077273, "p": [ 17093.49609375, 14490.05078125, 41251.61328125 ], "wind_a": 0.0 }, "80097": { "creation_time": 1779568077273, "p": [ 17065.083984375, 14490.05078125, 41359.84765625 ], "wind_a": 0.0 }, "80098": { "creation_time": 1779568077273, "p": [ 17055.947265625, 14490.05078125, 41476.0625 ], "wind_a": 0.0 }, "80099": { "creation_time": 1779568077273, "p": [ 17065.083984375, 14490.05078125, 41592.27734375 ], "wind_a": 0.0 }, "80100": { "creation_time": 1779568077273, "p": [ 17083.357421875, 14490.05078125, 41704.70703125 ], "wind_a": 0.0 }, "80101": { "creation_time": 1779568077273, "p": [ 17110.76953125, 14490.05078125, 41813.35546875 ], "wind_a": 0.0 }, "80102": { "creation_time": 1779568077273, "p": [ 17142.74609375, 14490.05078125, 41920.109375 ], "wind_a": 0.0 }, "80103": { "creation_time": 1779568077273, "p": [ 17160.125, 14490.05078125, 42032.91015625 ], "wind_a": 0.0 }, "80104": { "creation_time": 1779568077273, "p": [ 17199.751953125, 14490.05078125, 42136.49609375 ], "wind_a": 0.0 }, "80105": { "creation_time": 1779568077273, "p": [ 17252.38671875, 14490.05078125, 42234.6953125 ], "wind_a": 0.0 }, "80106": { "creation_time": 1779568077273, "p": [ 17311.77734375, 14490.05078125, 42330.09375 ], "wind_a": 0.0 }, "80107": { "creation_time": 1779568077273, "p": [ 17383.244140625, 14490.05078125, 42420.4921875 ], "wind_a": 0.0 }, "80108": { "creation_time": 1779568077273, "p": [ 17448.828125, 14490.05078125, 42513.32421875 ], "wind_a": 0.0 }, "80109": { "creation_time": 1779568077273, "p": [ 17485.11328125, 14490.05078125, 42618.296875 ], "wind_a": 0.0 }, "80110": { "creation_time": 1779568077273, "p": [ 17518.28125, 14490.05078125, 42724.55859375 ], "wind_a": 0.0 }, "80111": { "creation_time": 1779568077273, "p": [ 17526.490234375, 14490.05078125, 42841.15625 ], "wind_a": 0.0 }, "80112": { "creation_time": 1779568077273, "p": [ 17494.51171875, 14490.05078125, 42947.91015625 ], "wind_a": 0.0 }, "80113": { "creation_time": 1779568077273, "p": [ 17441.65625, 14490.05078125, 43046.015625 ], "wind_a": 0.0 }, "80114": { "creation_time": 1779568077273, "p": [ 17382.646484375, 14490.05078125, 43141.57421875 ], "wind_a": 0.0 }, "80115": { "creation_time": 1779568077273, "p": [ 17330.05078125, 14490.05078125, 43189.6015625 ], "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": [ 4285.6865234375, 3622.5126953125, 10480.02734375 ], "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": { "737": { "color": [ 0.250980406999588, 1.0, 0.6274510025978088 ], "metadata": { "winding_is_absolute": true }, "name": "same_wrap1807", "points": { "80088": { "creation_time": 1779568077273, "p": [ 4375.912109375, 3622.5126953125, 10116.7138671875 ], "wind_a": 0.0 }, "80089": { "creation_time": 1779568077273, "p": [ 4355.3544921875, 3622.5126953125, 10136.861328125 ], "wind_a": 0.0 }, "80090": { "creation_time": 1779568077273, "p": [ 4340.50732421875, 3622.5126953125, 10160.7109375 ], "wind_a": 0.0 }, "80091": { "creation_time": 1779568077273, "p": [ 4327.9443359375, 3622.5126953125, 10185.5068359375 ], "wind_a": 0.0 }, "80092": { "creation_time": 1779568077273, "p": [ 4317.84765625, 3622.5126953125, 10211.3251953125 ], "wind_a": 0.0 }, "80093": { "creation_time": 1779568077273, "p": [ 4307.13330078125, 3622.5126953125, 10236.88671875 ], "wind_a": 0.0 }, "80094": { "creation_time": 1779568077273, "p": [ 4297.22607421875, 3622.5126953125, 10262.783203125 ], "wind_a": 0.0 }, "80095": { "creation_time": 1779568077273, "p": [ 4284.896484375, 3622.5126953125, 10287.67578125 ], "wind_a": 0.0 }, "80096": { "creation_time": 1779568077273, "p": [ 4273.3740234375, 3622.5126953125, 10312.9033203125 ], "wind_a": 0.0 }, "80097": { "creation_time": 1779568077273, "p": [ 4266.27099609375, 3622.5126953125, 10339.9619140625 ], "wind_a": 0.0 }, "80098": { "creation_time": 1779568077273, "p": [ 4263.98681640625, 3622.5126953125, 10369.015625 ], "wind_a": 0.0 }, "80099": { "creation_time": 1779568077273, "p": [ 4266.27099609375, 3622.5126953125, 10398.0693359375 ], "wind_a": 0.0 }, "80100": { "creation_time": 1779568077273, "p": [ 4270.83935546875, 3622.5126953125, 10426.1767578125 ], "wind_a": 0.0 }, "80101": { "creation_time": 1779568077273, "p": [ 4277.6923828125, 3622.5126953125, 10453.3388671875 ], "wind_a": 0.0 }, "80102": { "creation_time": 1779568077273, "p": [ 4285.6865234375, 3622.5126953125, 10480.02734375 ], "wind_a": 0.0 }, "80103": { "creation_time": 1779568077273, "p": [ 4290.03125, 3622.5126953125, 10508.2275390625 ], "wind_a": 0.0 }, "80104": { "creation_time": 1779568077273, "p": [ 4299.93798828125, 3622.5126953125, 10534.1240234375 ], "wind_a": 0.0 }, "80105": { "creation_time": 1779568077273, "p": [ 4313.0966796875, 3622.5126953125, 10558.673828125 ], "wind_a": 0.0 }, "80106": { "creation_time": 1779568077273, "p": [ 4327.9443359375, 3622.5126953125, 10582.5234375 ], "wind_a": 0.0 }, "80107": { "creation_time": 1779568077273, "p": [ 4345.81103515625, 3622.5126953125, 10605.123046875 ], "wind_a": 0.0 }, "80108": { "creation_time": 1779568077273, "p": [ 4362.20703125, 3622.5126953125, 10628.3310546875 ], "wind_a": 0.0 }, "80109": { "creation_time": 1779568077273, "p": [ 4371.2783203125, 3622.5126953125, 10654.57421875 ], "wind_a": 0.0 }, "80110": { "creation_time": 1779568077273, "p": [ 4379.5703125, 3622.5126953125, 10681.1396484375 ], "wind_a": 0.0 }, "80111": { "creation_time": 1779568077273, "p": [ 4381.62255859375, 3622.5126953125, 10710.2890625 ], "wind_a": 0.0 }, "80112": { "creation_time": 1779568077273, "p": [ 4373.6279296875, 3622.5126953125, 10736.9775390625 ], "wind_a": 0.0 }, "80113": { "creation_time": 1779568077273, "p": [ 4360.4140625, 3622.5126953125, 10761.50390625 ], "wind_a": 0.0 }, "80114": { "creation_time": 1779568077273, "p": [ 4345.66162109375, 3622.5126953125, 10785.3935546875 ], "wind_a": 0.0 }, "80115": { "creation_time": 1779568077273, "p": [ 4332.5126953125, 3622.5126953125, 10797.400390625 ], "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_zq5cfx2i/model_reopt.pt", "scale": [ 0.07999999821186066, 0.07999999821186066 ], "tags": { "date_last_modified": "20260614185644410", "reviewed": { "date": "20260604080934246" } }, "type": "seg", "uuid": "same_wrap001807_lasagna" }