{ "area_vx2": 513750.0, "base_shape_zyx": [ 18946, 8174, 8174 ], "bbox": [ [ 4445.11572265625, 3489.2919921875, 6465.23681640625 ], [ 4865.4443359375, 3800.88232421875, 7050.97998046875 ] ], "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": [ 18988.50390625, 14512.8330078125, 26398.083984375 ], "final_anchor_h": 146.0, "final_anchor_w": 13.604552924633026, "final_shell_id": "shell_0000.tifxyz", "final_trim_bottom": 28, "final_trim_top": 27, "init_margin_grid_points": 80, "initial_seed": [ 18988.50390625, 14512.8330078125, 26398.083984375 ], "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": 25, "mode": "corr-point-roi", "model_h": 8413.46435546875, "model_w": 8037.326812744141, "model_w_unit": "voxels", "output_radius_grid_points": 20, "parsed_point_count": 25, "projected_h_span_grid": 8.269287109375, "projected_h_span_vx": 413.46435546875, "projected_points": [ { "collection_id": 3393, "direction_sign": -1, "grid_distance_to_anchor": 3.8272785903492608, "h": 149.74142456054688, "point_id": 145533, "row_index": 0, "w": 14.410656929016113 }, { "collection_id": 3393, "direction_sign": -1, "grid_distance_to_anchor": 3.499895191011309, "h": 149.42520141601563, "point_id": 145534, "row_index": 1, "w": 14.323761940002441 }, { "collection_id": 3393, "direction_sign": -1, "grid_distance_to_anchor": 3.166284653568145, "h": 149.10092163085938, "point_id": 145535, "row_index": 2, "w": 14.244586944580078 }, { "collection_id": 3393, "direction_sign": -1, "grid_distance_to_anchor": 2.8917099770307706, "h": 148.83424377441406, "point_id": 145536, "row_index": 3, "w": 14.178180694580078 }, { "collection_id": 3393, "direction_sign": -1, "grid_distance_to_anchor": 2.399919410194536, "h": 148.35147094726563, "point_id": 145537, "row_index": 4, "w": 14.084342002868652 }, { "collection_id": 3393, "direction_sign": -1, "grid_distance_to_anchor": 2.1889277589308915, "h": 148.1509246826172, "point_id": 145538, "row_index": 5, "w": 14.010665893554688 }, { "collection_id": 3393, "direction_sign": -1, "grid_distance_to_anchor": 1.8560569993681744, "h": 147.82464599609375, "point_id": 145539, "row_index": 6, "w": 13.944574356079102 }, { "collection_id": 3393, "direction_sign": -1, "grid_distance_to_anchor": 1.6346108506118355, "h": 147.603515625, "point_id": 145540, "row_index": 7, "w": 13.921870231628418 }, { "collection_id": 3393, "direction_sign": -1, "grid_distance_to_anchor": 1.1552028431003896, "h": 147.12254333496094, "point_id": 145541, "row_index": 8, "w": 13.877298355102539 }, { "collection_id": 3393, "direction_sign": 1, "grid_distance_to_anchor": 0.8650247253601054, "h": 146.84375, "point_id": 145542, "row_index": 9, "w": 13.795219421386719 }, { "collection_id": 3393, "direction_sign": 1, "grid_distance_to_anchor": 0.48746090873165643, "h": 146.46759033203125, "point_id": 145543, "row_index": 10, "w": 13.742311477661133 }, { "collection_id": 3393, "direction_sign": 1, "grid_distance_to_anchor": 0.25546271110815855, "h": 146.23536682128906, "point_id": 145544, "row_index": 11, "w": 13.703868865966797 }, { "collection_id": 3393, "direction_sign": 1, "grid_distance_to_anchor": 0.1395079405035316, "h": 146.00970458984375, "point_id": 145545, "row_index": 12, "w": 13.743722915649414 }, { "collection_id": 3393, "direction_sign": 1, "grid_distance_to_anchor": 0.4111041925379217, "h": 145.6152801513672, "point_id": 145546, "row_index": 13, "w": 13.749457359313965 }, { "collection_id": 3393, "direction_sign": 1, "grid_distance_to_anchor": 0.6508053961889998, "h": 145.37100219726563, "point_id": 145547, "row_index": 14, "w": 13.771614074707031 }, { "collection_id": 3393, "direction_sign": 1, "grid_distance_to_anchor": 0.88832263255991, "h": 145.14125061035156, "point_id": 145548, "row_index": 15, "w": 13.831855773925781 }, { "collection_id": 3393, "direction_sign": 1, "grid_distance_to_anchor": 1.185491119225916, "h": 144.85586547851563, "point_id": 145549, "row_index": 16, "w": 13.914948463439941 }, { "collection_id": 3393, "direction_sign": 1, "grid_distance_to_anchor": 1.5516228869387236, "h": 144.50244140625, "point_id": 145550, "row_index": 17, "w": 14.01057243347168 }, { "collection_id": 3393, "direction_sign": 1, "grid_distance_to_anchor": 1.845919499989687, "h": 144.22117614746094, "point_id": 145551, "row_index": 18, "w": 14.097710609436035 }, { "collection_id": 3393, "direction_sign": 1, "grid_distance_to_anchor": 2.0237971196402142, "h": 144.07421875, "point_id": 145552, "row_index": 19, "w": 14.226743698120117 }, { "collection_id": 3393, "direction_sign": 1, "grid_distance_to_anchor": 2.3856545162528775, "h": 143.7290802001953, "point_id": 145553, "row_index": 20, "w": 14.335491180419922 }, { "collection_id": 3393, "direction_sign": 1, "grid_distance_to_anchor": 2.7619128256596803, "h": 143.3519287109375, "point_id": 145554, "row_index": 21, "w": 14.389333724975586 }, { "collection_id": 3393, "direction_sign": 1, "grid_distance_to_anchor": 3.229691456643352, "h": 142.871337890625, "point_id": 145555, "row_index": 22, "w": 14.406039237976074 }, { "collection_id": 3393, "direction_sign": 1, "grid_distance_to_anchor": 4.582671722483222, "h": 141.47213745117188, "point_id": 145556, "row_index": 23, "w": 14.311193466186523 }, { "collection_id": 3393, "direction_sign": 1, "grid_distance_to_anchor": 4.3026655998743095, "h": 141.7812957763672, "point_id": 145557, "row_index": 24, "w": 14.45040512084961 } ], "projected_w_span_grid": 0.7465362548828125, "projected_w_span_vx": 37.326812744140625, "projection_mode": "normal-line", "skipped_point_count": 0, "skipped_points": [], "skipped_reasons": {}, "usable_point_count": 25, "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_3393/point_strip.lasagna.json", "mesh-h": 32, "mesh-step": 50, "mesh-w": 32, "model-h": 8413.46435546875, "model-init": "seed", "model-input": null, "model-output": "/tmp/fit_reopt_qmr9obl2/model_reopt.pt", "model-w": 8037.326812744141, "model-w-unit": "voxels", "normal-mask-zero": 0, "out-dir": null, "progress": true, "pyramid-d": false, "seed": [ 18988.50390625, 14512.8330078125, 26398.083984375 ], "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": { "3393": { "color": [ 1.0, 0.501960813999176, 0.0 ], "metadata": { "winding_is_absolute": true }, "name": "same_wrap3104", "points": { "145533": { "creation_time": 1779830043269, "p": [ 18883.5078125, 14585.6708984375, 27289.5859375 ], "wind_a": 0.0 }, "145534": { "creation_time": 1779830043269, "p": [ 18905.125, 14570.6748046875, 27220.484375 ], "wind_a": 0.0 }, "145535": { "creation_time": 1779830043269, "p": [ 18920.56640625, 14559.962890625, 27151.380859375 ], "wind_a": 0.0 }, "145536": { "creation_time": 1779830043269, "p": [ 18936.005859375, 14549.251953125, 27079.1640625 ], "wind_a": 0.0 }, "145537": { "creation_time": 1779830043269, "p": [ 18951.447265625, 14538.5400390625, 27006.94921875 ], "wind_a": 0.0 }, "145538": { "creation_time": 1779830043269, "p": [ 18965.611328125, 14528.7138671875, 26934.08984375 ], "wind_a": 0.0 }, "145539": { "creation_time": 1779830043269, "p": [ 18977.15234375, 14520.70703125, 26859.908203125 ], "wind_a": 0.0 }, "145540": { "creation_time": 1779830043269, "p": [ 18982.328125, 14517.1171875, 26782.515625 ], "wind_a": 0.0 }, "145541": { "creation_time": 1779830043269, "p": [ 18982.328125, 14517.1171875, 26702.515625 ], "wind_a": 0.0 }, "145542": { "creation_time": 1779830043269, "p": [ 18985.416015625, 14514.9755859375, 26624.07421875 ], "wind_a": 0.0 }, "145543": { "creation_time": 1779830043269, "p": [ 18988.50390625, 14512.8330078125, 26545.62890625 ], "wind_a": 0.0 }, "145544": { "creation_time": 1779830043269, "p": [ 18997.767578125, 14506.40625, 26473.4140625 ], "wind_a": 0.0 }, "145545": { "creation_time": 1779830043269, "p": [ 18988.50390625, 14512.8330078125, 26398.083984375 ], "wind_a": 0.0 }, "145546": { "creation_time": 1779830043269, "p": [ 18976.150390625, 14521.40234375, 26324.3125 ], "wind_a": 0.0 }, "145547": { "creation_time": 1779830043269, "p": [ 18954.0625, 14536.7265625, 26255.447265625 ], "wind_a": 0.0 }, "145548": { "creation_time": 1779830043269, "p": [ 18926.7421875, 14555.6787109375, 26189.21875 ], "wind_a": 0.0 }, "145549": { "creation_time": 1779830043269, "p": [ 18902.037109375, 14572.8173828125, 26121.673828125 ], "wind_a": 0.0 }, "145550": { "creation_time": 1779830043269, "p": [ 18871.396484375, 14594.072265625, 26057.12109375 ], "wind_a": 0.0 }, "145551": { "creation_time": 1779830043269, "p": [ 18843.36328125, 14613.5205078125, 25991.25390625 ], "wind_a": 0.0 }, "145552": { "creation_time": 1779830043269, "p": [ 18811.193359375, 14635.837890625, 25927.47265625 ], "wind_a": 0.0 }, "145553": { "creation_time": 1779830043269, "p": [ 18775.630859375, 14660.5078125, 25865.3984375 ], "wind_a": 0.0 }, "145554": { "creation_time": 1779830043269, "p": [ 18737.88671875, 14686.6923828125, 25804.42578125 ], "wind_a": 0.0 }, "145555": { "creation_time": 1779830043269, "p": [ 18702.32421875, 14711.3623046875, 25742.35546875 ], "wind_a": 0.0 }, "145556": { "creation_time": 1779830043269, "p": [ 18673.314453125, 14731.4873046875, 25676.98046875 ], "wind_a": 0.0 }, "145557": { "creation_time": 1779830043269, "p": [ 18664.25390625, 14737.7724609375, 25658.435546875 ], "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": [ 4747.1259765625, 3628.208251953125, 6599.52099609375 ], "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": { "3393": { "color": [ 1.0, 0.501960813999176, 0.0 ], "metadata": { "winding_is_absolute": true }, "name": "same_wrap3104", "points": { "145533": { "creation_time": 1779830043269, "p": [ 4720.876953125, 3646.417724609375, 6822.396484375 ], "wind_a": 0.0 }, "145534": { "creation_time": 1779830043269, "p": [ 4726.28125, 3642.668701171875, 6805.12109375 ], "wind_a": 0.0 }, "145535": { "creation_time": 1779830043269, "p": [ 4730.1416015625, 3639.99072265625, 6787.84521484375 ], "wind_a": 0.0 }, "145536": { "creation_time": 1779830043269, "p": [ 4734.00146484375, 3637.31298828125, 6769.791015625 ], "wind_a": 0.0 }, "145537": { "creation_time": 1779830043269, "p": [ 4737.86181640625, 3634.635009765625, 6751.7373046875 ], "wind_a": 0.0 }, "145538": { "creation_time": 1779830043269, "p": [ 4741.40283203125, 3632.178466796875, 6733.5224609375 ], "wind_a": 0.0 }, "145539": { "creation_time": 1779830043269, "p": [ 4744.2880859375, 3630.1767578125, 6714.97705078125 ], "wind_a": 0.0 }, "145540": { "creation_time": 1779830043269, "p": [ 4745.58203125, 3629.279296875, 6695.62890625 ], "wind_a": 0.0 }, "145541": { "creation_time": 1779830043269, "p": [ 4745.58203125, 3629.279296875, 6675.62890625 ], "wind_a": 0.0 }, "145542": { "creation_time": 1779830043269, "p": [ 4746.35400390625, 3628.743896484375, 6656.0185546875 ], "wind_a": 0.0 }, "145543": { "creation_time": 1779830043269, "p": [ 4747.1259765625, 3628.208251953125, 6636.4072265625 ], "wind_a": 0.0 }, "145544": { "creation_time": 1779830043269, "p": [ 4749.44189453125, 3626.6015625, 6618.353515625 ], "wind_a": 0.0 }, "145545": { "creation_time": 1779830043269, "p": [ 4747.1259765625, 3628.208251953125, 6599.52099609375 ], "wind_a": 0.0 }, "145546": { "creation_time": 1779830043269, "p": [ 4744.03759765625, 3630.3505859375, 6581.078125 ], "wind_a": 0.0 }, "145547": { "creation_time": 1779830043269, "p": [ 4738.515625, 3634.181640625, 6563.86181640625 ], "wind_a": 0.0 }, "145548": { "creation_time": 1779830043269, "p": [ 4731.685546875, 3638.919677734375, 6547.3046875 ], "wind_a": 0.0 }, "145549": { "creation_time": 1779830043269, "p": [ 4725.50927734375, 3643.204345703125, 6530.41845703125 ], "wind_a": 0.0 }, "145550": { "creation_time": 1779830043269, "p": [ 4717.84912109375, 3648.51806640625, 6514.2802734375 ], "wind_a": 0.0 }, "145551": { "creation_time": 1779830043269, "p": [ 4710.8408203125, 3653.380126953125, 6497.8134765625 ], "wind_a": 0.0 }, "145552": { "creation_time": 1779830043269, "p": [ 4702.79833984375, 3658.95947265625, 6481.8681640625 ], "wind_a": 0.0 }, "145553": { "creation_time": 1779830043269, "p": [ 4693.90771484375, 3665.126953125, 6466.349609375 ], "wind_a": 0.0 }, "145554": { "creation_time": 1779830043269, "p": [ 4684.4716796875, 3671.673095703125, 6451.1064453125 ], "wind_a": 0.0 }, "145555": { "creation_time": 1779830043269, "p": [ 4675.5810546875, 3677.840576171875, 6435.5888671875 ], "wind_a": 0.0 }, "145556": { "creation_time": 1779830043269, "p": [ 4668.32861328125, 3682.871826171875, 6419.2451171875 ], "wind_a": 0.0 }, "145557": { "creation_time": 1779830043269, "p": [ 4666.0634765625, 3684.443115234375, 6414.60888671875 ], "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_qmr9obl2/model_reopt.pt", "scale": [ 0.07999999821186066, 0.07999999821186066 ], "tags": { "date_last_modified": "20260614185644711", "reviewed": { "date": "20260604080934310" } }, "type": "seg", "uuid": "same_wrap003104_lasagna" }