{ "area_vx2": 669375.0, "base_shape_zyx": [ 18946, 8174, 8174 ], "bbox": [ [ 4555.91748046875, 3429.080078125, 8712.3193359375 ], [ 5218.1943359375, 3962.76513671875, 9295.9970703125 ] ], "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": [ 19815.15625, 15382.9736328125, 36000.0 ], "final_anchor_h": 195.60172525048256, "final_anchor_w": 14.446807831525803, "final_shell_id": "shell_0000.tifxyz", "final_trim_bottom": 28, "final_trim_top": 27, "init_margin_grid_points": 80, "initial_seed": [ 20105.49609375, 15551.150390625, 36000.0 ], "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": 27, "mode": "corr-point-roi", "model_h": 8126.316833496094, "model_w": 8563.300657272339, "model_w_unit": "voxels", "output_radius_grid_points": 20, "parsed_point_count": 27, "projected_h_span_grid": 2.526336669921875, "projected_h_span_vx": 126.31683349609375, "projected_points": [ { "collection_id": 2464, "direction_sign": -1, "grid_distance_to_anchor": 3.9019552988674073, "h": 193.2016143798828, "point_id": 76187, "row_index": 0, "w": 17.523286819458008 }, { "collection_id": 2464, "direction_sign": -1, "grid_distance_to_anchor": 3.1021033352775937, "h": 193.88238525390625, "point_id": 76188, "row_index": 1, "w": 17.028844833374023 }, { "collection_id": 2464, "direction_sign": -1, "grid_distance_to_anchor": 3.072023615729166, "h": 193.82196044921875, "point_id": 76189, "row_index": 2, "w": 16.95075798034668 }, { "collection_id": 2464, "direction_sign": -1, "grid_distance_to_anchor": 2.722257028020028, "h": 193.87733459472656, "point_id": 76190, "row_index": 3, "w": 16.553264617919922 }, { "collection_id": 2464, "direction_sign": -1, "grid_distance_to_anchor": 1.6335975798961848, "h": 194.32162475585938, "point_id": 76191, "row_index": 4, "w": 15.461688995361328 }, { "collection_id": 2464, "direction_sign": -1, "grid_distance_to_anchor": 1.32535346800222, "h": 194.400634765625, "point_id": 76192, "row_index": 5, "w": 15.00711441040039 }, { "collection_id": 2464, "direction_sign": 1, "grid_distance_to_anchor": 0.1911788818540529, "h": 195.6035919189453, "point_id": 76193, "row_index": 6, "w": 14.637977600097656 }, { "collection_id": 2464, "direction_sign": 1, "grid_distance_to_anchor": 3.6559405311070425, "h": 194.98464965820313, "point_id": 76194, "row_index": 7, "w": 18.050294876098633 }, { "collection_id": 2464, "direction_sign": -1, "grid_distance_to_anchor": 7.111926939811374, "h": 195.55677795410156, "point_id": 76195, "row_index": 8, "w": 7.335022926330566 }, { "collection_id": 2464, "direction_sign": -1, "grid_distance_to_anchor": 6.178100349465215, "h": 195.53114318847656, "point_id": 76196, "row_index": 9, "w": 8.269110679626465 }, { "collection_id": 2464, "direction_sign": -1, "grid_distance_to_anchor": 5.012793246419603, "h": 195.53952026367188, "point_id": 76197, "row_index": 10, "w": 9.43440055847168 }, { "collection_id": 2464, "direction_sign": 1, "grid_distance_to_anchor": 4.169895745048473, "h": 195.5851287841797, "point_id": 76198, "row_index": 11, "w": 10.276945114135742 }, { "collection_id": 2464, "direction_sign": 1, "grid_distance_to_anchor": 3.5503521222576437, "h": 195.65997314453125, "point_id": 76199, "row_index": 12, "w": 10.896933555603027 }, { "collection_id": 2464, "direction_sign": 1, "grid_distance_to_anchor": 2.8432766185810974, "h": 195.64942932128906, "point_id": 76200, "row_index": 13, "w": 11.603931427001953 }, { "collection_id": 2464, "direction_sign": 1, "grid_distance_to_anchor": 2.2569057032748194, "h": 195.7279510498047, "point_id": 76201, "row_index": 14, "w": 12.193434715270996 }, { "collection_id": 2464, "direction_sign": 1, "grid_distance_to_anchor": 1.7024517146018419, "h": 195.65037536621094, "point_id": 76202, "row_index": 15, "w": 12.745051383972168 }, { "collection_id": 2464, "direction_sign": 1, "grid_distance_to_anchor": 1.1346820982868144, "h": 195.6062469482422, "point_id": 76203, "row_index": 16, "w": 13.312134742736816 }, { "collection_id": 2464, "direction_sign": 1, "grid_distance_to_anchor": 0.4769415454214385, "h": 195.48204040527344, "point_id": 76204, "row_index": 17, "w": 13.985127449035645 }, { "collection_id": 2464, "direction_sign": 1, "grid_distance_to_anchor": 0.20817674600563904, "h": 195.48704528808594, "point_id": 76205, "row_index": 18, "w": 14.620549201965332 }, { "collection_id": 2464, "direction_sign": 1, "grid_distance_to_anchor": 0.744286518779284, "h": 195.49757385253906, "point_id": 76206, "row_index": 19, "w": 15.183771133422852 }, { "collection_id": 2464, "direction_sign": 1, "grid_distance_to_anchor": 1.2765143213691974, "h": 195.4829559326172, "point_id": 76207, "row_index": 20, "w": 15.717784881591797 }, { "collection_id": 2464, "direction_sign": 1, "grid_distance_to_anchor": 1.7929350144593639, "h": 195.4217987060547, "point_id": 76208, "row_index": 21, "w": 16.23069190979004 }, { "collection_id": 2464, "direction_sign": 1, "grid_distance_to_anchor": 2.316910128238886, "h": 195.43321228027344, "point_id": 76209, "row_index": 22, "w": 16.75758171081543 }, { "collection_id": 2464, "direction_sign": 1, "grid_distance_to_anchor": 2.8507674148754996, "h": 195.36773681640625, "point_id": 76210, "row_index": 23, "w": 17.28795623779297 }, { "collection_id": 2464, "direction_sign": 1, "grid_distance_to_anchor": 3.5024521663776644, "h": 195.3031463623047, "point_id": 76211, "row_index": 24, "w": 17.93651008605957 }, { "collection_id": 2464, "direction_sign": 1, "grid_distance_to_anchor": 4.062001125496094, "h": 195.2405242919922, "point_id": 76212, "row_index": 25, "w": 18.492717742919922 }, { "collection_id": 2464, "direction_sign": 1, "grid_distance_to_anchor": 4.174132180882331, "h": 195.194580078125, "point_id": 76213, "row_index": 26, "w": 18.601036071777344 } ], "projected_w_span_grid": 11.266013145446777, "projected_w_span_vx": 563.3006572723389, "projection_mode": "normal-line", "skipped_point_count": 0, "skipped_points": [], "skipped_reasons": {}, "usable_point_count": 27, "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_2464/point_strip.lasagna.json", "mesh-h": 32, "mesh-step": 50, "mesh-w": 32, "model-h": 8126.316833496094, "model-init": "seed", "model-input": null, "model-output": "/tmp/fit_reopt_tasjdb21/model_reopt.pt", "model-w": 8563.300657272339, "model-w-unit": "voxels", "normal-mask-zero": 0, "out-dir": null, "progress": true, "pyramid-d": false, "seed": [ 19815.15625, 15382.9736328125, 36000.0 ], "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": { "2464": { "color": [ 1.0, 0.9019607901573181, 0.0 ], "metadata": { "winding_is_absolute": true }, "name": "same_wrap1686", "points": { "76187": { "creation_time": 1779555042453, "p": [ 20695.25, 14763.7978515625, 36000.0 ], "wind_a": 0.0 }, "76188": { "creation_time": 1779555042453, "p": [ 20723.013671875, 14872.2978515625, 36000.0 ], "wind_a": 0.0 }, "76189": { "creation_time": 1779555042453, "p": [ 20756.330078125, 14978.4970703125, 36000.0 ], "wind_a": 0.0 }, "76190": { "creation_time": 1779555042453, "p": [ 20772.98828125, 15091.5966796875, 36000.0 ], "wind_a": 0.0 }, "76191": { "creation_time": 1779555042453, "p": [ 20795.19921875, 15202.396484375, 36000.0 ], "wind_a": 0.0 }, "76192": { "creation_time": 1779555042453, "p": [ 20817.412109375, 15313.1962890625, 36000.0 ], "wind_a": 0.0 }, "76193": { "creation_time": 1779555042453, "p": [ 20828.517578125, 15428.5966796875, 36000.0 ], "wind_a": 0.0 }, "76194": { "creation_time": 1779555042453, "p": [ 20828.517578125, 15543.99609375, 36000.0 ], "wind_a": 0.0 }, "76195": { "creation_time": 1779555042453, "p": [ 20792.728515625, 15649.171875, 36000.0 ], "wind_a": 0.0 }, "76196": { "creation_time": 1779555042453, "p": [ 20723.58203125, 15740.5302734375, 36000.0 ], "wind_a": 0.0 }, "76197": { "creation_time": 1779555042453, "p": [ 20615.31640625, 15768.8623046875, 36000.0 ], "wind_a": 0.0 }, "76198": { "creation_time": 1779555042453, "p": [ 20504.517578125, 15746.6513671875, 36000.0 ], "wind_a": 0.0 }, "76199": { "creation_time": 1779555042453, "p": [ 20400.6171875, 15707.78125, 36000.0 ], "wind_a": 0.0 }, "76200": { "creation_time": 1779555042453, "p": [ 20301.224609375, 15658.0322265625, 36000.0 ], "wind_a": 0.0 }, "76201": { "creation_time": 1779555042453, "p": [ 20204.318359375, 15602.27734375, 36000.0 ], "wind_a": 0.0 }, "76202": { "creation_time": 1779555042453, "p": [ 20105.49609375, 15551.150390625, 36000.0 ], "wind_a": 0.0 }, "76203": { "creation_time": 1779555042453, "p": [ 20005.71875, 15502.326171875, 36000.0 ], "wind_a": 0.0 }, "76204": { "creation_time": 1779555042453, "p": [ 19908.720703125, 15446.7978515625, 36000.0 ], "wind_a": 0.0 }, "76205": { "creation_time": 1779555042453, "p": [ 19815.15625, 15382.9736328125, 36000.0 ], "wind_a": 0.0 }, "76206": { "creation_time": 1779555042453, "p": [ 19723.798828125, 15313.826171875, 36000.0 ], "wind_a": 0.0 }, "76207": { "creation_time": 1779555042453, "p": [ 19629.22265625, 15252.4482421875, 36000.0 ], "wind_a": 0.0 }, "76208": { "creation_time": 1779555042453, "p": [ 19536.203125, 15187.3125, 36000.0 ], "wind_a": 0.0 }, "76209": { "creation_time": 1779555042453, "p": [ 19437.5234375, 15135.837890625, 36000.0 ], "wind_a": 0.0 }, "76210": { "creation_time": 1779555042453, "p": [ 19338.224609375, 15085.86328125, 36000.0 ], "wind_a": 0.0 }, "76211": { "creation_time": 1779555042453, "p": [ 19240.984375, 15030.9150390625, 36000.0 ], "wind_a": 0.0 }, "76212": { "creation_time": 1779555042453, "p": [ 19144.74609375, 14973.546875, 36000.0 ], "wind_a": 0.0 }, "76213": { "creation_time": 1779555042453, "p": [ 19123.794921875, 14963.7001953125, 36000.0 ], "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": [ 5075.30615234375, 3914.508056640625, 9000.0 ], "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": { "2464": { "color": [ 1.0, 0.9019607901573181, 0.0 ], "metadata": { "winding_is_absolute": true }, "name": "same_wrap1686", "points": { "76187": { "creation_time": 1779555042453, "p": [ 5173.8125, 3690.949462890625, 9000.0 ], "wind_a": 0.0 }, "76188": { "creation_time": 1779555042453, "p": [ 5180.75341796875, 3718.074462890625, 9000.0 ], "wind_a": 0.0 }, "76189": { "creation_time": 1779555042453, "p": [ 5189.08251953125, 3744.624267578125, 9000.0 ], "wind_a": 0.0 }, "76190": { "creation_time": 1779555042453, "p": [ 5193.2470703125, 3772.899169921875, 9000.0 ], "wind_a": 0.0 }, "76191": { "creation_time": 1779555042453, "p": [ 5198.7998046875, 3800.59912109375, 9000.0 ], "wind_a": 0.0 }, "76192": { "creation_time": 1779555042453, "p": [ 5204.35302734375, 3828.299072265625, 9000.0 ], "wind_a": 0.0 }, "76193": { "creation_time": 1779555042453, "p": [ 5207.12939453125, 3857.149169921875, 9000.0 ], "wind_a": 0.0 }, "76194": { "creation_time": 1779555042453, "p": [ 5207.12939453125, 3885.9990234375, 9000.0 ], "wind_a": 0.0 }, "76195": { "creation_time": 1779555042453, "p": [ 5198.18212890625, 3912.29296875, 9000.0 ], "wind_a": 0.0 }, "76196": { "creation_time": 1779555042453, "p": [ 5180.8955078125, 3935.132568359375, 9000.0 ], "wind_a": 0.0 }, "76197": { "creation_time": 1779555042453, "p": [ 5153.8291015625, 3942.215576171875, 9000.0 ], "wind_a": 0.0 }, "76198": { "creation_time": 1779555042453, "p": [ 5126.12939453125, 3936.662841796875, 9000.0 ], "wind_a": 0.0 }, "76199": { "creation_time": 1779555042453, "p": [ 5100.154296875, 3926.9453125, 9000.0 ], "wind_a": 0.0 }, "76200": { "creation_time": 1779555042453, "p": [ 5075.30615234375, 3914.508056640625, 9000.0 ], "wind_a": 0.0 }, "76201": { "creation_time": 1779555042453, "p": [ 5051.07958984375, 3900.5693359375, 9000.0 ], "wind_a": 0.0 }, "76202": { "creation_time": 1779555042453, "p": [ 5026.3740234375, 3887.78759765625, 9000.0 ], "wind_a": 0.0 }, "76203": { "creation_time": 1779555042453, "p": [ 5001.4296875, 3875.58154296875, 9000.0 ], "wind_a": 0.0 }, "76204": { "creation_time": 1779555042453, "p": [ 4977.18017578125, 3861.699462890625, 9000.0 ], "wind_a": 0.0 }, "76205": { "creation_time": 1779555042453, "p": [ 4953.7890625, 3845.743408203125, 9000.0 ], "wind_a": 0.0 }, "76206": { "creation_time": 1779555042453, "p": [ 4930.94970703125, 3828.45654296875, 9000.0 ], "wind_a": 0.0 }, "76207": { "creation_time": 1779555042453, "p": [ 4907.3056640625, 3813.112060546875, 9000.0 ], "wind_a": 0.0 }, "76208": { "creation_time": 1779555042453, "p": [ 4884.05078125, 3796.828125, 9000.0 ], "wind_a": 0.0 }, "76209": { "creation_time": 1779555042453, "p": [ 4859.380859375, 3783.95947265625, 9000.0 ], "wind_a": 0.0 }, "76210": { "creation_time": 1779555042453, "p": [ 4834.55615234375, 3771.4658203125, 9000.0 ], "wind_a": 0.0 }, "76211": { "creation_time": 1779555042453, "p": [ 4810.24609375, 3757.728759765625, 9000.0 ], "wind_a": 0.0 }, "76212": { "creation_time": 1779555042453, "p": [ 4786.1865234375, 3743.38671875, 9000.0 ], "wind_a": 0.0 }, "76213": { "creation_time": 1779555042453, "p": [ 4780.94873046875, 3740.925048828125, 9000.0 ], "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_tasjdb21/model_reopt.pt", "scale": [ 0.07999999821186066, 0.07999999821186066 ], "tags": { "date_last_modified": "20260614185644396", "reviewed": { "date": "20260604080934243" } }, "type": "seg", "uuid": "same_wrap001686_lasagna" }