{ "area_vx2": 659062.5, "base_shape_zyx": [ 18946, 8174, 8174 ], "bbox": [ [ 3799.924560546875, 3603.370361328125, 11947.0556640625 ], [ 4396.3662109375, 4129.43310546875, 13046.455078125 ] ], "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": [ 16245.9892578125, 15224.8505859375, 50396.22265625 ], "final_anchor_h": 269.77725572139025, "final_anchor_w": 42.714477241039276, "final_shell_id": "shell_0000.tifxyz", "final_trim_bottom": 28, "final_trim_top": 27, "init_margin_grid_points": 80, "initial_seed": [ 16227.439453125, 15338.75, 50407.328125 ], "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": 8617.155456542969, "model_w": 8058.736038208008, "model_w_unit": "voxels", "output_radius_grid_points": 20, "parsed_point_count": 27, "projected_h_span_grid": 12.343109130859375, "projected_h_span_vx": 617.1554565429688, "projected_points": [ { "collection_id": 2870, "direction_sign": -1, "grid_distance_to_anchor": 6.98929722856714, "h": 262.8663330078125, "point_id": 113770, "row_index": 0, "w": 41.67072296142578 }, { "collection_id": 2870, "direction_sign": 1, "grid_distance_to_anchor": 6.26915335548399, "h": 263.5522155761719, "point_id": 113771, "row_index": 1, "w": 41.972076416015625 }, { "collection_id": 2870, "direction_sign": 1, "grid_distance_to_anchor": 5.571825827385372, "h": 264.23663330078125, "point_id": 113772, "row_index": 2, "w": 42.12562561035156 }, { "collection_id": 2870, "direction_sign": 1, "grid_distance_to_anchor": 5.044737258749985, "h": 264.7614440917969, "point_id": 113773, "row_index": 3, "w": 42.175025939941406 }, { "collection_id": 2870, "direction_sign": 1, "grid_distance_to_anchor": 4.519491528404913, "h": 265.27947998046875, "point_id": 113774, "row_index": 4, "w": 42.27196502685547 }, { "collection_id": 2870, "direction_sign": 1, "grid_distance_to_anchor": 3.9731448685158894, "h": 265.8204040527344, "point_id": 113775, "row_index": 5, "w": 42.35502624511719 }, { "collection_id": 2870, "direction_sign": 1, "grid_distance_to_anchor": 3.445238133998817, "h": 266.3423156738281, "point_id": 113776, "row_index": 6, "w": 42.44829559326172 }, { "collection_id": 2870, "direction_sign": 1, "grid_distance_to_anchor": 2.8358297258303495, "h": 266.94537353515625, "point_id": 113777, "row_index": 7, "w": 42.56489944458008 }, { "collection_id": 2870, "direction_sign": 1, "grid_distance_to_anchor": 2.342946603684544, "h": 267.4367980957031, "point_id": 113778, "row_index": 8, "w": 42.606510162353516 }, { "collection_id": 2870, "direction_sign": 1, "grid_distance_to_anchor": 1.8894518201247592, "h": 267.8878173828125, "point_id": 113779, "row_index": 9, "w": 42.721614837646484 }, { "collection_id": 2870, "direction_sign": 1, "grid_distance_to_anchor": 1.3075818458672288, "h": 268.47430419921875, "point_id": 113780, "row_index": 10, "w": 42.82442092895508 }, { "collection_id": 2870, "direction_sign": 1, "grid_distance_to_anchor": 0.6933024809572534, "h": 269.096435546875, "point_id": 113781, "row_index": 11, "w": 42.84544372558594 }, { "collection_id": 2870, "direction_sign": 1, "grid_distance_to_anchor": 0.15974460446302957, "h": 269.9364013671875, "point_id": 113782, "row_index": 12, "w": 42.70065689086914 }, { "collection_id": 2870, "direction_sign": 1, "grid_distance_to_anchor": 0.8155401208129252, "h": 270.54608154296875, "point_id": 113783, "row_index": 13, "w": 42.44242477416992 }, { "collection_id": 2870, "direction_sign": 1, "grid_distance_to_anchor": 1.305651127652903, "h": 270.9730529785156, "point_id": 113784, "row_index": 14, "w": 42.190269470214844 }, { "collection_id": 2870, "direction_sign": 1, "grid_distance_to_anchor": 1.7346687470640947, "h": 271.361328125, "point_id": 113785, "row_index": 15, "w": 42.00751876831055 }, { "collection_id": 2870, "direction_sign": 1, "grid_distance_to_anchor": 2.2497369291496807, "h": 271.8427734375, "point_id": 113786, "row_index": 16, "w": 41.8228759765625 }, { "collection_id": 2870, "direction_sign": 1, "grid_distance_to_anchor": 2.5188061343040293, "h": 272.0999450683594, "point_id": 113787, "row_index": 17, "w": 41.740055084228516 }, { "collection_id": 2870, "direction_sign": 1, "grid_distance_to_anchor": 2.8738546355237213, "h": 272.4717712402344, "point_id": 113788, "row_index": 18, "w": 41.71516418457031 }, { "collection_id": 2870, "direction_sign": 1, "grid_distance_to_anchor": 3.3118900066502457, "h": 272.93963623046875, "point_id": 113789, "row_index": 19, "w": 41.73062515258789 }, { "collection_id": 2870, "direction_sign": 1, "grid_distance_to_anchor": 4.089068796409962, "h": 273.74664306640625, "point_id": 113790, "row_index": 20, "w": 41.73241424560547 }, { "collection_id": 2870, "direction_sign": 1, "grid_distance_to_anchor": 4.501659580215921, "h": 274.1585693359375, "point_id": 113791, "row_index": 21, "w": 41.680538177490234 }, { "collection_id": 2870, "direction_sign": -1, "grid_distance_to_anchor": 4.090066929394917, "h": 273.7933654785156, "point_id": 113792, "row_index": 22, "w": 41.9401969909668 }, { "collection_id": 2870, "direction_sign": -1, "grid_distance_to_anchor": 4.523623888133381, "h": 274.2705078125, "point_id": 113793, "row_index": 23, "w": 42.191162109375 }, { "collection_id": 2870, "direction_sign": -1, "grid_distance_to_anchor": 4.9585820975069215, "h": 274.72723388671875, "point_id": 113794, "row_index": 24, "w": 42.4224967956543 }, { "collection_id": 2870, "direction_sign": -1, "grid_distance_to_anchor": 5.404706085698565, "h": 275.1816101074219, "point_id": 113795, "row_index": 25, "w": 42.6528205871582 }, { "collection_id": 2870, "direction_sign": -1, "grid_distance_to_anchor": 5.4324000361003915, "h": 275.2094421386719, "point_id": 113796, "row_index": 26, "w": 42.66630172729492 } ], "projected_w_span_grid": 1.1747207641601563, "projected_w_span_vx": 58.73603820800781, "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_2870/point_strip.lasagna.json", "mesh-h": 32, "mesh-step": 50, "mesh-w": 32, "model-h": 8617.155456542969, "model-init": "seed", "model-input": null, "model-output": "/tmp/fit_reopt_z7mr41h4/model_reopt.pt", "model-w": 8058.736038208008, "model-w-unit": "voxels", "normal-mask-zero": 0, "out-dir": null, "progress": true, "pyramid-d": false, "seed": [ 16245.9892578125, 15224.8505859375, 50396.22265625 ], "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": { "2870": { "color": [ 1.0, 0.7058823704719543, 0.3137255012989044 ], "metadata": { "winding_is_absolute": true }, "name": "same_wrap2625", "points": { "113770": { "creation_time": 1779686178846, "p": [ 16314.2119140625, 14805.9521484375, 49152.38671875 ], "wind_a": 0.0 }, "113771": { "creation_time": 1779686178846, "p": [ 16314.2412109375, 14805.7724609375, 49263.26171875 ], "wind_a": 0.0 }, "113772": { "creation_time": 1779686178846, "p": [ 16310.7001953125, 14827.515625, 49374.13671875 ], "wind_a": 0.0 }, "113773": { "creation_time": 1779686178846, "p": [ 16304.3935546875, 14866.23828125, 49477.88671875 ], "wind_a": 0.0 }, "113774": { "creation_time": 1779686178846, "p": [ 16299.8310546875, 14894.2548828125, 49586.12890625 ], "wind_a": 0.0 }, "113775": { "creation_time": 1779686178846, "p": [ 16294.5751953125, 14926.525390625, 49692.5859375 ], "wind_a": 0.0 }, "113776": { "creation_time": 1779686178846, "p": [ 16289.5927734375, 14957.1181640625, 49799.75 ], "wind_a": 0.0 }, "113777": { "creation_time": 1779686178846, "p": [ 16282.9716796875, 14997.7734375, 49902.6875 ], "wind_a": 0.0 }, "113778": { "creation_time": 1779686178846, "p": [ 16275.8310546875, 15041.6181640625, 50004.28515625 ], "wind_a": 0.0 }, "113779": { "creation_time": 1779686178846, "p": [ 16271.3681640625, 15069.021484375, 50112.78515625 ], "wind_a": 0.0 }, "113780": { "creation_time": 1779686178846, "p": [ 16267.2236328125, 15094.470703125, 50222.10546875 ], "wind_a": 0.0 }, "113781": { "creation_time": 1779686178846, "p": [ 16260.5263671875, 15135.58984375, 50324.84765625 ], "wind_a": 0.0 }, "113782": { "creation_time": 1779686178846, "p": [ 16245.9892578125, 15224.8505859375, 50396.22265625 ], "wind_a": 0.0 }, "113783": { "creation_time": 1779686178846, "p": [ 16227.439453125, 15338.75, 50407.328125 ], "wind_a": 0.0 }, "113784": { "creation_time": 1779686178846, "p": [ 16209.150390625, 15451.0478515625, 50422.34765625 ], "wind_a": 0.0 }, "113785": { "creation_time": 1779686178846, "p": [ 16191.8515625, 15557.2705078125, 50452.23046875 ], "wind_a": 0.0 }, "113786": { "creation_time": 1779686178846, "p": [ 16175.1181640625, 15660.015625, 50490.6171875 ], "wind_a": 0.0 }, "113787": { "creation_time": 1779686178846, "p": [ 16161.2822265625, 15744.97265625, 50564.6640625 ], "wind_a": 0.0 }, "113788": { "creation_time": 1779686178846, "p": [ 16152.69140625, 15797.71875, 50662.53125 ], "wind_a": 0.0 }, "113789": { "creation_time": 1779686178846, "p": [ 16146.6259765625, 15834.9638671875, 50766.8984375 ], "wind_a": 0.0 }, "113790": { "creation_time": 1779686178846, "p": [ 16139.2978515625, 15879.9599609375, 50868.015625 ], "wind_a": 0.0 }, "113791": { "creation_time": 1779686178846, "p": [ 16131.2333984375, 15929.4775390625, 50967.234375 ], "wind_a": 0.0 }, "113792": { "creation_time": 1779686178846, "p": [ 16132.8837890625, 15919.34375, 51078.3828125 ], "wind_a": 0.0 }, "113793": { "creation_time": 1779686178846, "p": [ 16141.0517578125, 15869.19140625, 51177.3359375 ], "wind_a": 0.0 }, "113794": { "creation_time": 1779686178846, "p": [ 16150.6953125, 15809.9755859375, 51272.484375 ], "wind_a": 0.0 }, "113795": { "creation_time": 1779686178846, "p": [ 16160.6884765625, 15748.6181640625, 51366.734375 ], "wind_a": 0.0 }, "113796": { "creation_time": 1779686178846, "p": [ 16161.5810546875, 15743.13671875, 51373.51953125 ], "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": [ 4056.85986328125, 3834.6875, 12601.83203125 ], "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": { "2870": { "color": [ 1.0, 0.7058823704719543, 0.3137255012989044 ], "metadata": { "winding_is_absolute": true }, "name": "same_wrap2625", "points": { "113770": { "creation_time": 1779686178846, "p": [ 4078.552978515625, 3701.488037109375, 12288.0966796875 ], "wind_a": 0.0 }, "113771": { "creation_time": 1779686178846, "p": [ 4078.560302734375, 3701.443115234375, 12315.8154296875 ], "wind_a": 0.0 }, "113772": { "creation_time": 1779686178846, "p": [ 4077.675048828125, 3706.87890625, 12343.5341796875 ], "wind_a": 0.0 }, "113773": { "creation_time": 1779686178846, "p": [ 4076.098388671875, 3716.5595703125, 12369.4716796875 ], "wind_a": 0.0 }, "113774": { "creation_time": 1779686178846, "p": [ 4074.957763671875, 3723.563720703125, 12396.5322265625 ], "wind_a": 0.0 }, "113775": { "creation_time": 1779686178846, "p": [ 4073.643798828125, 3731.63134765625, 12423.146484375 ], "wind_a": 0.0 }, "113776": { "creation_time": 1779686178846, "p": [ 4072.398193359375, 3739.279541015625, 12449.9375 ], "wind_a": 0.0 }, "113777": { "creation_time": 1779686178846, "p": [ 4070.742919921875, 3749.443359375, 12475.671875 ], "wind_a": 0.0 }, "113778": { "creation_time": 1779686178846, "p": [ 4068.957763671875, 3760.404541015625, 12501.0712890625 ], "wind_a": 0.0 }, "113779": { "creation_time": 1779686178846, "p": [ 4067.842041015625, 3767.25537109375, 12528.1962890625 ], "wind_a": 0.0 }, "113780": { "creation_time": 1779686178846, "p": [ 4066.805908203125, 3773.61767578125, 12555.5263671875 ], "wind_a": 0.0 }, "113781": { "creation_time": 1779686178846, "p": [ 4065.131591796875, 3783.8974609375, 12581.2119140625 ], "wind_a": 0.0 }, "113782": { "creation_time": 1779686178846, "p": [ 4061.497314453125, 3806.212646484375, 12599.0556640625 ], "wind_a": 0.0 }, "113783": { "creation_time": 1779686178846, "p": [ 4056.85986328125, 3834.6875, 12601.83203125 ], "wind_a": 0.0 }, "113784": { "creation_time": 1779686178846, "p": [ 4052.28759765625, 3862.761962890625, 12605.5869140625 ], "wind_a": 0.0 }, "113785": { "creation_time": 1779686178846, "p": [ 4047.962890625, 3889.317626953125, 12613.0576171875 ], "wind_a": 0.0 }, "113786": { "creation_time": 1779686178846, "p": [ 4043.779541015625, 3915.00390625, 12622.654296875 ], "wind_a": 0.0 }, "113787": { "creation_time": 1779686178846, "p": [ 4040.320556640625, 3936.2431640625, 12641.166015625 ], "wind_a": 0.0 }, "113788": { "creation_time": 1779686178846, "p": [ 4038.1728515625, 3949.4296875, 12665.6328125 ], "wind_a": 0.0 }, "113789": { "creation_time": 1779686178846, "p": [ 4036.656494140625, 3958.740966796875, 12691.724609375 ], "wind_a": 0.0 }, "113790": { "creation_time": 1779686178846, "p": [ 4034.824462890625, 3969.989990234375, 12717.00390625 ], "wind_a": 0.0 }, "113791": { "creation_time": 1779686178846, "p": [ 4032.808349609375, 3982.369384765625, 12741.80859375 ], "wind_a": 0.0 }, "113792": { "creation_time": 1779686178846, "p": [ 4033.220947265625, 3979.8359375, 12769.595703125 ], "wind_a": 0.0 }, "113793": { "creation_time": 1779686178846, "p": [ 4035.262939453125, 3967.2978515625, 12794.333984375 ], "wind_a": 0.0 }, "113794": { "creation_time": 1779686178846, "p": [ 4037.673828125, 3952.493896484375, 12818.12109375 ], "wind_a": 0.0 }, "113795": { "creation_time": 1779686178846, "p": [ 4040.172119140625, 3937.154541015625, 12841.68359375 ], "wind_a": 0.0 }, "113796": { "creation_time": 1779686178846, "p": [ 4040.395263671875, 3935.7841796875, 12843.3798828125 ], "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_z7mr41h4/model_reopt.pt", "scale": [ 0.07999999821186066, 0.07999999821186066 ], "tags": { "date_last_modified": "20260614185644598", "reviewed": { "date": "20260604080934286" } }, "type": "seg", "uuid": "same_wrap002625_lasagna" }