{ "area_vx2": 480156.25, "base_shape_zyx": [ 18946, 8174, 8174 ], "bbox": [ [ 4813.51513671875, 3190.682373046875, 6494.25048828125 ], [ 5126.58056640625, 3705.569580078125, 7078.22265625 ] ], "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": [ 19902.771484375, 13878.583984375, 26318.28515625 ], "final_anchor_h": 151.87956658005714, "final_anchor_w": 13.593695044517517, "final_shell_id": "shell_0007.tifxyz", "final_trim_bottom": 21, "final_trim_top": 20, "init_margin_grid_points": 80, "initial_seed": [ 19902.771484375, 13878.583984375, 26318.28515625 ], "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": 25, "mode": "corr-point-roi", "model_h": 8434.637451171875, "model_w": 8059.100675582886, "model_w_unit": "voxels", "output_radius_grid_points": 20, "parsed_point_count": 25, "projected_h_span_grid": 8.6927490234375, "projected_h_span_vx": 434.637451171875, "projected_points": [ { "collection_id": 3394, "direction_sign": 1, "grid_distance_to_anchor": 4.845025996536854, "h": 156.67559814453125, "point_id": 145558, "row_index": 0, "w": 14.280978202819824 }, { "collection_id": 3394, "direction_sign": 1, "grid_distance_to_anchor": 4.419186353351943, "h": 156.25416564941406, "point_id": 145559, "row_index": 1, "w": 14.219866752624512 }, { "collection_id": 3394, "direction_sign": 1, "grid_distance_to_anchor": 3.8461800966910915, "h": 155.68460083007813, "point_id": 145560, "row_index": 2, "w": 14.154779434204102 }, { "collection_id": 3394, "direction_sign": 1, "grid_distance_to_anchor": 3.406117603744973, "h": 155.24630737304688, "point_id": 145561, "row_index": 3, "w": 14.110118865966797 }, { "collection_id": 3394, "direction_sign": 1, "grid_distance_to_anchor": 3.1094096323507343, "h": 154.95709228515625, "point_id": 145562, "row_index": 4, "w": 14.03783893585205 }, { "collection_id": 3394, "direction_sign": 1, "grid_distance_to_anchor": 2.784690423873152, "h": 154.63323974609375, "point_id": 145563, "row_index": 5, "w": 14.008164405822754 }, { "collection_id": 3394, "direction_sign": 1, "grid_distance_to_anchor": 2.393489163342227, "h": 154.24778747558594, "point_id": 145564, "row_index": 6, "w": 13.940567016601563 }, { "collection_id": 3394, "direction_sign": 1, "grid_distance_to_anchor": 1.9729963104415373, "h": 153.8359375, "point_id": 145565, "row_index": 7, "w": 13.849287033081055 }, { "collection_id": 3394, "direction_sign": 1, "grid_distance_to_anchor": 1.5881638149216795, "h": 153.45758056640625, "point_id": 145566, "row_index": 8, "w": 13.772960662841797 }, { "collection_id": 3394, "direction_sign": 1, "grid_distance_to_anchor": 1.0382073148861781, "h": 152.91091918945313, "point_id": 145567, "row_index": 9, "w": 13.712800979614258 }, { "collection_id": 3394, "direction_sign": 1, "grid_distance_to_anchor": 0.7137291524134414, "h": 152.59002685546875, "point_id": 145568, "row_index": 10, "w": 13.66192626953125 }, { "collection_id": 3394, "direction_sign": 1, "grid_distance_to_anchor": 0.3559825847993937, "h": 152.23475646972656, "point_id": 145569, "row_index": 11, "w": 13.617438316345215 }, { "collection_id": 3394, "direction_sign": 1, "grid_distance_to_anchor": 0.0729079938535083, "h": 151.9493865966797, "point_id": 145570, "row_index": 12, "w": 13.614688873291016 }, { "collection_id": 3394, "direction_sign": 1, "grid_distance_to_anchor": 0.3487063135267001, "h": 151.5338897705078, "point_id": 145571, "row_index": 13, "w": 13.547829627990723 }, { "collection_id": 3394, "direction_sign": 1, "grid_distance_to_anchor": 0.6811289302062136, "h": 151.20518493652344, "point_id": 145572, "row_index": 14, "w": 13.49806022644043 }, { "collection_id": 3394, "direction_sign": 1, "grid_distance_to_anchor": 0.8934100755580154, "h": 150.99313354492188, "point_id": 145573, "row_index": 15, "w": 13.482258796691895 }, { "collection_id": 3394, "direction_sign": 1, "grid_distance_to_anchor": 1.208241189581291, "h": 150.68128967285156, "point_id": 145574, "row_index": 16, "w": 13.4388427734375 }, { "collection_id": 3394, "direction_sign": 1, "grid_distance_to_anchor": 1.5748873252721671, "h": 150.32070922851563, "point_id": 145575, "row_index": 17, "w": 13.369565963745117 }, { "collection_id": 3394, "direction_sign": 1, "grid_distance_to_anchor": 1.866198332729136, "h": 150.03521728515625, "point_id": 145576, "row_index": 18, "w": 13.308963775634766 }, { "collection_id": 3394, "direction_sign": 1, "grid_distance_to_anchor": 2.4596028540086308, "h": 149.4521942138672, "point_id": 145577, "row_index": 19, "w": 13.196820259094238 }, { "collection_id": 3394, "direction_sign": 1, "grid_distance_to_anchor": 2.72108604960921, "h": 149.19004821777344, "point_id": 145578, "row_index": 20, "w": 13.180415153503418 }, { "collection_id": 3394, "direction_sign": 1, "grid_distance_to_anchor": 3.0736004970980213, "h": 148.83787536621094, "point_id": 145579, "row_index": 21, "w": 13.151954650878906 }, { "collection_id": 3394, "direction_sign": 1, "grid_distance_to_anchor": 3.4941407234632584, "h": 148.41680908203125, "point_id": 145580, "row_index": 22, "w": 13.126437187194824 }, { "collection_id": 3394, "direction_sign": 1, "grid_distance_to_anchor": 3.843153124823048, "h": 148.06787109375, "point_id": 145581, "row_index": 23, "w": 13.102977752685547 }, { "collection_id": 3394, "direction_sign": 1, "grid_distance_to_anchor": 3.9279975913334386, "h": 147.98284912109375, "point_id": 145582, "row_index": 24, "w": 13.09896469116211 } ], "projected_w_span_grid": 1.1820135116577148, "projected_w_span_vx": 59.10067558288574, "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_3394/point_strip.lasagna.json", "mesh-h": 32, "mesh-step": 50, "mesh-w": 32, "model-h": 8434.637451171875, "model-init": "seed", "model-input": null, "model-output": "/tmp/fit_reopt_xz7kfi4c/model_reopt.pt", "model-w": 8059.100675582886, "model-w-unit": "voxels", "normal-mask-zero": 0, "out-dir": null, "progress": true, "pyramid-d": false, "seed": [ 19902.771484375, 13878.583984375, 26318.28515625 ], "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": { "3394": { "color": [ 0.0, 0.7450980544090271, 0.6274510025978088 ], "metadata": { "winding_is_absolute": true }, "name": "same_wrap3105", "points": { "145558": { "creation_time": 1779830056342, "p": [ 20084.96875, 13752.189453125, 27186.435546875 ], "wind_a": 0.0 }, "145559": { "creation_time": 1779830056342, "p": [ 20060.263671875, 13769.3271484375, 27118.890625 ], "wind_a": 0.0 }, "145560": { "creation_time": 1779830056342, "p": [ 20040.048828125, 13783.3505859375, 27049.08203125 ], "wind_a": 0.0 }, "145561": { "creation_time": 1779830056342, "p": [ 20026.32421875, 13792.8720703125, 26976.0 ], "wind_a": 0.0 }, "145562": { "creation_time": 1779830056342, "p": [ 20010.853515625, 13803.603515625, 26903.798828125 ], "wind_a": 0.0 }, "145563": { "creation_time": 1779830056342, "p": [ 19992.326171875, 13816.4580078125, 26833.138671875 ], "wind_a": 0.0 }, "145564": { "creation_time": 1779830056342, "p": [ 19974.23046875, 13829.0107421875, 26762.26171875 ], "wind_a": 0.0 }, "145565": { "creation_time": 1779830056342, "p": [ 19964.533203125, 13835.73828125, 26687.150390625 ], "wind_a": 0.0 }, "145566": { "creation_time": 1779830056342, "p": [ 19949.091796875, 13846.44921875, 26614.93359375 ], "wind_a": 0.0 }, "145567": { "creation_time": 1779830056342, "p": [ 19937.421875, 13854.5458984375, 26540.818359375 ], "wind_a": 0.0 }, "145568": { "creation_time": 1779830056342, "p": [ 19930.564453125, 13859.302734375, 26464.2734375 ], "wind_a": 0.0 }, "145569": { "creation_time": 1779830056342, "p": [ 19918.2109375, 13867.8720703125, 26390.501953125 ], "wind_a": 0.0 }, "145570": { "creation_time": 1779830056342, "p": [ 19902.771484375, 13878.583984375, 26318.28515625 ], "wind_a": 0.0 }, "145571": { "creation_time": 1779830056342, "p": [ 19889.0703125, 13888.087890625, 26245.19140625 ], "wind_a": 0.0 }, "145572": { "creation_time": 1779830056342, "p": [ 19873.162109375, 13899.1240234375, 26173.212890625 ], "wind_a": 0.0 }, "145573": { "creation_time": 1779830056342, "p": [ 19855.0703125, 13911.67578125, 26102.33203125 ], "wind_a": 0.0 }, "145574": { "creation_time": 1779830056342, "p": [ 19826.05859375, 13931.80078125, 26036.95703125 ], "wind_a": 0.0 }, "145575": { "creation_time": 1779830056342, "p": [ 19797.048828125, 13951.92578125, 25971.58203125 ], "wind_a": 0.0 }, "145576": { "creation_time": 1779830056342, "p": [ 19765.85546875, 13973.56640625, 25907.30859375 ], "wind_a": 0.0 }, "145577": { "creation_time": 1779830056342, "p": [ 19739.103515625, 13992.1240234375, 25840.794921875 ], "wind_a": 0.0 }, "145578": { "creation_time": 1779830056342, "p": [ 19717.486328125, 14007.1201171875, 25771.693359375 ], "wind_a": 0.0 }, "145579": { "creation_time": 1779830056342, "p": [ 19687.556640625, 14027.8828125, 25706.78125 ], "wind_a": 0.0 }, "145580": { "creation_time": 1779830056342, "p": [ 19651.99609375, 14052.552734375, 25644.70703125 ], "wind_a": 0.0 }, "145581": { "creation_time": 1779830056342, "p": [ 19618.619140625, 14075.70703125, 25581.53515625 ], "wind_a": 0.0 }, "145582": { "creation_time": 1779830056342, "p": [ 19609.40234375, 14082.1005859375, 25566.560546875 ], "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": [ 4975.69287109375, 3469.64599609375, 6579.5712890625 ], "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": { "3394": { "color": [ 0.0, 0.7450980544090271, 0.6274510025978088 ], "metadata": { "winding_is_absolute": true }, "name": "same_wrap3105", "points": { "145558": { "creation_time": 1779830056342, "p": [ 5021.2421875, 3438.04736328125, 6796.60888671875 ], "wind_a": 0.0 }, "145559": { "creation_time": 1779830056342, "p": [ 5015.06591796875, 3442.331787109375, 6779.72265625 ], "wind_a": 0.0 }, "145560": { "creation_time": 1779830056342, "p": [ 5010.01220703125, 3445.837646484375, 6762.2705078125 ], "wind_a": 0.0 }, "145561": { "creation_time": 1779830056342, "p": [ 5006.5810546875, 3448.218017578125, 6744.0 ], "wind_a": 0.0 }, "145562": { "creation_time": 1779830056342, "p": [ 5002.71337890625, 3450.90087890625, 6725.94970703125 ], "wind_a": 0.0 }, "145563": { "creation_time": 1779830056342, "p": [ 4998.08154296875, 3454.114501953125, 6708.28466796875 ], "wind_a": 0.0 }, "145564": { "creation_time": 1779830056342, "p": [ 4993.5576171875, 3457.252685546875, 6690.5654296875 ], "wind_a": 0.0 }, "145565": { "creation_time": 1779830056342, "p": [ 4991.13330078125, 3458.9345703125, 6671.78759765625 ], "wind_a": 0.0 }, "145566": { "creation_time": 1779830056342, "p": [ 4987.27294921875, 3461.6123046875, 6653.7333984375 ], "wind_a": 0.0 }, "145567": { "creation_time": 1779830056342, "p": [ 4984.35546875, 3463.636474609375, 6635.20458984375 ], "wind_a": 0.0 }, "145568": { "creation_time": 1779830056342, "p": [ 4982.64111328125, 3464.82568359375, 6616.068359375 ], "wind_a": 0.0 }, "145569": { "creation_time": 1779830056342, "p": [ 4979.552734375, 3466.968017578125, 6597.62548828125 ], "wind_a": 0.0 }, "145570": { "creation_time": 1779830056342, "p": [ 4975.69287109375, 3469.64599609375, 6579.5712890625 ], "wind_a": 0.0 }, "145571": { "creation_time": 1779830056342, "p": [ 4972.267578125, 3472.02197265625, 6561.2978515625 ], "wind_a": 0.0 }, "145572": { "creation_time": 1779830056342, "p": [ 4968.29052734375, 3474.781005859375, 6543.30322265625 ], "wind_a": 0.0 }, "145573": { "creation_time": 1779830056342, "p": [ 4963.767578125, 3477.9189453125, 6525.5830078125 ], "wind_a": 0.0 }, "145574": { "creation_time": 1779830056342, "p": [ 4956.5146484375, 3482.9501953125, 6509.2392578125 ], "wind_a": 0.0 }, "145575": { "creation_time": 1779830056342, "p": [ 4949.26220703125, 3487.9814453125, 6492.8955078125 ], "wind_a": 0.0 }, "145576": { "creation_time": 1779830056342, "p": [ 4941.4638671875, 3493.3916015625, 6476.8271484375 ], "wind_a": 0.0 }, "145577": { "creation_time": 1779830056342, "p": [ 4934.77587890625, 3498.031005859375, 6460.19873046875 ], "wind_a": 0.0 }, "145578": { "creation_time": 1779830056342, "p": [ 4929.37158203125, 3501.780029296875, 6442.92333984375 ], "wind_a": 0.0 }, "145579": { "creation_time": 1779830056342, "p": [ 4921.88916015625, 3506.970703125, 6426.6953125 ], "wind_a": 0.0 }, "145580": { "creation_time": 1779830056342, "p": [ 4912.9990234375, 3513.13818359375, 6411.1767578125 ], "wind_a": 0.0 }, "145581": { "creation_time": 1779830056342, "p": [ 4904.65478515625, 3518.9267578125, 6395.3837890625 ], "wind_a": 0.0 }, "145582": { "creation_time": 1779830056342, "p": [ 4902.3505859375, 3520.525146484375, 6391.64013671875 ], "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_xz7kfi4c/model_reopt.pt", "scale": [ 0.07999999821186066, 0.07999999821186066 ], "tags": { "date_last_modified": "20260614185644712", "reviewed": { "date": "20260604080934311" } }, "type": "seg", "uuid": "same_wrap003105_lasagna" }