{ "area_vx2": 646093.75, "base_shape_zyx": [ 18946, 8174, 8174 ], "bbox": [ [ 4475.8173828125, 2776.5029296875, 8723.2607421875 ], [ 5242.140625, 3400.4462890625, 9269.8671875 ] ], "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": [ 19499.861328125, 11585.083984375, 36000.0 ], "final_anchor_h": 201.0, "final_anchor_w": 8.75806337594986, "final_shell_id": "shell_0007.tifxyz", "final_trim_bottom": 21, "final_trim_top": 20, "init_margin_grid_points": 80, "initial_seed": [ 19499.861328125, 11585.083984375, 36000.0 ], "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": 27, "mode": "corr-point-roi", "model_h": 8298.046112060547, "model_w": 8543.13759803772, "model_w_unit": "voxels", "output_radius_grid_points": 20, "parsed_point_count": 27, "projected_h_span_grid": 5.9609222412109375, "projected_h_span_vx": 298.0461120605469, "projected_points": [ { "collection_id": 621, "direction_sign": -1, "grid_distance_to_anchor": 5.241361598807891, "h": 201.4587860107422, "point_id": 74187, "row_index": 0, "w": 13.979307174682617 }, { "collection_id": 621, "direction_sign": 1, "grid_distance_to_anchor": 5.281434488508488, "h": 202.87217712402344, "point_id": 74188, "row_index": 1, "w": 13.696535110473633 }, { "collection_id": 621, "direction_sign": 1, "grid_distance_to_anchor": 4.292327216376496, "h": 201.54757690429688, "point_id": 74189, "row_index": 2, "w": 13.01531982421875 }, { "collection_id": 621, "direction_sign": 1, "grid_distance_to_anchor": 3.816791168425042, "h": 201.3630828857422, "point_id": 74190, "row_index": 3, "w": 12.55754566192627 }, { "collection_id": 621, "direction_sign": 1, "grid_distance_to_anchor": 3.3302676702104885, "h": 201.48345947265625, "point_id": 74191, "row_index": 4, "w": 12.053051948547363 }, { "collection_id": 621, "direction_sign": 1, "grid_distance_to_anchor": 2.8848827439586597, "h": 201.6111297607422, "point_id": 74192, "row_index": 5, "w": 11.577472686767578 }, { "collection_id": 621, "direction_sign": 1, "grid_distance_to_anchor": 2.7529431490147727, "h": 201.6407012939453, "point_id": 74193, "row_index": 6, "w": 11.435412406921387 }, { "collection_id": 621, "direction_sign": 1, "grid_distance_to_anchor": 2.485278941381906, "h": 201.59149169921875, "point_id": 74194, "row_index": 7, "w": 11.171929359436035 }, { "collection_id": 621, "direction_sign": 1, "grid_distance_to_anchor": 1.9611499822736775, "h": 201.53952026367188, "point_id": 74195, "row_index": 8, "w": 10.64354133605957 }, { "collection_id": 621, "direction_sign": 1, "grid_distance_to_anchor": 1.692561056927404, "h": 201.38671875, "point_id": 74196, "row_index": 9, "w": 10.405853271484375 }, { "collection_id": 621, "direction_sign": 1, "grid_distance_to_anchor": 1.2452055967743423, "h": 201.5004425048828, "point_id": 74197, "row_index": 10, "w": 9.898280143737793 }, { "collection_id": 621, "direction_sign": 1, "grid_distance_to_anchor": 0.7723303616436159, "h": 201.1332550048828, "point_id": 74198, "row_index": 11, "w": 9.518811225891113 }, { "collection_id": 621, "direction_sign": -1, "grid_distance_to_anchor": 0.4928284945467239, "h": 201.1085968017578, "point_id": 74199, "row_index": 12, "w": 9.238778114318848 }, { "collection_id": 621, "direction_sign": 1, "grid_distance_to_anchor": 0.07435132914511025, "h": 201.06365966796875, "point_id": 74200, "row_index": 13, "w": 8.719650268554688 }, { "collection_id": 621, "direction_sign": 1, "grid_distance_to_anchor": 0.9926384178368919, "h": 201.38999938964844, "point_id": 74201, "row_index": 14, "w": 7.845248222351074 }, { "collection_id": 621, "direction_sign": 1, "grid_distance_to_anchor": 1.1739483662704564, "h": 201.2255401611328, "point_id": 74202, "row_index": 15, "w": 7.605984210968018 }, { "collection_id": 621, "direction_sign": 1, "grid_distance_to_anchor": 1.3856141439035607, "h": 200.9453582763672, "point_id": 74203, "row_index": 16, "w": 7.3735270500183105 }, { "collection_id": 621, "direction_sign": 1, "grid_distance_to_anchor": 5.983695791459145, "h": 206.85890197753906, "point_id": 74204, "row_index": 17, "w": 7.542381286621094 }, { "collection_id": 621, "direction_sign": 1, "grid_distance_to_anchor": 1.945692613212899, "h": 200.89797973632813, "point_id": 74205, "row_index": 18, "w": 6.815047264099121 }, { "collection_id": 621, "direction_sign": 1, "grid_distance_to_anchor": 2.4888843587969527, "h": 201.16397094726563, "point_id": 74206, "row_index": 19, "w": 6.274586200714111 }, { "collection_id": 621, "direction_sign": 1, "grid_distance_to_anchor": 2.8394856980482017, "h": 201.36923217773438, "point_id": 74207, "row_index": 20, "w": 5.942686557769775 }, { "collection_id": 621, "direction_sign": 1, "grid_distance_to_anchor": 3.187577413732346, "h": 201.14231872558594, "point_id": 74208, "row_index": 21, "w": 5.573664665222168 }, { "collection_id": 621, "direction_sign": 1, "grid_distance_to_anchor": 3.680068073186271, "h": 201.12640380859375, "point_id": 74209, "row_index": 22, "w": 5.080166816711426 }, { "collection_id": 621, "direction_sign": 1, "grid_distance_to_anchor": 4.184819928297703, "h": 201.0970916748047, "point_id": 74210, "row_index": 23, "w": 4.57436990737915 }, { "collection_id": 621, "direction_sign": 1, "grid_distance_to_anchor": 4.743358976015508, "h": 201.06137084960938, "point_id": 74211, "row_index": 24, "w": 4.015101432800293 }, { "collection_id": 621, "direction_sign": 1, "grid_distance_to_anchor": 5.530445782709052, "h": 200.91329956054688, "point_id": 74212, "row_index": 25, "w": 3.228297233581543 }, { "collection_id": 621, "direction_sign": 1, "grid_distance_to_anchor": 5.642280241779086, "h": 200.9066619873047, "point_id": 74213, "row_index": 26, "w": 3.1165552139282227 } ], "projected_w_span_grid": 10.862751960754395, "projected_w_span_vx": 543.1375980377197, "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_621/point_strip.lasagna.json", "mesh-h": 32, "mesh-step": 50, "mesh-w": 32, "model-h": 8298.046112060547, "model-init": "seed", "model-input": null, "model-output": "/tmp/fit_reopt_qsbxsmu_/model_reopt.pt", "model-w": 8543.13759803772, "model-w-unit": "voxels", "normal-mask-zero": 0, "out-dir": null, "progress": true, "pyramid-d": false, "seed": [ 19499.861328125, 11585.083984375, 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": { "621": { "color": [ 1.0, 0.3137255012989044, 0.47058823704719543 ], "metadata": { "winding_is_absolute": true }, "name": "same_wrap1620", "points": { "74187": { "creation_time": 1779554417387, "p": [ 20521.7734375, 12601.44140625, 36000.0 ], "wind_a": 0.0 }, "74188": { "creation_time": 1779554417387, "p": [ 20466.244140625, 12504.4423828125, 36000.0 ], "wind_a": 0.0 }, "74189": { "creation_time": 1779554417387, "p": [ 20407.037109375, 12408.966796875, 36000.0 ], "wind_a": 0.0 }, "74190": { "creation_time": 1779554417387, "p": [ 20349.634765625, 12312.744140625, 36000.0 ], "wind_a": 0.0 }, "74191": { "creation_time": 1779554417387, "p": [ 20284.44921875, 12219.744140625, 36000.0 ], "wind_a": 0.0 }, "74192": { "creation_time": 1779554417387, "p": [ 20227.470703125, 12123.345703125, 36000.0 ], "wind_a": 0.0 }, "74193": { "creation_time": 1779554417387, "p": [ 20154.0078125, 12033.775390625, 36000.0 ], "wind_a": 0.0 }, "74194": { "creation_time": 1779554417387, "p": [ 20067.98046875, 11951.7578125, 36000.0 ], "wind_a": 0.0 }, "74195": { "creation_time": 1779554417387, "p": [ 19981.05078125, 11871.921875, 36000.0 ], "wind_a": 0.0 }, "74196": { "creation_time": 1779554417387, "p": [ 19888.064453125, 11806.701171875, 36000.0 ], "wind_a": 0.0 }, "74197": { "creation_time": 1779554417387, "p": [ 19795.3828125, 11740.75, 36000.0 ], "wind_a": 0.0 }, "74198": { "creation_time": 1779554417387, "p": [ 19700.46875, 11680.1875, 36000.0 ], "wind_a": 0.0 }, "74199": { "creation_time": 1779554417387, "p": [ 19600.978515625, 11630.671875, 36000.0 ], "wind_a": 0.0 }, "74200": { "creation_time": 1779554417387, "p": [ 19499.861328125, 11585.083984375, 36000.0 ], "wind_a": 0.0 }, "74201": { "creation_time": 1779554417387, "p": [ 19403.625, 11527.716796875, 36000.0 ], "wind_a": 0.0 }, "74202": { "creation_time": 1779554417387, "p": [ 19307.38671875, 11470.3486328125, 36000.0 ], "wind_a": 0.0 }, "74203": { "creation_time": 1779554417387, "p": [ 19204.1875, 11429.7900390625, 36000.0 ], "wind_a": 0.0 }, "74204": { "creation_time": 1779554417387, "p": [ 19097.021484375, 11398.8046875, 36000.0 ], "wind_a": 0.0 }, "74205": { "creation_time": 1779554417387, "p": [ 18984.88671875, 11379.814453125, 36000.0 ], "wind_a": 0.0 }, "74206": { "creation_time": 1779554417387, "p": [ 18874.087890625, 11357.603515625, 36000.0 ], "wind_a": 0.0 }, "74207": { "creation_time": 1779554417387, "p": [ 18760.98828125, 11340.9453125, 36000.0 ], "wind_a": 0.0 }, "74208": { "creation_time": 1779554417387, "p": [ 18645.587890625, 11329.8388671875, 36000.0 ], "wind_a": 0.0 }, "74209": { "creation_time": 1779554417387, "p": [ 18527.88671875, 11324.2861328125, 36000.0 ], "wind_a": 0.0 }, "74210": { "creation_time": 1779554417387, "p": [ 18407.88671875, 11324.2861328125, 36000.0 ], "wind_a": 0.0 }, "74211": { "creation_time": 1779554417387, "p": [ 18289.994140625, 11319.201171875, 36000.0 ], "wind_a": 0.0 }, "74212": { "creation_time": 1779554417387, "p": [ 18174.240234375, 11308.951171875, 36000.0 ], "wind_a": 0.0 }, "74213": { "creation_time": 1779554417387, "p": [ 18150.705078125, 11307.626953125, 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": [ 4874.96533203125, 2896.27099609375, 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": { "621": { "color": [ 1.0, 0.3137255012989044, 0.47058823704719543 ], "metadata": { "winding_is_absolute": true }, "name": "same_wrap1620", "points": { "74187": { "creation_time": 1779554417387, "p": [ 5130.443359375, 3150.3603515625, 9000.0 ], "wind_a": 0.0 }, "74188": { "creation_time": 1779554417387, "p": [ 5116.56103515625, 3126.110595703125, 9000.0 ], "wind_a": 0.0 }, "74189": { "creation_time": 1779554417387, "p": [ 5101.75927734375, 3102.24169921875, 9000.0 ], "wind_a": 0.0 }, "74190": { "creation_time": 1779554417387, "p": [ 5087.40869140625, 3078.18603515625, 9000.0 ], "wind_a": 0.0 }, "74191": { "creation_time": 1779554417387, "p": [ 5071.1123046875, 3054.93603515625, 9000.0 ], "wind_a": 0.0 }, "74192": { "creation_time": 1779554417387, "p": [ 5056.86767578125, 3030.83642578125, 9000.0 ], "wind_a": 0.0 }, "74193": { "creation_time": 1779554417387, "p": [ 5038.501953125, 3008.44384765625, 9000.0 ], "wind_a": 0.0 }, "74194": { "creation_time": 1779554417387, "p": [ 5016.9951171875, 2987.939453125, 9000.0 ], "wind_a": 0.0 }, "74195": { "creation_time": 1779554417387, "p": [ 4995.2626953125, 2967.98046875, 9000.0 ], "wind_a": 0.0 }, "74196": { "creation_time": 1779554417387, "p": [ 4972.01611328125, 2951.67529296875, 9000.0 ], "wind_a": 0.0 }, "74197": { "creation_time": 1779554417387, "p": [ 4948.845703125, 2935.1875, 9000.0 ], "wind_a": 0.0 }, "74198": { "creation_time": 1779554417387, "p": [ 4925.1171875, 2920.046875, 9000.0 ], "wind_a": 0.0 }, "74199": { "creation_time": 1779554417387, "p": [ 4900.24462890625, 2907.66796875, 9000.0 ], "wind_a": 0.0 }, "74200": { "creation_time": 1779554417387, "p": [ 4874.96533203125, 2896.27099609375, 9000.0 ], "wind_a": 0.0 }, "74201": { "creation_time": 1779554417387, "p": [ 4850.90625, 2881.92919921875, 9000.0 ], "wind_a": 0.0 }, "74202": { "creation_time": 1779554417387, "p": [ 4826.8466796875, 2867.587158203125, 9000.0 ], "wind_a": 0.0 }, "74203": { "creation_time": 1779554417387, "p": [ 4801.046875, 2857.447509765625, 9000.0 ], "wind_a": 0.0 }, "74204": { "creation_time": 1779554417387, "p": [ 4774.25537109375, 2849.701171875, 9000.0 ], "wind_a": 0.0 }, "74205": { "creation_time": 1779554417387, "p": [ 4746.2216796875, 2844.95361328125, 9000.0 ], "wind_a": 0.0 }, "74206": { "creation_time": 1779554417387, "p": [ 4718.52197265625, 2839.40087890625, 9000.0 ], "wind_a": 0.0 }, "74207": { "creation_time": 1779554417387, "p": [ 4690.2470703125, 2835.236328125, 9000.0 ], "wind_a": 0.0 }, "74208": { "creation_time": 1779554417387, "p": [ 4661.39697265625, 2832.459716796875, 9000.0 ], "wind_a": 0.0 }, "74209": { "creation_time": 1779554417387, "p": [ 4631.9716796875, 2831.071533203125, 9000.0 ], "wind_a": 0.0 }, "74210": { "creation_time": 1779554417387, "p": [ 4601.9716796875, 2831.071533203125, 9000.0 ], "wind_a": 0.0 }, "74211": { "creation_time": 1779554417387, "p": [ 4572.49853515625, 2829.80029296875, 9000.0 ], "wind_a": 0.0 }, "74212": { "creation_time": 1779554417387, "p": [ 4543.56005859375, 2827.23779296875, 9000.0 ], "wind_a": 0.0 }, "74213": { "creation_time": 1779554417387, "p": [ 4537.67626953125, 2826.90673828125, 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_qsbxsmu_/model_reopt.pt", "scale": [ 0.07999999821186066, 0.07999999821186066 ], "tags": { "date_last_modified": "20260614185644378", "reviewed": { "date": "20260604080934240" } }, "type": "seg", "uuid": "same_wrap001620_lasagna" }