{ "area_vx2": 531093.75, "base_shape_zyx": [ 18946, 8174, 8174 ], "bbox": [ [ 4485.36669921875, 3376.671142578125, 8699.0771484375 ], [ 4998.7998046875, 3811.90625, 9695.802734375 ] ], "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": [ 18989.078125, 14512.43359375, 36848.28125 ], "final_anchor_h": 199.11942917108536, "final_anchor_w": 21.119429171085358, "final_shell_id": "shell_0000.tifxyz", "final_trim_bottom": 28, "final_trim_top": 27, "init_margin_grid_points": 80, "initial_seed": [ 18989.078125, 14512.43359375, 36848.28125 ], "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": 8497.095489501953, "model_w": 8048.472595214844, "model_w_unit": "voxels", "output_radius_grid_points": 20, "parsed_point_count": 27, "projected_h_span_grid": 9.941909790039063, "projected_h_span_vx": 497.0954895019531, "projected_points": [ { "collection_id": 3376, "direction_sign": 1, "grid_distance_to_anchor": 5.347722754450765, "h": 204.41323852539063, "point_id": 144971, "row_index": 0, "w": 21.876873016357422 }, { "collection_id": 3376, "direction_sign": 1, "grid_distance_to_anchor": 5.0603634178889, "h": 204.1167449951172, "point_id": 144972, "row_index": 1, "w": 21.915740966796875 }, { "collection_id": 3376, "direction_sign": 1, "grid_distance_to_anchor": 4.83431894240465, "h": 203.89035034179688, "point_id": 144973, "row_index": 2, "w": 21.899782180786133 }, { "collection_id": 3376, "direction_sign": 1, "grid_distance_to_anchor": 4.299183947274656, "h": 203.35865783691406, "point_id": 144974, "row_index": 3, "w": 21.834917068481445 }, { "collection_id": 3376, "direction_sign": -1, "grid_distance_to_anchor": 3.52934046954895, "h": 202.59329223632813, "point_id": 144975, "row_index": 4, "w": 21.74274253845215 }, { "collection_id": 3376, "direction_sign": -1, "grid_distance_to_anchor": 2.6460314980019817, "h": 201.72433471679688, "point_id": 144976, "row_index": 5, "w": 21.58413314819336 }, { "collection_id": 3376, "direction_sign": -1, "grid_distance_to_anchor": 2.2802341693539043, "h": 201.36936950683594, "point_id": 144977, "row_index": 6, "w": 21.489883422851563 }, { "collection_id": 3376, "direction_sign": -1, "grid_distance_to_anchor": 1.794789746081, "h": 200.89309692382813, "point_id": 144978, "row_index": 7, "w": 21.393970489501953 }, { "collection_id": 3376, "direction_sign": -1, "grid_distance_to_anchor": 1.7026319812390496, "h": 200.8076171875, "point_id": 144979, "row_index": 8, "w": 21.340736389160156 }, { "collection_id": 3376, "direction_sign": -1, "grid_distance_to_anchor": 1.453969045122497, "h": 200.55686950683594, "point_id": 144980, "row_index": 9, "w": 21.338041305541992 }, { "collection_id": 3376, "direction_sign": -1, "grid_distance_to_anchor": 1.1528426595173953, "h": 200.24969482421875, "point_id": 144981, "row_index": 10, "w": 21.346466064453125 }, { "collection_id": 3376, "direction_sign": 1, "grid_distance_to_anchor": 2.6390360530983887, "h": 201.73300170898438, "point_id": 144982, "row_index": 11, "w": 21.48514747619629 }, { "collection_id": 3376, "direction_sign": 1, "grid_distance_to_anchor": 0.4244789132068899, "h": 199.53187561035156, "point_id": 144983, "row_index": 12, "w": 21.21977996826172 }, { "collection_id": 3376, "direction_sign": 1, "grid_distance_to_anchor": 0.2632982759472095, "h": 199.37319946289063, "point_id": 144984, "row_index": 13, "w": 21.189619064331055 }, { "collection_id": 3376, "direction_sign": 1, "grid_distance_to_anchor": 0.0910328666402084, "h": 199.0289306640625, "point_id": 144985, "row_index": 14, "w": 21.1292781829834 }, { "collection_id": 3376, "direction_sign": 1, "grid_distance_to_anchor": 0.4016765356895865, "h": 198.72073364257813, "point_id": 144986, "row_index": 15, "w": 21.07058334350586 }, { "collection_id": 3376, "direction_sign": 1, "grid_distance_to_anchor": 0.6132477132537143, "h": 198.50885009765625, "point_id": 144987, "row_index": 16, "w": 21.062280654907227 }, { "collection_id": 3376, "direction_sign": 1, "grid_distance_to_anchor": 0.974101595762118, "h": 198.15145874023438, "point_id": 144988, "row_index": 17, "w": 21.01030921936035 }, { "collection_id": 3376, "direction_sign": 1, "grid_distance_to_anchor": 1.4352743743969238, "h": 197.6934814453125, "point_id": 144989, "row_index": 18, "w": 20.956071853637695 }, { "collection_id": 3376, "direction_sign": 1, "grid_distance_to_anchor": 1.8065932691380162, "h": 197.32115173339844, "point_id": 144990, "row_index": 19, "w": 20.9462890625 }, { "collection_id": 3376, "direction_sign": 1, "grid_distance_to_anchor": 2.1899704705970695, "h": 196.93515014648438, "point_id": 144991, "row_index": 20, "w": 20.961645126342773 }, { "collection_id": 3376, "direction_sign": 1, "grid_distance_to_anchor": 2.57834651787053, "h": 196.5444793701172, "point_id": 144992, "row_index": 21, "w": 20.987125396728516 }, { "collection_id": 3376, "direction_sign": 1, "grid_distance_to_anchor": 3.055239541156331, "h": 196.0661163330078, "point_id": 144993, "row_index": 22, "w": 21.010942459106445 }, { "collection_id": 3376, "direction_sign": 1, "grid_distance_to_anchor": 3.4011957127711074, "h": 195.71910095214844, "point_id": 144994, "row_index": 23, "w": 21.04261589050293 }, { "collection_id": 3376, "direction_sign": 1, "grid_distance_to_anchor": 3.7293855399833915, "h": 195.39083862304688, "point_id": 144995, "row_index": 24, "w": 21.042428970336914 }, { "collection_id": 3376, "direction_sign": 1, "grid_distance_to_anchor": 4.0861595563096325, "h": 195.03359985351563, "point_id": 144996, "row_index": 25, "w": 21.067480087280273 }, { "collection_id": 3376, "direction_sign": 1, "grid_distance_to_anchor": 4.649053080548554, "h": 194.47132873535156, "point_id": 144997, "row_index": 26, "w": 21.025318145751953 } ], "projected_w_span_grid": 0.969451904296875, "projected_w_span_vx": 48.47259521484375, "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_3376/point_strip.lasagna.json", "mesh-h": 32, "mesh-step": 50, "mesh-w": 32, "model-h": 8497.095489501953, "model-init": "seed", "model-input": null, "model-output": "/tmp/fit_reopt_hr6yasqm/model_reopt.pt", "model-w": 8048.472595214844, "model-w-unit": "voxels", "normal-mask-zero": 0, "out-dir": null, "progress": true, "pyramid-d": false, "seed": [ 18989.078125, 14512.43359375, 36848.28125 ], "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": { "3376": { "color": [ 0.0, 0.7450980544090271, 0.6274510025978088 ], "metadata": { "winding_is_absolute": true }, "name": "same_wrap3089", "points": { "144971": { "creation_time": 1779829915669, "p": [ 18973.63671875, 14523.1455078125, 37827.5703125 ], "wind_a": 0.0 }, "144972": { "creation_time": 1779829915669, "p": [ 18964.279296875, 14529.63671875, 37752.28515625 ], "wind_a": 0.0 }, "144973": { "creation_time": 1779829915669, "p": [ 18948.37109375, 14540.6728515625, 37680.3046875 ], "wind_a": 0.0 }, "144974": { "creation_time": 1779829915669, "p": [ 18933.4921875, 14550.9951171875, 37607.80859375 ], "wind_a": 0.0 }, "144975": { "creation_time": 1779829915669, "p": [ 18930.404296875, 14553.13671875, 37529.36328125 ], "wind_a": 0.0 }, "144976": { "creation_time": 1779829915669, "p": [ 18942.755859375, 14544.5673828125, 37455.58984375 ], "wind_a": 0.0 }, "144977": { "creation_time": 1779829915669, "p": [ 18958.197265625, 14533.8564453125, 37383.375 ], "wind_a": 0.0 }, "144978": { "creation_time": 1779829915669, "p": [ 18970.548828125, 14525.287109375, 37309.6015625 ], "wind_a": 0.0 }, "144979": { "creation_time": 1779829915669, "p": [ 18985.990234375, 14514.576171875, 37237.38671875 ], "wind_a": 0.0 }, "144980": { "creation_time": 1779829915669, "p": [ 18995.25390625, 14508.1494140625, 37162.0546875 ], "wind_a": 0.0 }, "144981": { "creation_time": 1779829915669, "p": [ 18998.220703125, 14506.0908203125, 37083.55078125 ], "wind_a": 0.0 }, "144982": { "creation_time": 1779829915669, "p": [ 18998.341796875, 14506.0068359375, 37003.61328125 ], "wind_a": 0.0 }, "144983": { "creation_time": 1779829915669, "p": [ 18995.25390625, 14508.1494140625, 36925.16796875 ], "wind_a": 0.0 }, "144984": { "creation_time": 1779829915669, "p": [ 18989.078125, 14512.43359375, 36848.28125 ], "wind_a": 0.0 }, "144985": { "creation_time": 1779829915669, "p": [ 18982.90234375, 14516.7177734375, 36771.3984375 ], "wind_a": 0.0 }, "144986": { "creation_time": 1779829915669, "p": [ 18973.63671875, 14523.1455078125, 36696.06640625 ], "wind_a": 0.0 }, "144987": { "creation_time": 1779829915669, "p": [ 18957.6015625, 14534.2705078125, 36624.15234375 ], "wind_a": 0.0 }, "144988": { "creation_time": 1779829915669, "p": [ 18937.32421875, 14548.3359375, 36554.375 ], "wind_a": 0.0 }, "144989": { "creation_time": 1779829915669, "p": [ 18918.05078125, 14561.7060546875, 36484.08984375 ], "wind_a": 0.0 }, "144990": { "creation_time": 1779829915669, "p": [ 18902.611328125, 14572.41796875, 36411.875 ], "wind_a": 0.0 }, "144991": { "creation_time": 1779829915669, "p": [ 18887.171875, 14583.12890625, 36339.65625 ], "wind_a": 0.0 }, "144992": { "creation_time": 1779829915669, "p": [ 18868.642578125, 14595.982421875, 36268.99609375 ], "wind_a": 0.0 }, "144993": { "creation_time": 1779829915669, "p": [ 18849.046875, 14609.5771484375, 36198.875 ], "wind_a": 0.0 }, "144994": { "creation_time": 1779829915669, "p": [ 18833.13671875, 14620.61328125, 36126.8984375 ], "wind_a": 0.0 }, "144995": { "creation_time": 1779829915669, "p": [ 18819.412109375, 14630.134765625, 36053.81640625 ], "wind_a": 0.0 }, "144996": { "creation_time": 1779829915669, "p": [ 18805.685546875, 14639.65625, 35980.734375 ], "wind_a": 0.0 }, "144997": { "creation_time": 1779829915669, "p": [ 18797.6171875, 14645.2548828125, 35907.01953125 ], "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": [ 4747.26953125, 3628.1083984375, 9212.0703125 ], "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": { "3376": { "color": [ 0.0, 0.7450980544090271, 0.6274510025978088 ], "metadata": { "winding_is_absolute": true }, "name": "same_wrap3089", "points": { "144971": { "creation_time": 1779829915669, "p": [ 4743.4091796875, 3630.786376953125, 9456.892578125 ], "wind_a": 0.0 }, "144972": { "creation_time": 1779829915669, "p": [ 4741.06982421875, 3632.4091796875, 9438.0712890625 ], "wind_a": 0.0 }, "144973": { "creation_time": 1779829915669, "p": [ 4737.0927734375, 3635.168212890625, 9420.076171875 ], "wind_a": 0.0 }, "144974": { "creation_time": 1779829915669, "p": [ 4733.373046875, 3637.748779296875, 9401.9521484375 ], "wind_a": 0.0 }, "144975": { "creation_time": 1779829915669, "p": [ 4732.60107421875, 3638.2841796875, 9382.3408203125 ], "wind_a": 0.0 }, "144976": { "creation_time": 1779829915669, "p": [ 4735.68896484375, 3636.141845703125, 9363.8974609375 ], "wind_a": 0.0 }, "144977": { "creation_time": 1779829915669, "p": [ 4739.54931640625, 3633.464111328125, 9345.84375 ], "wind_a": 0.0 }, "144978": { "creation_time": 1779829915669, "p": [ 4742.63720703125, 3631.32177734375, 9327.400390625 ], "wind_a": 0.0 }, "144979": { "creation_time": 1779829915669, "p": [ 4746.49755859375, 3628.64404296875, 9309.3466796875 ], "wind_a": 0.0 }, "144980": { "creation_time": 1779829915669, "p": [ 4748.8134765625, 3627.037353515625, 9290.513671875 ], "wind_a": 0.0 }, "144981": { "creation_time": 1779829915669, "p": [ 4749.55517578125, 3626.522705078125, 9270.8876953125 ], "wind_a": 0.0 }, "144982": { "creation_time": 1779829915669, "p": [ 4749.58544921875, 3626.501708984375, 9250.9033203125 ], "wind_a": 0.0 }, "144983": { "creation_time": 1779829915669, "p": [ 4748.8134765625, 3627.037353515625, 9231.2919921875 ], "wind_a": 0.0 }, "144984": { "creation_time": 1779829915669, "p": [ 4747.26953125, 3628.1083984375, 9212.0703125 ], "wind_a": 0.0 }, "144985": { "creation_time": 1779829915669, "p": [ 4745.7255859375, 3629.179443359375, 9192.849609375 ], "wind_a": 0.0 }, "144986": { "creation_time": 1779829915669, "p": [ 4743.4091796875, 3630.786376953125, 9174.0166015625 ], "wind_a": 0.0 }, "144987": { "creation_time": 1779829915669, "p": [ 4739.400390625, 3633.567626953125, 9156.0380859375 ], "wind_a": 0.0 }, "144988": { "creation_time": 1779829915669, "p": [ 4734.3310546875, 3637.083984375, 9138.59375 ], "wind_a": 0.0 }, "144989": { "creation_time": 1779829915669, "p": [ 4729.5126953125, 3640.426513671875, 9121.0224609375 ], "wind_a": 0.0 }, "144990": { "creation_time": 1779829915669, "p": [ 4725.65283203125, 3643.1044921875, 9102.96875 ], "wind_a": 0.0 }, "144991": { "creation_time": 1779829915669, "p": [ 4721.79296875, 3645.7822265625, 9084.9140625 ], "wind_a": 0.0 }, "144992": { "creation_time": 1779829915669, "p": [ 4717.16064453125, 3648.99560546875, 9067.2490234375 ], "wind_a": 0.0 }, "144993": { "creation_time": 1779829915669, "p": [ 4712.26171875, 3652.394287109375, 9049.71875 ], "wind_a": 0.0 }, "144994": { "creation_time": 1779829915669, "p": [ 4708.2841796875, 3655.1533203125, 9031.724609375 ], "wind_a": 0.0 }, "144995": { "creation_time": 1779829915669, "p": [ 4704.85302734375, 3657.53369140625, 9013.4541015625 ], "wind_a": 0.0 }, "144996": { "creation_time": 1779829915669, "p": [ 4701.42138671875, 3659.9140625, 8995.18359375 ], "wind_a": 0.0 }, "144997": { "creation_time": 1779829915669, "p": [ 4699.404296875, 3661.313720703125, 8976.7548828125 ], "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_hr6yasqm/model_reopt.pt", "scale": [ 0.07999999821186066, 0.07999999821186066 ], "tags": { "date_last_modified": "20260614185644699", "reviewed": { "date": "20260604080934308" } }, "type": "seg", "uuid": "same_wrap003089_lasagna" }