{ "area_vx2": 611718.75, "base_shape_zyx": [ 18946, 8174, 8174 ], "bbox": [ [ 3546.33251953125, 2320.270263671875, 8211.626953125 ], [ 4476.95849609375, 2467.8115234375, 8747.439453125 ] ], "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": [ 15617.7138671875, 9330.69921875, 34000.0 ], "final_anchor_h": 207.15018670260906, "final_anchor_w": 183.78518180549145, "final_shell_id": "shell_0002.tifxyz", "final_trim_bottom": 28, "final_trim_top": 0, "init_margin_grid_points": 80, "initial_seed": [ 15617.7138671875, 9330.69921875, 34000.0 ], "initial_shell_id": "shell_0002.tifxyz", "initial_skipped_point_count": 0, "initial_skipped_reasons": {}, "initial_trim_bottom": 28, "initial_trim_top": 0, "initial_usable_point_count": 24, "mode": "corr-point-roi", "model_h": 8110.599517822266, "model_w": 8634.673309326172, "model_w_unit": "voxels", "output_radius_grid_points": 20, "parsed_point_count": 24, "projected_h_span_grid": 2.2119903564453125, "projected_h_span_vx": 110.59951782226563, "projected_points": [ { "collection_id": 2770, "direction_sign": -1, "grid_distance_to_anchor": 6.229129691020947, "h": 207.04708862304688, "point_id": 111992, "row_index": 0, "w": 190.01345825195313 }, { "collection_id": 2770, "direction_sign": -1, "grid_distance_to_anchor": 5.682623689024127, "h": 207.06077575683594, "point_id": 111993, "row_index": 1, "w": 189.46710205078125 }, { "collection_id": 2770, "direction_sign": -1, "grid_distance_to_anchor": 5.077354661102929, "h": 207.0693359375, "point_id": 111994, "row_index": 2, "w": 188.8618927001953 }, { "collection_id": 2770, "direction_sign": -1, "grid_distance_to_anchor": 4.515205789672162, "h": 207.05911254882813, "point_id": 111995, "row_index": 3, "w": 188.29946899414063 }, { "collection_id": 2770, "direction_sign": -1, "grid_distance_to_anchor": 3.9710498354327632, "h": 207.0274200439453, "point_id": 111996, "row_index": 4, "w": 187.75433349609375 }, { "collection_id": 2770, "direction_sign": -1, "grid_distance_to_anchor": 3.4395857501835114, "h": 207.04063415527344, "point_id": 111997, "row_index": 5, "w": 187.2230224609375 }, { "collection_id": 2770, "direction_sign": -1, "grid_distance_to_anchor": 2.880489462786167, "h": 207.07611083984375, "point_id": 111998, "row_index": 6, "w": 186.6647186279297 }, { "collection_id": 2770, "direction_sign": -1, "grid_distance_to_anchor": 2.369684616689762, "h": 207.10824584960938, "point_id": 111999, "row_index": 7, "w": 186.1544952392578 }, { "collection_id": 2770, "direction_sign": -1, "grid_distance_to_anchor": 1.8303760044853614, "h": 207.105224609375, "point_id": 112000, "row_index": 8, "w": 185.61500549316406 }, { "collection_id": 2770, "direction_sign": 1, "grid_distance_to_anchor": 2.4098903469654367, "h": 209.23941040039063, "point_id": 112001, "row_index": 9, "w": 184.98631286621094 }, { "collection_id": 2770, "direction_sign": 1, "grid_distance_to_anchor": 0.5735272953606433, "h": 207.1850128173828, "point_id": 112002, "row_index": 10, "w": 184.35765075683594 }, { "collection_id": 2770, "direction_sign": 1, "grid_distance_to_anchor": 0.03562739535707223, "h": 207.18360900878906, "point_id": 112003, "row_index": 11, "w": 183.77284240722656 }, { "collection_id": 2770, "direction_sign": 1, "grid_distance_to_anchor": 0.619204999118545, "h": 207.16676330566406, "point_id": 112004, "row_index": 12, "w": 183.16619873046875 }, { "collection_id": 2770, "direction_sign": 1, "grid_distance_to_anchor": 1.244005665102415, "h": 207.2128448486328, "point_id": 112005, "row_index": 13, "w": 182.54275512695313 }, { "collection_id": 2770, "direction_sign": 1, "grid_distance_to_anchor": 1.7935563294907686, "h": 207.30325317382813, "point_id": 112006, "row_index": 14, "w": 181.9981689453125 }, { "collection_id": 2770, "direction_sign": 1, "grid_distance_to_anchor": 2.33096914132143, "h": 207.3612823486328, "point_id": 112007, "row_index": 15, "w": 181.4637908935547 }, { "collection_id": 2770, "direction_sign": 1, "grid_distance_to_anchor": 2.838480482013172, "h": 207.44410705566406, "point_id": 112008, "row_index": 16, "w": 180.9619598388672 }, { "collection_id": 2770, "direction_sign": 1, "grid_distance_to_anchor": 3.3607795462674552, "h": 207.5109100341797, "point_id": 112009, "row_index": 17, "w": 180.44381713867188 }, { "collection_id": 2770, "direction_sign": 1, "grid_distance_to_anchor": 3.893718786911766, "h": 207.645263671875, "point_id": 112010, "row_index": 18, "w": 179.92306518554688 }, { "collection_id": 2770, "direction_sign": 1, "grid_distance_to_anchor": 4.3685162464015335, "h": 207.70477294921875, "point_id": 112011, "row_index": 19, "w": 179.45201110839844 }, { "collection_id": 2770, "direction_sign": 1, "grid_distance_to_anchor": 4.920968468056868, "h": 207.6697998046875, "point_id": 112012, "row_index": 20, "w": 178.8917236328125 }, { "collection_id": 2770, "direction_sign": 1, "grid_distance_to_anchor": 5.503415124137668, "h": 207.48501586914063, "point_id": 112013, "row_index": 21, "w": 178.29196166992188 }, { "collection_id": 2770, "direction_sign": 1, "grid_distance_to_anchor": 6.065294389168924, "h": 207.43789672851563, "point_id": 112014, "row_index": 22, "w": 177.72671508789063 }, { "collection_id": 2770, "direction_sign": 1, "grid_distance_to_anchor": 6.469672158439992, "h": 207.39097595214844, "point_id": 112015, "row_index": 23, "w": 177.3199920654297 } ], "projected_w_span_grid": 12.693466186523438, "projected_w_span_vx": 634.6733093261719, "projection_mode": "normal-line", "skipped_point_count": 0, "skipped_points": [], "skipped_reasons": {}, "usable_point_count": 24, "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_2770/point_strip.lasagna.json", "mesh-h": 32, "mesh-step": 50, "mesh-w": 32, "model-h": 8110.599517822266, "model-init": "seed", "model-input": null, "model-output": "/tmp/fit_reopt_e6ejad94/model_reopt.pt", "model-w": 8634.673309326172, "model-w-unit": "voxels", "normal-mask-zero": 0, "out-dir": null, "progress": true, "pyramid-d": false, "seed": [ 15617.7138671875, 9330.69921875, 34000.0 ], "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": { "2770": { "color": [ 0.0, 0.47058823704719543, 1.0 ], "metadata": { "winding_is_absolute": true }, "name": "same_wrap2552", "points": { "111992": { "creation_time": 1779685508313, "p": [ 16862.0234375, 9440.337890625, 34000.0 ], "wind_a": 0.0 }, "111993": { "creation_time": 1779685508313, "p": [ 16755.26953125, 9408.3603515625, 34000.0 ], "wind_a": 0.0 }, "111994": { "creation_time": 1779685508313, "p": [ 16640.947265625, 9394.6552734375, 34000.0 ], "wind_a": 0.0 }, "111995": { "creation_time": 1779685508313, "p": [ 16526.623046875, 9399.2236328125, 34000.0 ], "wind_a": 0.0 }, "111996": { "creation_time": 1779685508313, "p": [ 16410.408203125, 9399.2236328125, 34000.0 ], "wind_a": 0.0 }, "111997": { "creation_time": 1779685508313, "p": [ 16296.083984375, 9385.5185546875, 34000.0 ], "wind_a": 0.0 }, "111998": { "creation_time": 1779685508313, "p": [ 16181.7607421875, 9371.8134765625, 34000.0 ], "wind_a": 0.0 }, "111999": { "creation_time": 1779685508313, "p": [ 16069.330078125, 9353.541015625, 34000.0 ], "wind_a": 0.0 }, "112000": { "creation_time": 1779685508313, "p": [ 15962.576171875, 9321.5625, 34000.0 ], "wind_a": 0.0 }, "112001": { "creation_time": 1779685508313, "p": [ 15848.2529296875, 9307.857421875, 34000.0 ], "wind_a": 0.0 }, "112002": { "creation_time": 1779685508313, "p": [ 15732.037109375, 9316.994140625, 34000.0 ], "wind_a": 0.0 }, "112003": { "creation_time": 1779685508313, "p": [ 15617.7138671875, 9330.69921875, 34000.0 ], "wind_a": 0.0 }, "112004": { "creation_time": 1779685508313, "p": [ 15503.390625, 9344.404296875, 34000.0 ], "wind_a": 0.0 }, "112005": { "creation_time": 1779685508313, "p": [ 15400.4208984375, 9385.5185546875, 34000.0 ], "wind_a": 0.0 }, "112006": { "creation_time": 1779685508313, "p": [ 15300.77734375, 9434.6650390625, 34000.0 ], "wind_a": 0.0 }, "112007": { "creation_time": 1779685508313, "p": [ 15198.5302734375, 9477.5244140625, 34000.0 ], "wind_a": 0.0 }, "112008": { "creation_time": 1779685508313, "p": [ 15098.958984375, 9526.84375, 34000.0 ], "wind_a": 0.0 }, "112009": { "creation_time": 1779685508313, "p": [ 14996.1103515625, 9568.25, 34000.0 ], "wind_a": 0.0 }, "112010": { "creation_time": 1779685508313, "p": [ 14889.35546875, 9600.2275390625, 34000.0 ], "wind_a": 0.0 }, "112011": { "creation_time": 1779685508313, "p": [ 14782.6015625, 9632.2060546875, 34000.0 ], "wind_a": 0.0 }, "112012": { "creation_time": 1779685508313, "p": [ 14668.2783203125, 9645.91015625, 34000.0 ], "wind_a": 0.0 }, "112013": { "creation_time": 1779685508313, "p": [ 14559.6318359375, 9673.3203125, 34000.0 ], "wind_a": 0.0 }, "112014": { "creation_time": 1779685508313, "p": [ 14452.8779296875, 9705.2978515625, 34000.0 ], "wind_a": 0.0 }, "112015": { "creation_time": 1779685508313, "p": [ 14376.880859375, 9732.7080078125, 34000.0 ], "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": [ 3875.84765625, 2336.10107421875, 8500.0 ], "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": { "2770": { "color": [ 0.0, 0.47058823704719543, 1.0 ], "metadata": { "winding_is_absolute": true }, "name": "same_wrap2552", "points": { "111992": { "creation_time": 1779685508313, "p": [ 4215.505859375, 2360.08447265625, 8500.0 ], "wind_a": 0.0 }, "111993": { "creation_time": 1779685508313, "p": [ 4188.8173828125, 2352.090087890625, 8500.0 ], "wind_a": 0.0 }, "111994": { "creation_time": 1779685508313, "p": [ 4160.23681640625, 2348.663818359375, 8500.0 ], "wind_a": 0.0 }, "111995": { "creation_time": 1779685508313, "p": [ 4131.65576171875, 2349.805908203125, 8500.0 ], "wind_a": 0.0 }, "111996": { "creation_time": 1779685508313, "p": [ 4102.60205078125, 2349.805908203125, 8500.0 ], "wind_a": 0.0 }, "111997": { "creation_time": 1779685508313, "p": [ 4074.02099609375, 2346.379638671875, 8500.0 ], "wind_a": 0.0 }, "111998": { "creation_time": 1779685508313, "p": [ 4045.440185546875, 2342.953369140625, 8500.0 ], "wind_a": 0.0 }, "111999": { "creation_time": 1779685508313, "p": [ 4017.33251953125, 2338.38525390625, 8500.0 ], "wind_a": 0.0 }, "112000": { "creation_time": 1779685508313, "p": [ 3990.64404296875, 2330.390625, 8500.0 ], "wind_a": 0.0 }, "112001": { "creation_time": 1779685508313, "p": [ 3962.063232421875, 2326.96435546875, 8500.0 ], "wind_a": 0.0 }, "112002": { "creation_time": 1779685508313, "p": [ 3933.00927734375, 2329.24853515625, 8500.0 ], "wind_a": 0.0 }, "112003": { "creation_time": 1779685508313, "p": [ 3904.428466796875, 2332.6748046875, 8500.0 ], "wind_a": 0.0 }, "112004": { "creation_time": 1779685508313, "p": [ 3875.84765625, 2336.10107421875, 8500.0 ], "wind_a": 0.0 }, "112005": { "creation_time": 1779685508313, "p": [ 3850.105224609375, 2346.379638671875, 8500.0 ], "wind_a": 0.0 }, "112006": { "creation_time": 1779685508313, "p": [ 3825.1943359375, 2358.666259765625, 8500.0 ], "wind_a": 0.0 }, "112007": { "creation_time": 1779685508313, "p": [ 3799.632568359375, 2369.381103515625, 8500.0 ], "wind_a": 0.0 }, "112008": { "creation_time": 1779685508313, "p": [ 3774.73974609375, 2381.7109375, 8500.0 ], "wind_a": 0.0 }, "112009": { "creation_time": 1779685508313, "p": [ 3749.027587890625, 2392.0625, 8500.0 ], "wind_a": 0.0 }, "112010": { "creation_time": 1779685508313, "p": [ 3722.3388671875, 2400.056884765625, 8500.0 ], "wind_a": 0.0 }, "112011": { "creation_time": 1779685508313, "p": [ 3695.650390625, 2408.051513671875, 8500.0 ], "wind_a": 0.0 }, "112012": { "creation_time": 1779685508313, "p": [ 3667.069580078125, 2411.4775390625, 8500.0 ], "wind_a": 0.0 }, "112013": { "creation_time": 1779685508313, "p": [ 3639.907958984375, 2418.330078125, 8500.0 ], "wind_a": 0.0 }, "112014": { "creation_time": 1779685508313, "p": [ 3613.219482421875, 2426.324462890625, 8500.0 ], "wind_a": 0.0 }, "112015": { "creation_time": 1779685508313, "p": [ 3594.22021484375, 2433.177001953125, 8500.0 ], "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_e6ejad94/model_reopt.pt", "scale": [ 0.07999999821186066, 0.07999999821186066 ], "tags": { "date_last_modified": "20260614185644563", "reviewed": { "date": "20260604080934278" } }, "type": "seg", "uuid": "same_wrap002552_lasagna" }