{ "area_vx2": 417812.5, "base_shape_zyx": [ 18946, 8174, 8174 ], "bbox": [ [ 4191.4912109375, 3757.24560546875, 14027.599609375 ], [ 4691.43994140625, 3909.41796875, 14823.638671875 ] ], "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": [ 17726.140625, 15377.5224609375, 57888.3671875 ], "final_anchor_h": 320.56005880236626, "final_anchor_w": 21.442312568426132, "final_shell_id": "shell_0007.tifxyz", "final_trim_bottom": 21, "final_trim_top": 20, "init_margin_grid_points": 80, "initial_seed": [ 17748.39453125, 15311.01953125, 57677.4140625 ], "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": 18, "mode": "corr-point-roi", "model_h": 8327.35595703125, "model_w": 8058.862495422363, "model_w_unit": "voxels", "output_radius_grid_points": 20, "parsed_point_count": 18, "projected_h_span_grid": 6.547119140625, "projected_h_span_vx": 327.35595703125, "projected_points": [ { "collection_id": 879, "direction_sign": 1, "grid_distance_to_anchor": 2.3776021105597795, "h": 318.1832580566406, "point_id": 61134, "row_index": 0, "w": 21.504037857055664 }, { "collection_id": 879, "direction_sign": 1, "grid_distance_to_anchor": 2.3308227543892, "h": 318.2301940917969, "point_id": 61135, "row_index": 1, "w": 21.50913429260254 }, { "collection_id": 879, "direction_sign": 1, "grid_distance_to_anchor": 2.076207894844463, "h": 318.48858642578125, "point_id": 61136, "row_index": 2, "w": 21.582460403442383 }, { "collection_id": 879, "direction_sign": 1, "grid_distance_to_anchor": 2.4073106215724054, "h": 318.1648864746094, "point_id": 61137, "row_index": 3, "w": 21.683753967285156 }, { "collection_id": 879, "direction_sign": 1, "grid_distance_to_anchor": 2.296323207646691, "h": 318.27471923828125, "point_id": 61138, "row_index": 4, "w": 21.666641235351563 }, { "collection_id": 879, "direction_sign": -1, "grid_distance_to_anchor": 3.1827798324067587, "h": 317.3772888183594, "point_id": 61139, "row_index": 5, "w": 21.43439483642578 }, { "collection_id": 879, "direction_sign": -1, "grid_distance_to_anchor": 3.586637331839205, "h": 316.99273681640625, "point_id": 61140, "row_index": 6, "w": 21.070585250854492 }, { "collection_id": 879, "direction_sign": -1, "grid_distance_to_anchor": 3.4641614328112094, "h": 317.1539611816406, "point_id": 61141, "row_index": 7, "w": 20.81071662902832 }, { "collection_id": 879, "direction_sign": -1, "grid_distance_to_anchor": 3.841832079027131, "h": 316.7884826660156, "point_id": 61142, "row_index": 8, "w": 20.710952758789063 }, { "collection_id": 879, "direction_sign": -1, "grid_distance_to_anchor": 3.100239019574035, "h": 317.55572509765625, "point_id": 61143, "row_index": 9, "w": 20.67715835571289 }, { "collection_id": 879, "direction_sign": -1, "grid_distance_to_anchor": 2.348008962961603, "h": 318.3833312988281, "point_id": 61144, "row_index": 10, "w": 20.561969757080078 }, { "collection_id": 879, "direction_sign": -1, "grid_distance_to_anchor": 2.009463701096517, "h": 318.78179931640625, "point_id": 61145, "row_index": 11, "w": 20.50650405883789 }, { "collection_id": 879, "direction_sign": -1, "grid_distance_to_anchor": 1.8105499786934378, "h": 319.0015563964844, "point_id": 61146, "row_index": 12, "w": 20.52081298828125 }, { "collection_id": 879, "direction_sign": -1, "grid_distance_to_anchor": 1.168536312801896, "h": 319.79852294921875, "point_id": 61147, "row_index": 13, "w": 20.556005477905273 }, { "collection_id": 879, "direction_sign": 1, "grid_distance_to_anchor": 1.2808140410833573, "h": 321.59332275390625, "point_id": 61148, "row_index": 14, "w": 20.685443878173828 }, { "collection_id": 879, "direction_sign": 1, "grid_distance_to_anchor": 2.0949711764101777, "h": 322.5323486328125, "point_id": 61149, "row_index": 15, "w": 20.735929489135742 }, { "collection_id": 879, "direction_sign": 1, "grid_distance_to_anchor": 2.4729202239238557, "h": 322.9424133300781, "point_id": 61150, "row_index": 16, "w": 20.779197692871094 }, { "collection_id": 879, "direction_sign": 1, "grid_distance_to_anchor": 2.8534633425973843, "h": 323.3356018066406, "point_id": 61151, "row_index": 17, "w": 20.780033111572266 } ], "projected_w_span_grid": 1.1772499084472656, "projected_w_span_vx": 58.86249542236328, "projection_mode": "normal-line", "skipped_point_count": 0, "skipped_points": [], "skipped_reasons": {}, "usable_point_count": 18, "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_879/point_strip.lasagna.json", "mesh-h": 32, "mesh-step": 50, "mesh-w": 32, "model-h": 8327.35595703125, "model-init": "seed", "model-input": null, "model-output": "/tmp/fit_reopt_pngovp2l/model_reopt.pt", "model-w": 8058.862495422363, "model-w-unit": "voxels", "normal-mask-zero": 0, "out-dir": null, "progress": true, "pyramid-d": false, "seed": [ 17726.140625, 15377.5224609375, 57888.3671875 ], "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": { "879": { "color": [ 0.7058823704719543, 1.0, 0.3137255012989044 ], "metadata": { "winding_is_absolute": true }, "name": "same_wrap1255", "points": { "61134": { "creation_time": 61134, "p": [ 17758.033203125, 15282.212890625, 57089.69921875 ], "wind_a": 0.0 }, "61135": { "creation_time": 61135, "p": [ 17759.140625, 15278.9072265625, 57097.75390625 ], "wind_a": 0.0 }, "61136": { "creation_time": 61136, "p": [ 17766.732421875, 15256.2197265625, 57167.84375 ], "wind_a": 0.0 }, "61137": { "creation_time": 61137, "p": [ 17772.529296875, 15238.890625, 57240.2734375 ], "wind_a": 0.0 }, "61138": { "creation_time": 61138, "p": [ 17776.87890625, 15225.8935546875, 57314.59765625 ], "wind_a": 0.0 }, "61139": { "creation_time": 61139, "p": [ 17775.4296875, 15230.2255859375, 57392.703125 ], "wind_a": 0.0 }, "61140": { "creation_time": 61140, "p": [ 17771.080078125, 15243.22265625, 57467.02734375 ], "wind_a": 0.0 }, "61141": { "creation_time": 61141, "p": [ 17763.83203125, 15264.8837890625, 57537.56640625 ], "wind_a": 0.0 }, "61142": { "creation_time": 61142, "p": [ 17756.583984375, 15286.544921875, 57608.10546875 ], "wind_a": 0.0 }, "61143": { "creation_time": 61143, "p": [ 17748.39453125, 15311.01953125, 57677.4140625 ], "wind_a": 0.0 }, "61144": { "creation_time": 61144, "p": [ 17739.66796875, 15337.09375, 57746.02734375 ], "wind_a": 0.0 }, "61145": { "creation_time": 61145, "p": [ 17731.96875, 15360.10546875, 57815.9765625 ], "wind_a": 0.0 }, "61146": { "creation_time": 61146, "p": [ 17726.140625, 15377.5224609375, 57888.3671875 ], "wind_a": 0.0 }, "61147": { "creation_time": 61147, "p": [ 17720.341796875, 15394.8515625, 57960.796875 ], "wind_a": 0.0 }, "61148": { "creation_time": 61148, "p": [ 17718.892578125, 15399.18359375, 58038.90625 ], "wind_a": 0.0 }, "61149": { "creation_time": 61149, "p": [ 17721.791015625, 15390.51953125, 58115.12109375 ], "wind_a": 0.0 }, "61150": { "creation_time": 61150, "p": [ 17726.140625, 15377.5224609375, 58189.4453125 ], "wind_a": 0.0 }, "61151": { "creation_time": 61151, "p": [ 17730.490234375, 15364.525390625, 58263.76953125 ], "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": [ 4437.0986328125, 3827.7548828125, 14419.353515625 ], "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": { "879": { "color": [ 0.7058823704719543, 1.0, 0.3137255012989044 ], "metadata": { "winding_is_absolute": true }, "name": "same_wrap1255", "points": { "61134": { "creation_time": 61134, "p": [ 4439.50830078125, 3820.55322265625, 14272.4248046875 ], "wind_a": 0.0 }, "61135": { "creation_time": 61135, "p": [ 4439.78515625, 3819.726806640625, 14274.4384765625 ], "wind_a": 0.0 }, "61136": { "creation_time": 61136, "p": [ 4441.68310546875, 3814.054931640625, 14291.9609375 ], "wind_a": 0.0 }, "61137": { "creation_time": 61137, "p": [ 4443.13232421875, 3809.72265625, 14310.068359375 ], "wind_a": 0.0 }, "61138": { "creation_time": 61138, "p": [ 4444.2197265625, 3806.473388671875, 14328.6494140625 ], "wind_a": 0.0 }, "61139": { "creation_time": 61139, "p": [ 4443.857421875, 3807.556396484375, 14348.17578125 ], "wind_a": 0.0 }, "61140": { "creation_time": 61140, "p": [ 4442.77001953125, 3810.8056640625, 14366.7568359375 ], "wind_a": 0.0 }, "61141": { "creation_time": 61141, "p": [ 4440.9580078125, 3816.220947265625, 14384.3916015625 ], "wind_a": 0.0 }, "61142": { "creation_time": 61142, "p": [ 4439.14599609375, 3821.63623046875, 14402.0263671875 ], "wind_a": 0.0 }, "61143": { "creation_time": 61143, "p": [ 4437.0986328125, 3827.7548828125, 14419.353515625 ], "wind_a": 0.0 }, "61144": { "creation_time": 61144, "p": [ 4434.9169921875, 3834.2734375, 14436.5068359375 ], "wind_a": 0.0 }, "61145": { "creation_time": 61145, "p": [ 4432.9921875, 3840.0263671875, 14453.994140625 ], "wind_a": 0.0 }, "61146": { "creation_time": 61146, "p": [ 4431.53515625, 3844.380615234375, 14472.091796875 ], "wind_a": 0.0 }, "61147": { "creation_time": 61147, "p": [ 4430.08544921875, 3848.712890625, 14490.19921875 ], "wind_a": 0.0 }, "61148": { "creation_time": 61148, "p": [ 4429.72314453125, 3849.7958984375, 14509.7265625 ], "wind_a": 0.0 }, "61149": { "creation_time": 61149, "p": [ 4430.44775390625, 3847.6298828125, 14528.7802734375 ], "wind_a": 0.0 }, "61150": { "creation_time": 61150, "p": [ 4431.53515625, 3844.380615234375, 14547.361328125 ], "wind_a": 0.0 }, "61151": { "creation_time": 61151, "p": [ 4432.62255859375, 3841.13134765625, 14565.9423828125 ], "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_pngovp2l/model_reopt.pt", "scale": [ 0.07999999821186066, 0.07999999821186066 ], "tags": { "date_last_modified": "20260614185644289", "reviewed": { "date": "20260604080934221" } }, "type": "seg", "uuid": "same_wrap001255_lasagna" }