{ "area_vx2": 479687.5, "base_shape_zyx": [ 18946, 8174, 8174 ], "bbox": [ [ 5337.64794921875, 4125.60546875, 14975.9462890625 ], [ 5594.2578125, 4705.103515625, 15919.3046875 ] ], "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": [ 22279.380859375, 17676.28515625, 61778.41015625 ], "final_anchor_h": 351.48835080862045, "final_anchor_w": 14.90734413266182, "final_shell_id": "shell_0007.tifxyz", "final_trim_bottom": 11, "final_trim_top": 9, "init_margin_grid_points": 80, "initial_seed": [ 22279.380859375, 17676.28515625, 61778.41015625 ], "initial_shell_id": "shell_0007.tifxyz", "initial_skipped_point_count": 0, "initial_skipped_reasons": {}, "initial_trim_bottom": 11, "initial_trim_top": 9, "initial_usable_point_count": 21, "mode": "corr-point-roi", "model_h": 8702.153015136719, "model_w": 8247.003030776978, "model_w_unit": "voxels", "output_radius_grid_points": 20, "parsed_point_count": 21, "projected_h_span_grid": 14.043060302734375, "projected_h_span_vx": 702.1530151367188, "projected_points": [ { "collection_id": 2355, "direction_sign": -1, "grid_distance_to_anchor": 3.5437199100857413, "h": 348.2151794433594, "point_id": 87868, "row_index": 0, "w": 16.26539421081543 }, { "collection_id": 2355, "direction_sign": -1, "grid_distance_to_anchor": 3.357982919819438, "h": 348.4154968261719, "point_id": 87869, "row_index": 1, "w": 16.261455535888672 }, { "collection_id": 2355, "direction_sign": -1, "grid_distance_to_anchor": 2.928342258737458, "h": 348.90374755859375, "point_id": 87870, "row_index": 2, "w": 16.283939361572266 }, { "collection_id": 2355, "direction_sign": -1, "grid_distance_to_anchor": 2.327165678039486, "h": 349.6007080078125, "point_id": 87871, "row_index": 3, "w": 16.26841163635254 }, { "collection_id": 2355, "direction_sign": -1, "grid_distance_to_anchor": 2.29659577098338, "h": 349.7002258300781, "point_id": 87872, "row_index": 4, "w": 16.3485107421875 }, { "collection_id": 2355, "direction_sign": -1, "grid_distance_to_anchor": 2.171383512499933, "h": 350.0625915527344, "point_id": 87873, "row_index": 5, "w": 16.545061111450195 }, { "collection_id": 2355, "direction_sign": -1, "grid_distance_to_anchor": 2.438699852314917, "h": 350.3626403808594, "point_id": 87874, "row_index": 6, "w": 17.070682525634766 }, { "collection_id": 2355, "direction_sign": 1, "grid_distance_to_anchor": 3.0327116038947963, "h": 352.00555419921875, "point_id": 87875, "row_index": 7, "w": 17.895627975463867 }, { "collection_id": 2355, "direction_sign": 1, "grid_distance_to_anchor": 2.7809416179262296, "h": 353.0860290527344, "point_id": 87876, "row_index": 8, "w": 17.18353843688965 }, { "collection_id": 2355, "direction_sign": 1, "grid_distance_to_anchor": 2.1819233006512673, "h": 353.04180908203125, "point_id": 87877, "row_index": 9, "w": 16.439517974853516 }, { "collection_id": 2355, "direction_sign": 1, "grid_distance_to_anchor": 1.4162410776477075, "h": 352.7376403808594, "point_id": 87878, "row_index": 10, "w": 15.574438095092773 }, { "collection_id": 2355, "direction_sign": -1, "grid_distance_to_anchor": 0.46587611563700176, "h": 351.2157897949219, "point_id": 87879, "row_index": 11, "w": 14.529520034790039 }, { "collection_id": 2355, "direction_sign": -1, "grid_distance_to_anchor": 0.8261729192739607, "h": 351.5336608886719, "point_id": 87880, "row_index": 12, "w": 14.082414627075195 }, { "collection_id": 2355, "direction_sign": -1, "grid_distance_to_anchor": 1.4019665897951235, "h": 352.56317138671875, "point_id": 87881, "row_index": 13, "w": 14.007193565368652 }, { "collection_id": 2355, "direction_sign": 1, "grid_distance_to_anchor": 2.4021424408362173, "h": 353.7265625, "point_id": 87882, "row_index": 14, "w": 14.035164833068848 }, { "collection_id": 2355, "direction_sign": 1, "grid_distance_to_anchor": 2.615973516963271, "h": 353.85650634765625, "point_id": 87883, "row_index": 15, "w": 13.795968055725098 }, { "collection_id": 2355, "direction_sign": -1, "grid_distance_to_anchor": 2.873271248195902, "h": 354.0942077636719, "point_id": 87884, "row_index": 16, "w": 13.696890830993652 }, { "collection_id": 2355, "direction_sign": -1, "grid_distance_to_anchor": 1.3804969961566347, "h": 352.81353759765625, "point_id": 87885, "row_index": 17, "w": 14.520495414733887 }, { "collection_id": 2355, "direction_sign": 1, "grid_distance_to_anchor": 10.945315906638205, "h": 362.25823974609375, "point_id": 87886, "row_index": 18, "w": 12.955567359924316 }, { "collection_id": 2355, "direction_sign": -1, "grid_distance_to_anchor": 3.4904851853549492, "h": 354.9669494628906, "point_id": 87887, "row_index": 19, "w": 14.619527816772461 }, { "collection_id": 2355, "direction_sign": -1, "grid_distance_to_anchor": 3.569260398274576, "h": 355.0470275878906, "point_id": 87888, "row_index": 20, "w": 14.632681846618652 } ], "projected_w_span_grid": 4.940060615539551, "projected_w_span_vx": 247.00303077697754, "projection_mode": "normal-line", "skipped_point_count": 0, "skipped_points": [], "skipped_reasons": {}, "usable_point_count": 21, "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_2355/point_strip.lasagna.json", "mesh-h": 32, "mesh-step": 50, "mesh-w": 32, "model-h": 8702.153015136719, "model-init": "seed", "model-input": null, "model-output": "/tmp/fit_reopt__fgxzftj/model_reopt.pt", "model-w": 8247.003030776978, "model-w-unit": "voxels", "normal-mask-zero": 0, "out-dir": null, "progress": true, "pyramid-d": false, "seed": [ 22279.380859375, 17676.28515625, 61778.41015625 ], "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": { "2355": { "color": [ 0.7058823704719543, 0.0, 1.0 ], "metadata": { "winding_is_absolute": true }, "name": "same_wrap1993", "points": { "87868": { "creation_time": 1779581075204, "p": [ 22283.94921875, 17676.267578125, 61018.1484375 ], "wind_a": 0.0 }, "87869": { "creation_time": 1779581075204, "p": [ 22279.380859375, 17676.28515625, 61096.2578125 ], "wind_a": 0.0 }, "87870": { "creation_time": 1779581075204, "p": [ 22270.244140625, 17676.3203125, 61172.47265625 ], "wind_a": 0.0 }, "87871": { "creation_time": 1779581075204, "p": [ 22265.67578125, 17676.3359375, 61250.578125 ], "wind_a": 0.0 }, "87872": { "creation_time": 1779581075204, "p": [ 22256.5390625, 17676.37109375, 61326.796875 ], "wind_a": 0.0 }, "87873": { "creation_time": 1779581075204, "p": [ 22251.970703125, 17676.388671875, 61404.90234375 ], "wind_a": 0.0 }, "87874": { "creation_time": 1779581075204, "p": [ 22244.95703125, 17676.4140625, 61482.0 ], "wind_a": 0.0 }, "87875": { "creation_time": 1779581075204, "p": [ 22238.265625, 17676.439453125, 61559.2265625 ], "wind_a": 0.0 }, "87876": { "creation_time": 1779581075204, "p": [ 22247.40234375, 17676.404296875, 61631.65625 ], "wind_a": 0.0 }, "87877": { "creation_time": 1779581075204, "p": [ 22261.107421875, 17676.353515625, 61705.98046875 ], "wind_a": 0.0 }, "87878": { "creation_time": 1779581075204, "p": [ 22279.380859375, 17676.28515625, 61778.41015625 ], "wind_a": 0.0 }, "87879": { "creation_time": 1779581075204, "p": [ 22270.244140625, 17676.3203125, 61854.625 ], "wind_a": 0.0 }, "87880": { "creation_time": 1779581075204, "p": [ 22238.265625, 17676.439453125, 61921.3828125 ], "wind_a": 0.0 }, "87881": { "creation_time": 1779581075204, "p": [ 22224.560546875, 17676.490234375, 61995.703125 ], "wind_a": 0.0 }, "87882": { "creation_time": 1779581075204, "p": [ 22215.42578125, 17676.525390625, 62071.921875 ], "wind_a": 0.0 }, "87883": { "creation_time": 1779581075204, "p": [ 22224.560546875, 17676.490234375, 62148.1328125 ], "wind_a": 0.0 }, "87884": { "creation_time": 1779581075204, "p": [ 22224.560546875, 17676.490234375, 62228.1328125 ], "wind_a": 0.0 }, "87885": { "creation_time": 1779581075204, "p": [ 22229.12890625, 17676.474609375, 62306.2421875 ], "wind_a": 0.0 }, "87886": { "creation_time": 1779581075204, "p": [ 22233.697265625, 17676.45703125, 62384.3515625 ], "wind_a": 0.0 }, "87887": { "creation_time": 1779581075204, "p": [ 22238.265625, 17676.439453125, 62462.45703125 ], "wind_a": 0.0 }, "87888": { "creation_time": 1779581075204, "p": [ 22238.265625, 17676.439453125, 62470.8828125 ], "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": [ 5569.84521484375, 4419.0712890625, 15444.6025390625 ], "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": { "2355": { "color": [ 0.7058823704719543, 0.0, 1.0 ], "metadata": { "winding_is_absolute": true }, "name": "same_wrap1993", "points": { "87868": { "creation_time": 1779581075204, "p": [ 5570.9873046875, 4419.06689453125, 15254.537109375 ], "wind_a": 0.0 }, "87869": { "creation_time": 1779581075204, "p": [ 5569.84521484375, 4419.0712890625, 15274.064453125 ], "wind_a": 0.0 }, "87870": { "creation_time": 1779581075204, "p": [ 5567.56103515625, 4419.080078125, 15293.1181640625 ], "wind_a": 0.0 }, "87871": { "creation_time": 1779581075204, "p": [ 5566.4189453125, 4419.083984375, 15312.64453125 ], "wind_a": 0.0 }, "87872": { "creation_time": 1779581075204, "p": [ 5564.134765625, 4419.0927734375, 15331.69921875 ], "wind_a": 0.0 }, "87873": { "creation_time": 1779581075204, "p": [ 5562.99267578125, 4419.09716796875, 15351.2255859375 ], "wind_a": 0.0 }, "87874": { "creation_time": 1779581075204, "p": [ 5561.2392578125, 4419.103515625, 15370.5 ], "wind_a": 0.0 }, "87875": { "creation_time": 1779581075204, "p": [ 5559.56640625, 4419.10986328125, 15389.806640625 ], "wind_a": 0.0 }, "87876": { "creation_time": 1779581075204, "p": [ 5561.8505859375, 4419.10107421875, 15407.9140625 ], "wind_a": 0.0 }, "87877": { "creation_time": 1779581075204, "p": [ 5565.27685546875, 4419.08837890625, 15426.4951171875 ], "wind_a": 0.0 }, "87878": { "creation_time": 1779581075204, "p": [ 5569.84521484375, 4419.0712890625, 15444.6025390625 ], "wind_a": 0.0 }, "87879": { "creation_time": 1779581075204, "p": [ 5567.56103515625, 4419.080078125, 15463.65625 ], "wind_a": 0.0 }, "87880": { "creation_time": 1779581075204, "p": [ 5559.56640625, 4419.10986328125, 15480.345703125 ], "wind_a": 0.0 }, "87881": { "creation_time": 1779581075204, "p": [ 5556.14013671875, 4419.12255859375, 15498.92578125 ], "wind_a": 0.0 }, "87882": { "creation_time": 1779581075204, "p": [ 5553.8564453125, 4419.13134765625, 15517.98046875 ], "wind_a": 0.0 }, "87883": { "creation_time": 1779581075204, "p": [ 5556.14013671875, 4419.12255859375, 15537.033203125 ], "wind_a": 0.0 }, "87884": { "creation_time": 1779581075204, "p": [ 5556.14013671875, 4419.12255859375, 15557.033203125 ], "wind_a": 0.0 }, "87885": { "creation_time": 1779581075204, "p": [ 5557.2822265625, 4419.11865234375, 15576.560546875 ], "wind_a": 0.0 }, "87886": { "creation_time": 1779581075204, "p": [ 5558.42431640625, 4419.1142578125, 15596.087890625 ], "wind_a": 0.0 }, "87887": { "creation_time": 1779581075204, "p": [ 5559.56640625, 4419.10986328125, 15615.6142578125 ], "wind_a": 0.0 }, "87888": { "creation_time": 1779581075204, "p": [ 5559.56640625, 4419.10986328125, 15617.720703125 ], "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__fgxzftj/model_reopt.pt", "scale": [ 0.07999999821186066, 0.07999999821186066 ], "tags": { "date_last_modified": "20260614185644450", "reviewed": { "date": "20260604080934254" } }, "type": "seg", "uuid": "same_wrap001993_lasagna" }