{ "area_vx2": 945937.5, "base_shape_zyx": [ 18946, 8174, 8174 ], "bbox": [ [ 3305.617431640625, 2550.904296875, 6869.9794921875 ], [ 3837.56982421875, 2886.5478515625, 8578.240234375 ] ], "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": [ 13876.158203125, 10641.13671875, 31118.71484375 ], "final_anchor_h": 185.26853141188622, "final_anchor_w": 112.49742139875889, "final_shell_id": "shell_0007.tifxyz", "final_trim_bottom": 36, "final_trim_top": 5, "init_margin_grid_points": 80, "initial_seed": [ 13876.158203125, 10641.13671875, 31118.71484375 ], "initial_shell_id": "shell_0007.tifxyz", "initial_skipped_point_count": 0, "initial_skipped_reasons": {}, "initial_trim_bottom": 36, "initial_trim_top": 5, "initial_usable_point_count": 24, "mode": "corr-point-roi", "model_h": 9217.723846435547, "model_w": 8279.417037963867, "model_w_unit": "voxels", "output_radius_grid_points": 20, "parsed_point_count": 24, "projected_h_span_grid": 24.354476928710938, "projected_h_span_vx": 1217.7238464355469, "projected_points": [ { "collection_id": 3030, "direction_sign": 1, "grid_distance_to_anchor": 11.916366399664888, "h": 174.4147491455078, "point_id": 131375, "row_index": 0, "w": 107.57855987548828 }, { "collection_id": 3030, "direction_sign": -1, "grid_distance_to_anchor": 12.086785013909617, "h": 173.18585205078125, "point_id": 131376, "row_index": 1, "w": 112.18241119384766 }, { "collection_id": 3030, "direction_sign": -1, "grid_distance_to_anchor": 10.934557569442221, "h": 174.34535217285156, "point_id": 131377, "row_index": 2, "w": 112.99612426757813 }, { "collection_id": 3030, "direction_sign": 1, "grid_distance_to_anchor": 9.125915304726375, "h": 176.16720581054688, "point_id": 131378, "row_index": 3, "w": 113.16690063476563 }, { "collection_id": 3030, "direction_sign": -1, "grid_distance_to_anchor": 8.984640634880485, "h": 176.28709411621094, "point_id": 131379, "row_index": 4, "w": 112.25752258300781 }, { "collection_id": 3030, "direction_sign": -1, "grid_distance_to_anchor": 8.318906520632838, "h": 177.02096557617188, "point_id": 131380, "row_index": 5, "w": 111.41028594970703 }, { "collection_id": 3030, "direction_sign": 1, "grid_distance_to_anchor": 6.399104057184888, "h": 178.97328186035156, "point_id": 131381, "row_index": 6, "w": 111.3492202758789 }, { "collection_id": 3030, "direction_sign": -1, "grid_distance_to_anchor": 5.90894897420267, "h": 179.4501953125, "point_id": 131382, "row_index": 7, "w": 111.4665756225586 }, { "collection_id": 3030, "direction_sign": -1, "grid_distance_to_anchor": 4.555774293118556, "h": 180.7169647216797, "point_id": 131383, "row_index": 8, "w": 112.30166625976563 }, { "collection_id": 3030, "direction_sign": -1, "grid_distance_to_anchor": 3.2504162608814005, "h": 182.01901245117188, "point_id": 131384, "row_index": 9, "w": 112.57379150390625 }, { "collection_id": 3030, "direction_sign": -1, "grid_distance_to_anchor": 2.1483819894414045, "h": 183.12452697753906, "point_id": 131385, "row_index": 10, "w": 112.6344985961914 }, { "collection_id": 3030, "direction_sign": -1, "grid_distance_to_anchor": 1.0173264303811416, "h": 184.28346252441406, "point_id": 131386, "row_index": 11, "w": 112.75157165527344 }, { "collection_id": 3030, "direction_sign": -1, "grid_distance_to_anchor": 0.3488860040307593, "h": 185.02833557128906, "point_id": 131387, "row_index": 12, "w": 112.75045776367188 }, { "collection_id": 3030, "direction_sign": -1, "grid_distance_to_anchor": 1.279391586784711, "h": 186.54330444335938, "point_id": 131388, "row_index": 13, "w": 112.60603332519531 }, { "collection_id": 3030, "direction_sign": -1, "grid_distance_to_anchor": 2.4475227293556845, "h": 187.71511840820313, "point_id": 131389, "row_index": 14, "w": 112.56509399414063 }, { "collection_id": 3030, "direction_sign": -1, "grid_distance_to_anchor": 3.345943464851778, "h": 188.61447143554688, "point_id": 131390, "row_index": 15, "w": 112.5022201538086 }, { "collection_id": 3030, "direction_sign": -1, "grid_distance_to_anchor": 4.999065292138376, "h": 190.26754760742188, "point_id": 131391, "row_index": 16, "w": 112.51957702636719 }, { "collection_id": 3030, "direction_sign": -1, "grid_distance_to_anchor": 5.710810528511248, "h": 190.97802734375, "point_id": 131392, "row_index": 17, "w": 112.61994934082031 }, { "collection_id": 3030, "direction_sign": -1, "grid_distance_to_anchor": 6.927127324268641, "h": 192.19505310058594, "point_id": 131393, "row_index": 18, "w": 112.58901977539063 }, { "collection_id": 3030, "direction_sign": -1, "grid_distance_to_anchor": 8.182714265559705, "h": 193.45106506347656, "point_id": 131394, "row_index": 19, "w": 112.44305419921875 }, { "collection_id": 3030, "direction_sign": -1, "grid_distance_to_anchor": 9.004567095854684, "h": 194.26966857910156, "point_id": 131395, "row_index": 20, "w": 112.74593353271484 }, { "collection_id": 3030, "direction_sign": -1, "grid_distance_to_anchor": 9.991719167974566, "h": 195.2561798095703, "point_id": 131396, "row_index": 21, "w": 112.78260803222656 }, { "collection_id": 3030, "direction_sign": -1, "grid_distance_to_anchor": 11.271280050676744, "h": 196.53692626953125, "point_id": 131397, "row_index": 22, "w": 112.75243377685547 }, { "collection_id": 3030, "direction_sign": -1, "grid_distance_to_anchor": 12.273733898841481, "h": 197.5403289794922, "point_id": 131398, "row_index": 23, "w": 112.7154312133789 } ], "projected_w_span_grid": 5.588340759277344, "projected_w_span_vx": 279.4170379638672, "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_3030/point_strip.lasagna.json", "mesh-h": 32, "mesh-step": 50, "mesh-w": 32, "model-h": 9217.723846435547, "model-init": "seed", "model-input": null, "model-output": "/tmp/fit_reopt_peckb_c_/model_reopt.pt", "model-w": 8279.417037963867, "model-w-unit": "voxels", "normal-mask-zero": 0, "out-dir": null, "progress": true, "pyramid-d": false, "seed": [ 13876.158203125, 10641.13671875, 31118.71484375 ], "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": { "3030": { "color": [ 0.47058823704719543, 0.3137255012989044, 1.0 ], "metadata": { "winding_is_absolute": true }, "name": "same_wrap2996", "points": { "131375": { "creation_time": 1779734212746, "p": [ 13633.7822265625, 10489.6826171875, 28517.3671875 ], "wind_a": 0.0 }, "131376": { "creation_time": 1779734212746, "p": [ 13605.52734375, 10472.02734375, 28734.365234375 ], "wind_a": 0.0 }, "131377": { "creation_time": 1779734212746, "p": [ 13647.9091796875, 10498.5107421875, 28953.6640625 ], "wind_a": 0.0 }, "131378": { "creation_time": 1779734212746, "p": [ 13652.6181640625, 10501.453125, 29186.765625 ], "wind_a": 0.0 }, "131379": { "creation_time": 1779734212746, "p": [ 13662.0361328125, 10507.337890625, 29361.400390625 ], "wind_a": 0.0 }, "131380": { "creation_time": 1779734212746, "p": [ 13685.58203125, 10522.05078125, 29550.19921875 ], "wind_a": 0.0 }, "131381": { "creation_time": 1779734212746, "p": [ 13718.5458984375, 10542.6494140625, 29769.49609375 ], "wind_a": 0.0 }, "131382": { "creation_time": 1779734212746, "p": [ 13746.7998046875, 10560.3046875, 29991.09765625 ], "wind_a": 0.0 }, "131383": { "creation_time": 1779734212746, "p": [ 13752.7705078125, 10564.03515625, 30223.580078125 ], "wind_a": 0.0 }, "131384": { "creation_time": 1779734212746, "p": [ 13789.181640625, 10586.7880859375, 30445.796875 ], "wind_a": 0.0 }, "131385": { "creation_time": 1779734212746, "p": [ 13817.4365234375, 10604.443359375, 30671.99609375 ], "wind_a": 0.0 }, "131386": { "creation_time": 1779734212746, "p": [ 13835.46484375, 10615.7080078125, 30898.58984375 ], "wind_a": 0.0 }, "131387": { "creation_time": 1779734212746, "p": [ 13876.158203125, 10641.13671875, 31118.71484375 ], "wind_a": 0.0 }, "131388": { "creation_time": 1779734212746, "p": [ 13911.6181640625, 10663.2939453125, 31341.39453125 ], "wind_a": 0.0 }, "131389": { "creation_time": 1779734212746, "p": [ 13930.4541015625, 10675.064453125, 31572.193359375 ], "wind_a": 0.0 }, "131390": { "creation_time": 1779734212746, "p": [ 13963.41796875, 10695.6630859375, 31796.09375 ], "wind_a": 0.0 }, "131391": { "creation_time": 1779734212746, "p": [ 13996.3818359375, 10716.2607421875, 32019.9921875 ], "wind_a": 0.0 }, "131392": { "creation_time": 1779734212746, "p": [ 14034.0546875, 10739.8017578125, 32241.591796875 ], "wind_a": 0.0 }, "131393": { "creation_time": 1779734212746, "p": [ 14073.7041015625, 10764.5771484375, 32462.2265625 ], "wind_a": 0.0 }, "131394": { "creation_time": 1779734212746, "p": [ 14114.109375, 10789.8251953125, 32698.66796875 ], "wind_a": 0.0 }, "131395": { "creation_time": 1779734212746, "p": [ 14174.78125, 10827.7373046875, 32909.03515625 ], "wind_a": 0.0 }, "131396": { "creation_time": 1779734212746, "p": [ 14245.4443359375, 10871.892578125, 33114.51953125 ], "wind_a": 0.0 }, "131397": { "creation_time": 1779734212746, "p": [ 14326.095703125, 10922.2890625, 33315.125 ], "wind_a": 0.0 }, "131398": { "creation_time": 1779734212746, "p": [ 14424.9091796875, 10984.0341796875, 33506.86328125 ], "wind_a": 0.0 } }, "tags": { "same_wrap_direction": "z" } } } }, "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": [ 3469.03955078125, 2660.2841796875, 7779.6787109375 ], "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": { "3030": { "color": [ 0.47058823704719543, 0.3137255012989044, 1.0 ], "metadata": { "winding_is_absolute": true }, "name": "same_wrap2996", "points": { "131375": { "creation_time": 1779734212746, "p": [ 3408.445556640625, 2622.420654296875, 7129.341796875 ], "wind_a": 0.0 }, "131376": { "creation_time": 1779734212746, "p": [ 3401.3818359375, 2618.0068359375, 7183.59130859375 ], "wind_a": 0.0 }, "131377": { "creation_time": 1779734212746, "p": [ 3411.977294921875, 2624.627685546875, 7238.416015625 ], "wind_a": 0.0 }, "131378": { "creation_time": 1779734212746, "p": [ 3413.154541015625, 2625.36328125, 7296.69140625 ], "wind_a": 0.0 }, "131379": { "creation_time": 1779734212746, "p": [ 3415.509033203125, 2626.83447265625, 7340.35009765625 ], "wind_a": 0.0 }, "131380": { "creation_time": 1779734212746, "p": [ 3421.3955078125, 2630.5126953125, 7387.5498046875 ], "wind_a": 0.0 }, "131381": { "creation_time": 1779734212746, "p": [ 3429.636474609375, 2635.662353515625, 7442.3740234375 ], "wind_a": 0.0 }, "131382": { "creation_time": 1779734212746, "p": [ 3436.699951171875, 2640.076171875, 7497.7744140625 ], "wind_a": 0.0 }, "131383": { "creation_time": 1779734212746, "p": [ 3438.192626953125, 2641.0087890625, 7555.89501953125 ], "wind_a": 0.0 }, "131384": { "creation_time": 1779734212746, "p": [ 3447.29541015625, 2646.697021484375, 7611.44921875 ], "wind_a": 0.0 }, "131385": { "creation_time": 1779734212746, "p": [ 3454.359130859375, 2651.11083984375, 7667.9990234375 ], "wind_a": 0.0 }, "131386": { "creation_time": 1779734212746, "p": [ 3458.8662109375, 2653.927001953125, 7724.6474609375 ], "wind_a": 0.0 }, "131387": { "creation_time": 1779734212746, "p": [ 3469.03955078125, 2660.2841796875, 7779.6787109375 ], "wind_a": 0.0 }, "131388": { "creation_time": 1779734212746, "p": [ 3477.904541015625, 2665.823486328125, 7835.3486328125 ], "wind_a": 0.0 }, "131389": { "creation_time": 1779734212746, "p": [ 3482.613525390625, 2668.76611328125, 7893.04833984375 ], "wind_a": 0.0 }, "131390": { "creation_time": 1779734212746, "p": [ 3490.8544921875, 2673.915771484375, 7949.0234375 ], "wind_a": 0.0 }, "131391": { "creation_time": 1779734212746, "p": [ 3499.095458984375, 2679.065185546875, 8004.998046875 ], "wind_a": 0.0 }, "131392": { "creation_time": 1779734212746, "p": [ 3508.513671875, 2684.950439453125, 8060.39794921875 ], "wind_a": 0.0 }, "131393": { "creation_time": 1779734212746, "p": [ 3518.426025390625, 2691.144287109375, 8115.556640625 ], "wind_a": 0.0 }, "131394": { "creation_time": 1779734212746, "p": [ 3528.52734375, 2697.456298828125, 8174.6669921875 ], "wind_a": 0.0 }, "131395": { "creation_time": 1779734212746, "p": [ 3543.6953125, 2706.934326171875, 8227.2587890625 ], "wind_a": 0.0 }, "131396": { "creation_time": 1779734212746, "p": [ 3561.361083984375, 2717.97314453125, 8278.6298828125 ], "wind_a": 0.0 }, "131397": { "creation_time": 1779734212746, "p": [ 3581.52392578125, 2730.572265625, 8328.78125 ], "wind_a": 0.0 }, "131398": { "creation_time": 1779734212746, "p": [ 3606.227294921875, 2746.008544921875, 8376.7158203125 ], "wind_a": 0.0 } }, "tags": { "same_wrap_direction": "z" } } } }, "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_peckb_c_/model_reopt.pt", "scale": [ 0.07999999821186066, 0.07999999821186066 ], "tags": { "date_last_modified": "20260614185644654", "reviewed": { "date": "20260604080934298" } }, "type": "seg", "uuid": "same_wrap002996_lasagna" }