{ "area_vx2": 566562.5, "base_shape_zyx": [ 18946, 8174, 8174 ], "bbox": [ [ 5550.57763671875, 3977.061279296875, 8740.7802734375 ], [ 5843.392578125, 4482.27490234375, 9778.0146484375 ] ], "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": [ 23028.796875, 17017.35546875, 36983.765625 ], "final_anchor_h": 218.12480802834034, "final_anchor_w": 31.681411400437355, "final_shell_id": "shell_0002.tifxyz", "final_trim_bottom": 7, "final_trim_top": 8, "init_margin_grid_points": 80, "initial_seed": [ 23028.796875, 17017.35546875, 36906.8828125 ], "initial_shell_id": "shell_0002.tifxyz", "initial_skipped_point_count": 0, "initial_skipped_reasons": {}, "initial_trim_bottom": 7, "initial_trim_top": 8, "initial_usable_point_count": 29, "mode": "corr-point-roi", "model_h": 8521.570587158203, "model_w": 8028.985977172852, "model_w_unit": "voxels", "output_radius_grid_points": 20, "parsed_point_count": 29, "projected_h_span_grid": 10.431411743164063, "projected_h_span_vx": 521.5705871582031, "projected_points": [ { "collection_id": 916, "direction_sign": -1, "grid_distance_to_anchor": 5.613746855844268, "h": 212.51431274414063, "point_id": 89589, "row_index": 0, "w": 31.872451782226563 }, { "collection_id": 916, "direction_sign": 1, "grid_distance_to_anchor": 1.1523195669428083, "h": 216.99063110351563, "point_id": 89590, "row_index": 1, "w": 31.477737426757813 }, { "collection_id": 916, "direction_sign": 1, "grid_distance_to_anchor": 4.78005056657311, "h": 213.34567260742188, "point_id": 89591, "row_index": 2, "w": 31.77494239807129 }, { "collection_id": 916, "direction_sign": 1, "grid_distance_to_anchor": 4.363205288517348, "h": 213.7617950439453, "point_id": 89592, "row_index": 3, "w": 31.722375869750977 }, { "collection_id": 916, "direction_sign": 1, "grid_distance_to_anchor": 3.980787396730443, "h": 214.14402770996094, "point_id": 89593, "row_index": 4, "w": 31.673904418945313 }, { "collection_id": 916, "direction_sign": 1, "grid_distance_to_anchor": 3.590933572842394, "h": 214.53419494628906, "point_id": 89594, "row_index": 5, "w": 31.63343620300293 }, { "collection_id": 916, "direction_sign": 1, "grid_distance_to_anchor": 3.1930567924610433, "h": 214.93350219726563, "point_id": 89595, "row_index": 6, "w": 31.575681686401367 }, { "collection_id": 916, "direction_sign": 1, "grid_distance_to_anchor": 2.8389712537301075, "h": 215.29193115234375, "point_id": 89596, "row_index": 7, "w": 31.49549102783203 }, { "collection_id": 916, "direction_sign": 1, "grid_distance_to_anchor": 2.467544231389802, "h": 215.67105102539063, "point_id": 89597, "row_index": 8, "w": 31.420928955078125 }, { "collection_id": 916, "direction_sign": 1, "grid_distance_to_anchor": 2.127095252733467, "h": 216.0250244140625, "point_id": 89598, "row_index": 9, "w": 31.341642379760742 }, { "collection_id": 916, "direction_sign": -1, "grid_distance_to_anchor": 1.97027358622094, "h": 216.19325256347656, "point_id": 89599, "row_index": 10, "w": 31.29273223876953 }, { "collection_id": 916, "direction_sign": -1, "grid_distance_to_anchor": 1.5517709872491046, "h": 216.6160888671875, "point_id": 89600, "row_index": 11, "w": 31.318424224853516 }, { "collection_id": 916, "direction_sign": -1, "grid_distance_to_anchor": 1.1785024234544443, "h": 216.9680633544922, "point_id": 89601, "row_index": 12, "w": 31.45600128173828 }, { "collection_id": 916, "direction_sign": 1, "grid_distance_to_anchor": 0.7677812147163389, "h": 217.3602752685547, "point_id": 89602, "row_index": 13, "w": 31.610858917236328 }, { "collection_id": 916, "direction_sign": 1, "grid_distance_to_anchor": 0.4048581566343406, "h": 217.7200164794922, "point_id": 89603, "row_index": 14, "w": 31.68875503540039 }, { "collection_id": 916, "direction_sign": 1, "grid_distance_to_anchor": 0.001113103270010329, "h": 218.1237030029297, "point_id": 89604, "row_index": 15, "w": 31.68154525756836 }, { "collection_id": 916, "direction_sign": 1, "grid_distance_to_anchor": 0.40783673514573365, "h": 218.53237915039063, "point_id": 89605, "row_index": 16, "w": 31.66669464111328 }, { "collection_id": 916, "direction_sign": -1, "grid_distance_to_anchor": 0.7234980899507252, "h": 218.8480224609375, "point_id": 89606, "row_index": 17, "w": 31.66115379333496 }, { "collection_id": 916, "direction_sign": -1, "grid_distance_to_anchor": 1.204045131347569, "h": 219.32882690429688, "point_id": 89607, "row_index": 18, "w": 31.673460006713867 }, { "collection_id": 916, "direction_sign": 1, "grid_distance_to_anchor": 1.6002635168182333, "h": 219.72494506835938, "point_id": 89608, "row_index": 19, "w": 31.70153045654297 }, { "collection_id": 916, "direction_sign": 1, "grid_distance_to_anchor": 2.3289254756459306, "h": 220.45358276367188, "point_id": 89609, "row_index": 20, "w": 31.707908630371094 }, { "collection_id": 916, "direction_sign": -1, "grid_distance_to_anchor": 2.380776819294899, "h": 220.50558471679688, "point_id": 89610, "row_index": 21, "w": 31.680622100830078 }, { "collection_id": 916, "direction_sign": -1, "grid_distance_to_anchor": 2.763275647638596, "h": 220.88760375976563, "point_id": 89611, "row_index": 22, "w": 31.629913330078125 }, { "collection_id": 916, "direction_sign": -1, "grid_distance_to_anchor": 3.124391273511471, "h": 221.24720764160156, "point_id": 89612, "row_index": 23, "w": 31.569869995117188 }, { "collection_id": 916, "direction_sign": -1, "grid_distance_to_anchor": 3.493698380180978, "h": 221.6143035888672, "point_id": 89613, "row_index": 24, "w": 31.510095596313477 }, { "collection_id": 916, "direction_sign": -1, "grid_distance_to_anchor": 3.852971897954215, "h": 221.96957397460938, "point_id": 89614, "row_index": 25, "w": 31.43008041381836 }, { "collection_id": 916, "direction_sign": -1, "grid_distance_to_anchor": 4.220968706690241, "h": 222.3342742919922, "point_id": 89615, "row_index": 26, "w": 31.370010375976563 }, { "collection_id": 916, "direction_sign": -1, "grid_distance_to_anchor": 4.5970901459443985, "h": 222.70730590820313, "point_id": 89616, "row_index": 27, "w": 31.315418243408203 }, { "collection_id": 916, "direction_sign": -1, "grid_distance_to_anchor": 4.835166242829468, "h": 222.9457244873047, "point_id": 89617, "row_index": 28, "w": 31.310470581054688 } ], "projected_w_span_grid": 0.5797195434570313, "projected_w_span_vx": 28.985977172851563, "projection_mode": "normal-line", "skipped_point_count": 0, "skipped_points": [], "skipped_reasons": {}, "usable_point_count": 29, "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_916/point_strip.lasagna.json", "mesh-h": 32, "mesh-step": 50, "mesh-w": 32, "model-h": 8521.570587158203, "model-init": "seed", "model-input": null, "model-output": "/tmp/fit_reopt_cp_w4sfh/model_reopt.pt", "model-w": 8028.985977172852, "model-w-unit": "voxels", "normal-mask-zero": 0, "out-dir": null, "progress": true, "pyramid-d": false, "seed": [ 23028.796875, 17017.35546875, 36983.765625 ], "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": { "916": { "color": [ 0.47058823704719543, 0.7058823704719543, 1.0 ], "metadata": { "winding_is_absolute": true }, "name": "same_wrap2049", "points": { "89589": { "creation_time": 1779581657048, "p": [ 22988.896484375, 17006.533203125, 35928.015625 ], "wind_a": 0.0 }, "89590": { "creation_time": 1779581657048, "p": [ 22996.150390625, 17008.5, 36004.8984375 ], "wind_a": 0.0 }, "89591": { "creation_time": 1779581657048, "p": [ 22996.150390625, 17008.5, 36084.8984375 ], "wind_a": 0.0 }, "89592": { "creation_time": 1779581657048, "p": [ 22988.896484375, 17006.533203125, 36161.7890625 ], "wind_a": 0.0 }, "89593": { "creation_time": 1779581657048, "p": [ 22978.013671875, 17003.58203125, 36237.1171875 ], "wind_a": 0.0 }, "89594": { "creation_time": 1779581657048, "p": [ 22970.759765625, 17001.61328125, 36314.0 ], "wind_a": 0.0 }, "89595": { "creation_time": 1779581657048, "p": [ 22955.404296875, 16997.44921875, 36387.4140625 ], "wind_a": 0.0 }, "89596": { "creation_time": 1779581657048, "p": [ 22927.23046875, 16989.80859375, 36455.3203125 ], "wind_a": 0.0 }, "89597": { "creation_time": 1779581657048, "p": [ 22901.83984375, 16982.921875, 36524.421875 ], "wind_a": 0.0 }, "89598": { "creation_time": 1779581657048, "p": [ 22876.2578125, 16975.982421875, 36593.4453125 ], "wind_a": 0.0 }, "89599": { "creation_time": 1779581657048, "p": [ 22861.939453125, 16972.099609375, 36667.296875 ], "wind_a": 0.0 }, "89600": { "creation_time": 1779581657048, "p": [ 22884.994140625, 16978.3515625, 36737.40625 ], "wind_a": 0.0 }, "89601": { "creation_time": 1779581657048, "p": [ 22938.087890625, 16992.751953125, 36792.4140625 ], "wind_a": 0.0 }, "89602": { "creation_time": 1779581657048, "p": [ 22993.306640625, 17007.728515625, 36842.11328125 ], "wind_a": 0.0 }, "89603": { "creation_time": 1779581657048, "p": [ 23028.796875, 17017.35546875, 36906.8828125 ], "wind_a": 0.0 }, "89604": { "creation_time": 1779581657048, "p": [ 23028.796875, 17017.35546875, 36983.765625 ], "wind_a": 0.0 }, "89605": { "creation_time": 1779581657048, "p": [ 23025.169921875, 17016.37109375, 37062.2109375 ], "wind_a": 0.0 }, "89606": { "creation_time": 1779581657048, "p": [ 23025.169921875, 17016.37109375, 37139.09765625 ], "wind_a": 0.0 }, "89607": { "creation_time": 1779581657048, "p": [ 23031.634765625, 17018.125, 37216.3203125 ], "wind_a": 0.0 }, "89608": { "creation_time": 1779581657048, "p": [ 23043.306640625, 17021.291015625, 37291.3125 ], "wind_a": 0.0 }, "89609": { "creation_time": 1779581657048, "p": [ 23046.93359375, 17022.275390625, 37369.7578125 ], "wind_a": 0.0 }, "89610": { "creation_time": 1779581657048, "p": [ 23036.05078125, 17019.322265625, 37445.0859375 ], "wind_a": 0.0 }, "89611": { "creation_time": 1779581657048, "p": [ 23017.9140625, 17014.404296875, 37517.3046875 ], "wind_a": 0.0 }, "89612": { "creation_time": 1779581657048, "p": [ 22996.150390625, 17008.5, 37587.9609375 ], "wind_a": 0.0 }, "89613": { "creation_time": 1779581657048, "p": [ 22974.38671875, 17002.59765625, 37658.62109375 ], "wind_a": 0.0 }, "89614": { "creation_time": 1779581657048, "p": [ 22946.810546875, 16995.119140625, 37726.7890625 ], "wind_a": 0.0 }, "89615": { "creation_time": 1779581657048, "p": [ 22925.55859375, 16989.353515625, 37797.6640625 ], "wind_a": 0.0 }, "89616": { "creation_time": 1779581657048, "p": [ 22905.466796875, 16983.904296875, 37869.04296875 ], "wind_a": 0.0 }, "89617": { "creation_time": 1779581657048, "p": [ 22901.83984375, 16982.921875, 37916.203125 ], "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": [ 5757.19921875, 4254.3388671875, 9226.720703125 ], "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": { "916": { "color": [ 0.47058823704719543, 0.7058823704719543, 1.0 ], "metadata": { "winding_is_absolute": true }, "name": "same_wrap2049", "points": { "89589": { "creation_time": 1779581657048, "p": [ 5747.22412109375, 4251.63330078125, 8982.00390625 ], "wind_a": 0.0 }, "89590": { "creation_time": 1779581657048, "p": [ 5749.03759765625, 4252.125, 9001.224609375 ], "wind_a": 0.0 }, "89591": { "creation_time": 1779581657048, "p": [ 5749.03759765625, 4252.125, 9021.224609375 ], "wind_a": 0.0 }, "89592": { "creation_time": 1779581657048, "p": [ 5747.22412109375, 4251.63330078125, 9040.447265625 ], "wind_a": 0.0 }, "89593": { "creation_time": 1779581657048, "p": [ 5744.50341796875, 4250.8955078125, 9059.279296875 ], "wind_a": 0.0 }, "89594": { "creation_time": 1779581657048, "p": [ 5742.68994140625, 4250.4033203125, 9078.5 ], "wind_a": 0.0 }, "89595": { "creation_time": 1779581657048, "p": [ 5738.85107421875, 4249.3623046875, 9096.853515625 ], "wind_a": 0.0 }, "89596": { "creation_time": 1779581657048, "p": [ 5731.8076171875, 4247.4521484375, 9113.830078125 ], "wind_a": 0.0 }, "89597": { "creation_time": 1779581657048, "p": [ 5725.4599609375, 4245.73046875, 9131.10546875 ], "wind_a": 0.0 }, "89598": { "creation_time": 1779581657048, "p": [ 5719.064453125, 4243.99560546875, 9148.361328125 ], "wind_a": 0.0 }, "89599": { "creation_time": 1779581657048, "p": [ 5715.48486328125, 4243.02490234375, 9166.82421875 ], "wind_a": 0.0 }, "89600": { "creation_time": 1779581657048, "p": [ 5721.24853515625, 4244.587890625, 9184.3515625 ], "wind_a": 0.0 }, "89601": { "creation_time": 1779581657048, "p": [ 5734.52197265625, 4248.18798828125, 9198.103515625 ], "wind_a": 0.0 }, "89602": { "creation_time": 1779581657048, "p": [ 5748.32666015625, 4251.93212890625, 9210.5283203125 ], "wind_a": 0.0 }, "89603": { "creation_time": 1779581657048, "p": [ 5757.19921875, 4254.3388671875, 9226.720703125 ], "wind_a": 0.0 }, "89604": { "creation_time": 1779581657048, "p": [ 5757.19921875, 4254.3388671875, 9245.94140625 ], "wind_a": 0.0 }, "89605": { "creation_time": 1779581657048, "p": [ 5756.29248046875, 4254.0927734375, 9265.552734375 ], "wind_a": 0.0 }, "89606": { "creation_time": 1779581657048, "p": [ 5756.29248046875, 4254.0927734375, 9284.7744140625 ], "wind_a": 0.0 }, "89607": { "creation_time": 1779581657048, "p": [ 5757.90869140625, 4254.53125, 9304.080078125 ], "wind_a": 0.0 }, "89608": { "creation_time": 1779581657048, "p": [ 5760.82666015625, 4255.32275390625, 9322.828125 ], "wind_a": 0.0 }, "89609": { "creation_time": 1779581657048, "p": [ 5761.7333984375, 4255.56884765625, 9342.439453125 ], "wind_a": 0.0 }, "89610": { "creation_time": 1779581657048, "p": [ 5759.0126953125, 4254.83056640625, 9361.271484375 ], "wind_a": 0.0 }, "89611": { "creation_time": 1779581657048, "p": [ 5754.478515625, 4253.60107421875, 9379.326171875 ], "wind_a": 0.0 }, "89612": { "creation_time": 1779581657048, "p": [ 5749.03759765625, 4252.125, 9396.990234375 ], "wind_a": 0.0 }, "89613": { "creation_time": 1779581657048, "p": [ 5743.5966796875, 4250.6494140625, 9414.6552734375 ], "wind_a": 0.0 }, "89614": { "creation_time": 1779581657048, "p": [ 5736.70263671875, 4248.77978515625, 9431.697265625 ], "wind_a": 0.0 }, "89615": { "creation_time": 1779581657048, "p": [ 5731.3896484375, 4247.33837890625, 9449.416015625 ], "wind_a": 0.0 }, "89616": { "creation_time": 1779581657048, "p": [ 5726.36669921875, 4245.97607421875, 9467.2607421875 ], "wind_a": 0.0 }, "89617": { "creation_time": 1779581657048, "p": [ 5725.4599609375, 4245.73046875, 9479.05078125 ], "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_cp_w4sfh/model_reopt.pt", "scale": [ 0.07999999821186066, 0.07999999821186066 ], "tags": { "date_last_modified": "20260614185644482", "reviewed": { "date": "20260604080934261" } }, "type": "seg", "uuid": "same_wrap002049_lasagna" }