{ "area_vx2": 685937.5, "base_shape_zyx": [ 18946, 8174, 8174 ], "bbox": [ [ 3738.812744140625, 3608.663818359375, 12593.6474609375 ], [ 4405.07763671875, 3911.1357421875, 13529.9560546875 ] ], "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": [ 16258.8994140625, 15145.5830078125, 52402.98046875 ], "final_anchor_h": 291.0, "final_anchor_w": 13.935880899429321, "final_shell_id": "shell_0007.tifxyz", "final_trim_bottom": 21, "final_trim_top": 20, "init_margin_grid_points": 80, "initial_seed": [ 16297.9501953125, 14905.8056640625, 51883.00390625 ], "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": 27, "mode": "corr-point-roi", "model_h": 9526.698303222656, "model_w": 8433.110427856445, "model_w_unit": "voxels", "output_radius_grid_points": 20, "parsed_point_count": 27, "projected_h_span_grid": 30.533966064453125, "projected_h_span_vx": 1526.6983032226563, "projected_points": [ { "collection_id": 2871, "direction_sign": 1, "grid_distance_to_anchor": 5.006463034952948, "h": 295.98614501953125, "point_id": 113797, "row_index": 0, "w": 13.485292434692383 }, { "collection_id": 2871, "direction_sign": 1, "grid_distance_to_anchor": 6.15267662919498, "h": 297.077392578125, "point_id": 113798, "row_index": 1, "w": 12.976334571838379 }, { "collection_id": 2871, "direction_sign": 1, "grid_distance_to_anchor": 4.892130462535685, "h": 295.7978820800781, "point_id": 113799, "row_index": 2, "w": 12.980230331420898 }, { "collection_id": 2871, "direction_sign": 1, "grid_distance_to_anchor": 4.177156569794568, "h": 295.11029052734375, "point_id": 113800, "row_index": 3, "w": 13.191469192504883 }, { "collection_id": 2871, "direction_sign": 1, "grid_distance_to_anchor": 2.4584235761653033, "h": 293.38446044921875, "point_id": 113801, "row_index": 4, "w": 13.337387084960938 }, { "collection_id": 2871, "direction_sign": 1, "grid_distance_to_anchor": 16.747531221512403, "h": 307.5840759277344, "point_id": 113802, "row_index": 5, "w": 11.601737022399902 }, { "collection_id": 2871, "direction_sign": -1, "grid_distance_to_anchor": 2.8534277754872983, "h": 288.4822998046875, "point_id": 113803, "row_index": 6, "w": 12.593034744262695 }, { "collection_id": 2871, "direction_sign": -1, "grid_distance_to_anchor": 4.232147875170617, "h": 287.3736572265625, "point_id": 113804, "row_index": 7, "w": 11.753974914550781 }, { "collection_id": 2871, "direction_sign": -1, "grid_distance_to_anchor": 13.739264182792681, "h": 280.1605224609375, "point_id": 113805, "row_index": 8, "w": 5.4935407638549805 }, { "collection_id": 2871, "direction_sign": -1, "grid_distance_to_anchor": 11.602525103866308, "h": 280.5741271972656, "point_id": 113806, "row_index": 9, "w": 8.844735145568848 }, { "collection_id": 2871, "direction_sign": -1, "grid_distance_to_anchor": 4.8868802907649185, "h": 286.2538146972656, "point_id": 113807, "row_index": 10, "w": 12.771697044372559 }, { "collection_id": 2871, "direction_sign": -1, "grid_distance_to_anchor": 4.03995802972061, "h": 286.96368408203125, "point_id": 113808, "row_index": 11, "w": 13.764373779296875 }, { "collection_id": 2871, "direction_sign": 1, "grid_distance_to_anchor": 0.3108621833568045, "h": 290.7802429199219, "point_id": 113809, "row_index": 12, "w": 14.155749320983887 }, { "collection_id": 2871, "direction_sign": 1, "grid_distance_to_anchor": 0.10746069377673984, "h": 291.0425109863281, "point_id": 113810, "row_index": 13, "w": 14.034575462341309 }, { "collection_id": 2871, "direction_sign": 1, "grid_distance_to_anchor": 0.33453437291151217, "h": 290.713623046875, "point_id": 113811, "row_index": 14, "w": 13.762960433959961 }, { "collection_id": 2871, "direction_sign": 1, "grid_distance_to_anchor": 3.1312389810189525, "h": 287.8772277832031, "point_id": 113812, "row_index": 15, "w": 13.705769538879395 }, { "collection_id": 2871, "direction_sign": 1, "grid_distance_to_anchor": 4.121085006463777, "h": 286.89788818359375, "point_id": 113813, "row_index": 16, "w": 13.540886878967285 }, { "collection_id": 2871, "direction_sign": 1, "grid_distance_to_anchor": 4.4876995264999024, "h": 286.54559326171875, "point_id": 113814, "row_index": 17, "w": 13.390254974365234 }, { "collection_id": 2871, "direction_sign": 1, "grid_distance_to_anchor": 5.182951397655482, "h": 285.8730163574219, "point_id": 113815, "row_index": 18, "w": 13.176259994506836 }, { "collection_id": 2871, "direction_sign": 1, "grid_distance_to_anchor": 6.099451872827574, "h": 284.9778747558594, "point_id": 113816, "row_index": 19, "w": 12.967727661132813 }, { "collection_id": 2871, "direction_sign": 1, "grid_distance_to_anchor": 6.672848039124907, "h": 284.4158020019531, "point_id": 113817, "row_index": 20, "w": 12.851797103881836 }, { "collection_id": 2871, "direction_sign": -1, "grid_distance_to_anchor": 10.306486162447909, "h": 280.8448486328125, "point_id": 113818, "row_index": 21, "w": 12.176177024841309 }, { "collection_id": 2871, "direction_sign": -1, "grid_distance_to_anchor": 9.886976667130687, "h": 281.2257385253906, "point_id": 113819, "row_index": 22, "w": 12.447216987609863 }, { "collection_id": 2871, "direction_sign": -1, "grid_distance_to_anchor": 10.95625887424719, "h": 280.1221923828125, "point_id": 113820, "row_index": 23, "w": 12.62709903717041 }, { "collection_id": 2871, "direction_sign": -1, "grid_distance_to_anchor": 11.72473617278534, "h": 279.3280944824219, "point_id": 113821, "row_index": 24, "w": 12.824098587036133 }, { "collection_id": 2871, "direction_sign": -1, "grid_distance_to_anchor": 12.597688337512288, "h": 278.42633056640625, "point_id": 113822, "row_index": 25, "w": 13.15832805633545 }, { "collection_id": 2871, "direction_sign": -1, "grid_distance_to_anchor": 13.955990649075925, "h": 277.05010986328125, "point_id": 113823, "row_index": 26, "w": 13.523279190063477 } ], "projected_w_span_grid": 8.662208557128906, "projected_w_span_vx": 433.1104278564453, "projection_mode": "normal-line", "skipped_point_count": 0, "skipped_points": [], "skipped_reasons": {}, "usable_point_count": 27, "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_2871/point_strip.lasagna.json", "mesh-h": 32, "mesh-step": 50, "mesh-w": 32, "model-h": 9526.698303222656, "model-init": "seed", "model-input": null, "model-output": "/tmp/fit_reopt_7m5vmsjg/model_reopt.pt", "model-w": 8433.110427856445, "model-w-unit": "voxels", "normal-mask-zero": 0, "out-dir": null, "progress": true, "pyramid-d": false, "seed": [ 16258.8994140625, 15145.5830078125, 52402.98046875 ], "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": { "2871": { "color": [ 0.47058823704719543, 0.3137255012989044, 1.0 ], "metadata": { "winding_is_absolute": true }, "name": "same_wrap2626", "points": { "113797": { "creation_time": 1779686191489, "p": [ 16278.3125, 15026.37890625, 53063.765625 ], "wind_a": 0.0 }, "113798": { "creation_time": 1779686191489, "p": [ 16270.353515625, 15075.25, 52964.27734375 ], "wind_a": 0.0 }, "113799": { "creation_time": 1779686191489, "p": [ 16260.4609375, 15135.9912109375, 52869.76953125 ], "wind_a": 0.0 }, "113800": { "creation_time": 1779686191489, "p": [ 16250.6484375, 15196.244140625, 52775.0546875 ], "wind_a": 0.0 }, "113801": { "creation_time": 1779686191489, "p": [ 16243.951171875, 15237.3642578125, 52672.3125 ], "wind_a": 0.0 }, "113802": { "creation_time": 1779686191489, "p": [ 16240.41015625, 15259.107421875, 52561.4375 ], "wind_a": 0.0 }, "113803": { "creation_time": 1779686191489, "p": [ 16243.1025390625, 15242.5751953125, 52455.44140625 ], "wind_a": 0.0 }, "113804": { "creation_time": 1779686191489, "p": [ 16258.8994140625, 15145.5830078125, 52402.98046875 ], "wind_a": 0.0 }, "113805": { "creation_time": 1779686191489, "p": [ 16275.6005859375, 15043.03515625, 52364.109375 ], "wind_a": 0.0 }, "113806": { "creation_time": 1779686191489, "p": [ 16292.6484375, 14938.3544921875, 52330.453125 ], "wind_a": 0.0 }, "113807": { "creation_time": 1779686191489, "p": [ 16309.6865234375, 14833.7373046875, 52296.6484375 ], "wind_a": 0.0 }, "113808": { "creation_time": 1779686191489, "p": [ 16315.21875, 14799.7685546875, 52193.90234375 ], "wind_a": 0.0 }, "113809": { "creation_time": 1779686191489, "p": [ 16314.0166015625, 14807.154296875, 52081.6015625 ], "wind_a": 0.0 }, "113810": { "creation_time": 1779686191489, "p": [ 16306.765625, 14851.6708984375, 51980.28515625 ], "wind_a": 0.0 }, "113811": { "creation_time": 1779686191489, "p": [ 16297.9501953125, 14905.8056640625, 51883.00390625 ], "wind_a": 0.0 }, "113812": { "creation_time": 1779686191489, "p": [ 16290.216796875, 14953.2890625, 51782.9296875 ], "wind_a": 0.0 }, "113813": { "creation_time": 1779686191489, "p": [ 16285.453125, 14982.5341796875, 51675.203125 ], "wind_a": 0.0 }, "113814": { "creation_time": 1779686191489, "p": [ 16278.3125, 15026.37890625, 51573.60546875 ], "wind_a": 0.0 }, "113815": { "creation_time": 1779686191489, "p": [ 16271.388671875, 15068.8984375, 51471.44921875 ], "wind_a": 0.0 }, "113816": { "creation_time": 1779686191489, "p": [ 16267.2158203125, 15094.5166015625, 51362.19921875 ], "wind_a": 0.0 }, "113817": { "creation_time": 1779686191489, "p": [ 16264.03125, 15114.0693359375, 51250.40625 ], "wind_a": 0.0 }, "113818": { "creation_time": 1779686191489, "p": [ 16262.24609375, 15125.0302734375, 51135.0078125 ], "wind_a": 0.0 }, "113819": { "creation_time": 1779686191489, "p": [ 16267.900390625, 15090.3134765625, 51029.57421875 ], "wind_a": 0.0 }, "113820": { "creation_time": 1779686191489, "p": [ 16283.24609375, 14996.0869140625, 50970.3515625 ], "wind_a": 0.0 }, "113821": { "creation_time": 1779686191489, "p": [ 16301.056640625, 14886.7275390625, 50948.140625 ], "wind_a": 0.0 }, "113822": { "creation_time": 1779686191489, "p": [ 16319.236328125, 14775.0986328125, 50931.48046875 ], "wind_a": 0.0 }, "113823": { "creation_time": 1779686191489, "p": [ 16330.9755859375, 14703.0224609375, 50925.9296875 ], "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": [ 4076.69140625, 3712.917724609375, 12995.0712890625 ], "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": { "2871": { "color": [ 0.47058823704719543, 0.3137255012989044, 1.0 ], "metadata": { "winding_is_absolute": true }, "name": "same_wrap2626", "points": { "113797": { "creation_time": 1779686191489, "p": [ 4069.578125, 3756.5947265625, 13265.94140625 ], "wind_a": 0.0 }, "113798": { "creation_time": 1779686191489, "p": [ 4067.58837890625, 3768.8125, 13241.0693359375 ], "wind_a": 0.0 }, "113799": { "creation_time": 1779686191489, "p": [ 4065.115234375, 3783.997802734375, 13217.4423828125 ], "wind_a": 0.0 }, "113800": { "creation_time": 1779686191489, "p": [ 4062.662109375, 3799.06103515625, 13193.763671875 ], "wind_a": 0.0 }, "113801": { "creation_time": 1779686191489, "p": [ 4060.98779296875, 3809.341064453125, 13168.078125 ], "wind_a": 0.0 }, "113802": { "creation_time": 1779686191489, "p": [ 4060.1025390625, 3814.77685546875, 13140.359375 ], "wind_a": 0.0 }, "113803": { "creation_time": 1779686191489, "p": [ 4060.775634765625, 3810.643798828125, 13113.8603515625 ], "wind_a": 0.0 }, "113804": { "creation_time": 1779686191489, "p": [ 4064.724853515625, 3786.395751953125, 13100.7451171875 ], "wind_a": 0.0 }, "113805": { "creation_time": 1779686191489, "p": [ 4068.900146484375, 3760.7587890625, 13091.02734375 ], "wind_a": 0.0 }, "113806": { "creation_time": 1779686191489, "p": [ 4073.162109375, 3734.588623046875, 13082.61328125 ], "wind_a": 0.0 }, "113807": { "creation_time": 1779686191489, "p": [ 4077.421630859375, 3708.434326171875, 13074.162109375 ], "wind_a": 0.0 }, "113808": { "creation_time": 1779686191489, "p": [ 4078.8046875, 3699.942138671875, 13048.4755859375 ], "wind_a": 0.0 }, "113809": { "creation_time": 1779686191489, "p": [ 4078.504150390625, 3701.78857421875, 13020.400390625 ], "wind_a": 0.0 }, "113810": { "creation_time": 1779686191489, "p": [ 4076.69140625, 3712.917724609375, 12995.0712890625 ], "wind_a": 0.0 }, "113811": { "creation_time": 1779686191489, "p": [ 4074.487548828125, 3726.451416015625, 12970.7509765625 ], "wind_a": 0.0 }, "113812": { "creation_time": 1779686191489, "p": [ 4072.55419921875, 3738.322265625, 12945.732421875 ], "wind_a": 0.0 }, "113813": { "creation_time": 1779686191489, "p": [ 4071.36328125, 3745.633544921875, 12918.80078125 ], "wind_a": 0.0 }, "113814": { "creation_time": 1779686191489, "p": [ 4069.578125, 3756.5947265625, 12893.4013671875 ], "wind_a": 0.0 }, "113815": { "creation_time": 1779686191489, "p": [ 4067.84716796875, 3767.224609375, 12867.8623046875 ], "wind_a": 0.0 }, "113816": { "creation_time": 1779686191489, "p": [ 4066.803955078125, 3773.629150390625, 12840.5498046875 ], "wind_a": 0.0 }, "113817": { "creation_time": 1779686191489, "p": [ 4066.0078125, 3778.517333984375, 12812.6015625 ], "wind_a": 0.0 }, "113818": { "creation_time": 1779686191489, "p": [ 4065.5615234375, 3781.257568359375, 12783.751953125 ], "wind_a": 0.0 }, "113819": { "creation_time": 1779686191489, "p": [ 4066.97509765625, 3772.578369140625, 12757.3935546875 ], "wind_a": 0.0 }, "113820": { "creation_time": 1779686191489, "p": [ 4070.8115234375, 3749.021728515625, 12742.587890625 ], "wind_a": 0.0 }, "113821": { "creation_time": 1779686191489, "p": [ 4075.26416015625, 3721.681884765625, 12737.03515625 ], "wind_a": 0.0 }, "113822": { "creation_time": 1779686191489, "p": [ 4079.80908203125, 3693.774658203125, 12732.8701171875 ], "wind_a": 0.0 }, "113823": { "creation_time": 1779686191489, "p": [ 4082.743896484375, 3675.755615234375, 12731.482421875 ], "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_7m5vmsjg/model_reopt.pt", "scale": [ 0.07999999821186066, 0.07999999821186066 ], "tags": { "date_last_modified": "20260614185644599", "reviewed": { "date": "20260604080934286" } }, "type": "seg", "uuid": "same_wrap002626_lasagna" }