{ "area_vx2": 688281.25, "base_shape_zyx": [ 18946, 8174, 8174 ], "bbox": [ [ -0.250030517578125, -0.25, -0.25 ], [ 4866.56787109375, 3659.29248046875, 8783.62890625 ] ], "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": [ 17336.283203125, 12331.3134765625, 34000.0 ], "final_anchor_h": 183.17983536422253, "final_anchor_w": 40.93363146483898, "final_shell_id": "shell_0000.tifxyz", "final_trim_bottom": 28, "final_trim_top": 27, "init_margin_grid_points": 80, "initial_seed": [ 17166.90234375, 12482.4208984375, 34000.0 ], "initial_shell_id": "shell_0000.tifxyz", "initial_skipped_point_count": 0, "initial_skipped_reasons": {}, "initial_trim_bottom": 28, "initial_trim_top": 27, "initial_usable_point_count": 30, "mode": "corr-point-roi", "model_h": 8146.1761474609375, "model_w": 8953.868007659912, "model_w_unit": "voxels", "output_radius_grid_points": 20, "parsed_point_count": 30, "projected_h_span_grid": 2.92352294921875, "projected_h_span_vx": 146.1761474609375, "projected_points": [ { "collection_id": 2710, "direction_sign": -1, "grid_distance_to_anchor": 8.758686427770167, "h": 181.1114044189453, "point_id": 76510, "row_index": 0, "w": 49.444576263427734 }, { "collection_id": 2710, "direction_sign": -1, "grid_distance_to_anchor": 8.03713961206747, "h": 181.1934814453125, "point_id": 76511, "row_index": 1, "w": 48.72144317626953 }, { "collection_id": 2710, "direction_sign": -1, "grid_distance_to_anchor": 7.649889400803313, "h": 181.06027221679688, "point_id": 76512, "row_index": 2, "w": 48.28402328491211 }, { "collection_id": 2710, "direction_sign": -1, "grid_distance_to_anchor": 7.870285217561945, "h": 181.03564453125, "point_id": 76513, "row_index": 3, "w": 48.506202697753906 }, { "collection_id": 2710, "direction_sign": -1, "grid_distance_to_anchor": 7.98603992276444, "h": 181.49339294433594, "point_id": 76514, "row_index": 4, "w": 48.73957443237305 }, { "collection_id": 2710, "direction_sign": -1, "grid_distance_to_anchor": 9.136033104855263, "h": 181.95654296875, "point_id": 76515, "row_index": 5, "w": 49.987396240234375 }, { "collection_id": 2710, "direction_sign": -1, "grid_distance_to_anchor": 9.809592481838195, "h": 182.7587127685547, "point_id": 76516, "row_index": 6, "w": 50.73418045043945 }, { "collection_id": 2710, "direction_sign": 1, "grid_distance_to_anchor": 9.308439773423064, "h": 183.946533203125, "point_id": 76517, "row_index": 7, "w": 31.65682029724121 }, { "collection_id": 2710, "direction_sign": 1, "grid_distance_to_anchor": 8.677418070771575, "h": 183.8644256591797, "point_id": 76518, "row_index": 8, "w": 32.283260345458984 }, { "collection_id": 2710, "direction_sign": 1, "grid_distance_to_anchor": 8.017633545625468, "h": 183.95916748046875, "point_id": 76519, "row_index": 9, "w": 32.95396423339844 }, { "collection_id": 2710, "direction_sign": 1, "grid_distance_to_anchor": 6.979480010662963, "h": 183.7608642578125, "point_id": 76520, "row_index": 10, "w": 33.97837829589844 }, { "collection_id": 2710, "direction_sign": 1, "grid_distance_to_anchor": 5.859776209802725, "h": 183.88153076171875, "point_id": 76521, "row_index": 11, "w": 35.11602020263672 }, { "collection_id": 2710, "direction_sign": -1, "grid_distance_to_anchor": 4.803806935091271, "h": 183.51524353027344, "point_id": 76522, "row_index": 12, "w": 36.14154815673828 }, { "collection_id": 2710, "direction_sign": -1, "grid_distance_to_anchor": 4.046541507628639, "h": 183.4714813232422, "point_id": 76523, "row_index": 13, "w": 36.897613525390625 }, { "collection_id": 2710, "direction_sign": -1, "grid_distance_to_anchor": 3.0839605609867804, "h": 183.4358673095703, "point_id": 76524, "row_index": 14, "w": 37.86031723022461 }, { "collection_id": 2710, "direction_sign": -1, "grid_distance_to_anchor": 2.1720100678019856, "h": 183.40040588378906, "point_id": 76525, "row_index": 15, "w": 38.772850036621094 }, { "collection_id": 2710, "direction_sign": -1, "grid_distance_to_anchor": 1.580692951301674, "h": 183.43740844726563, "point_id": 76526, "row_index": 16, "w": 39.37406539916992 }, { "collection_id": 2710, "direction_sign": -1, "grid_distance_to_anchor": 1.1570121839919953, "h": 183.43746948242188, "point_id": 76527, "row_index": 17, "w": 39.805667877197266 }, { "collection_id": 2710, "direction_sign": -1, "grid_distance_to_anchor": 0.38538477530537973, "h": 183.31723022460938, "point_id": 76528, "row_index": 18, "w": 40.573570251464844 }, { "collection_id": 2710, "direction_sign": -1, "grid_distance_to_anchor": 0.4600138406577094, "h": 183.18727111816406, "point_id": 76529, "row_index": 19, "w": 41.393585205078125 }, { "collection_id": 2710, "direction_sign": -1, "grid_distance_to_anchor": 1.080249437180163, "h": 183.13987731933594, "point_id": 76530, "row_index": 20, "w": 42.01314163208008 }, { "collection_id": 2710, "direction_sign": -1, "grid_distance_to_anchor": 1.6762921833631408, "h": 183.12242126464844, "point_id": 76531, "row_index": 21, "w": 42.60894012451172 }, { "collection_id": 2710, "direction_sign": -1, "grid_distance_to_anchor": 2.2055114379609915, "h": 183.177001953125, "point_id": 76532, "row_index": 22, "w": 43.13914108276367 }, { "collection_id": 2710, "direction_sign": -1, "grid_distance_to_anchor": 2.7604395584715915, "h": 183.28611755371094, "point_id": 76533, "row_index": 23, "w": 43.69202423095703 }, { "collection_id": 2710, "direction_sign": -1, "grid_distance_to_anchor": 3.312634332371978, "h": 183.35086059570313, "point_id": 76534, "row_index": 24, "w": 44.24184799194336 }, { "collection_id": 2710, "direction_sign": -1, "grid_distance_to_anchor": 4.038031337696246, "h": 183.425048828125, "point_id": 76535, "row_index": 25, "w": 44.964210510253906 }, { "collection_id": 2710, "direction_sign": -1, "grid_distance_to_anchor": 4.631246679500704, "h": 183.4609375, "point_id": 76536, "row_index": 26, "w": 45.556339263916016 }, { "collection_id": 2710, "direction_sign": -1, "grid_distance_to_anchor": 5.243979316245641, "h": 183.55886840820313, "point_id": 76537, "row_index": 27, "w": 46.16389465332031 }, { "collection_id": 2710, "direction_sign": -1, "grid_distance_to_anchor": 6.005874130513916, "h": 183.6918487548828, "point_id": 76538, "row_index": 28, "w": 46.917640686035156 }, { "collection_id": 2710, "direction_sign": -1, "grid_distance_to_anchor": 6.241899887403323, "h": 183.790771484375, "point_id": 76539, "row_index": 29, "w": 47.14556121826172 } ], "projected_w_span_grid": 19.077360153198242, "projected_w_span_vx": 953.8680076599121, "projection_mode": "normal-line", "skipped_point_count": 0, "skipped_points": [], "skipped_reasons": {}, "usable_point_count": 30, "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_2710/point_strip.lasagna.json", "mesh-h": 32, "mesh-step": 50, "mesh-w": 32, "model-h": 8146.1761474609375, "model-init": "seed", "model-input": null, "model-output": "/tmp/fit_reopt_3calkjhk/model_reopt.pt", "model-w": 8953.868007659912, "model-w-unit": "voxels", "normal-mask-zero": 0, "out-dir": null, "progress": true, "pyramid-d": false, "seed": [ 17336.283203125, 12331.3134765625, 34000.0 ], "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": { "2710": { "color": [ 1.0, 0.7058823704719543, 0.3137255012989044 ], "metadata": { "winding_is_absolute": true }, "name": "same_wrap1698", "points": { "76510": { "creation_time": 1779555180309, "p": [ 17590.65625, 13872.296875, 34000.0 ], "wind_a": 0.0 }, "76511": { "creation_time": 1779555180309, "p": [ 17496.4375, 13810.056640625, 34000.0 ], "wind_a": 0.0 }, "76512": { "creation_time": 1779555180309, "p": [ 17400.880859375, 13751.0458984375, 34000.0 ], "wind_a": 0.0 }, "76513": { "creation_time": 1779555180309, "p": [ 17306.34765625, 13689.5634765625, 34000.0 ], "wind_a": 0.0 }, "76514": { "creation_time": 1779555180309, "p": [ 17213.779296875, 13623.333984375, 34000.0 ], "wind_a": 0.0 }, "76515": { "creation_time": 1779555180309, "p": [ 17128.927734375, 13538.4814453125, 34000.0 ], "wind_a": 0.0 }, "76516": { "creation_time": 1779555180309, "p": [ 17063.45703125, 13445.6005859375, 34000.0 ], "wind_a": 0.0 }, "76517": { "creation_time": 1779555180309, "p": [ 17001.33984375, 13351.330078125, 34000.0 ], "wind_a": 0.0 }, "76518": { "creation_time": 1779555180309, "p": [ 16942.205078125, 13255.82421875, 34000.0 ], "wind_a": 0.0 }, "76519": { "creation_time": 1779555180309, "p": [ 16891.701171875, 13156.744140625, 34000.0 ], "wind_a": 0.0 }, "76520": { "creation_time": 1779555180309, "p": [ 16859.72265625, 13049.990234375, 34000.0 ], "wind_a": 0.0 }, "76521": { "creation_time": 1779555180309, "p": [ 16859.72265625, 12933.7744140625, 34000.0 ], "wind_a": 0.0 }, "76522": { "creation_time": 1779555180309, "p": [ 16887.853515625, 12825.4267578125, 34000.0 ], "wind_a": 0.0 }, "76523": { "creation_time": 1779555180309, "p": [ 16930.712890625, 12723.1796875, 34000.0 ], "wind_a": 0.0 }, "76524": { "creation_time": 1779555180309, "p": [ 16991.060546875, 12630.8525390625, 34000.0 ], "wind_a": 0.0 }, "76525": { "creation_time": 1779555180309, "p": [ 17074.021484375, 12547.8916015625, 34000.0 ], "wind_a": 0.0 }, "76526": { "creation_time": 1779555180309, "p": [ 17166.90234375, 12482.4208984375, 34000.0 ], "wind_a": 0.0 }, "76527": { "creation_time": 1779555180309, "p": [ 17249.30859375, 12404.5830078125, 34000.0 ], "wind_a": 0.0 }, "76528": { "creation_time": 1779555180309, "p": [ 17336.283203125, 12331.3134765625, 34000.0 ], "wind_a": 0.0 }, "76529": { "creation_time": 1779555180309, "p": [ 17431.83984375, 12272.302734375, 34000.0 ], "wind_a": 0.0 }, "76530": { "creation_time": 1779555180309, "p": [ 17531.412109375, 12222.9833984375, 34000.0 ], "wind_a": 0.0 }, "76531": { "creation_time": 1779555180309, "p": [ 17634.998046875, 12183.35546875, 34000.0 ], "wind_a": 0.0 }, "76532": { "creation_time": 1779555180309, "p": [ 17737.244140625, 12140.49609375, 34000.0 ], "wind_a": 0.0 }, "76533": { "creation_time": 1779555180309, "p": [ 17839.4921875, 12097.63671875, 34000.0 ], "wind_a": 0.0 }, "76534": { "creation_time": 1779555180309, "p": [ 17939.56640625, 12049.53125, 34000.0 ], "wind_a": 0.0 }, "76535": { "creation_time": 1779555180309, "p": [ 18044.427734375, 12012.984375, 34000.0 ], "wind_a": 0.0 }, "76536": { "creation_time": 1779555180309, "p": [ 18154.26171875, 11988.4423828125, 34000.0 ], "wind_a": 0.0 }, "76537": { "creation_time": 1779555180309, "p": [ 18267.396484375, 11971.869140625, 34000.0 ], "wind_a": 0.0 }, "76538": { "creation_time": 1779555180309, "p": [ 18381.720703125, 11967.30078125, 34000.0 ], "wind_a": 0.0 }, "76539": { "creation_time": 1779555180309, "p": [ 18417.525390625, 11971.869140625, 34000.0 ], "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": [ 4268.50537109375, 3136.972900390625, 8500.0 ], "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": { "2710": { "color": [ 1.0, 0.7058823704719543, 0.3137255012989044 ], "metadata": { "winding_is_absolute": true }, "name": "same_wrap1698", "points": { "76510": { "creation_time": 1779555180309, "p": [ 4397.6640625, 3468.07421875, 8500.0 ], "wind_a": 0.0 }, "76511": { "creation_time": 1779555180309, "p": [ 4374.109375, 3452.51416015625, 8500.0 ], "wind_a": 0.0 }, "76512": { "creation_time": 1779555180309, "p": [ 4350.22021484375, 3437.761474609375, 8500.0 ], "wind_a": 0.0 }, "76513": { "creation_time": 1779555180309, "p": [ 4326.5869140625, 3422.390869140625, 8500.0 ], "wind_a": 0.0 }, "76514": { "creation_time": 1779555180309, "p": [ 4303.44482421875, 3405.83349609375, 8500.0 ], "wind_a": 0.0 }, "76515": { "creation_time": 1779555180309, "p": [ 4282.23193359375, 3384.620361328125, 8500.0 ], "wind_a": 0.0 }, "76516": { "creation_time": 1779555180309, "p": [ 4265.8642578125, 3361.400146484375, 8500.0 ], "wind_a": 0.0 }, "76517": { "creation_time": 1779555180309, "p": [ 4250.3349609375, 3337.83251953125, 8500.0 ], "wind_a": 0.0 }, "76518": { "creation_time": 1779555180309, "p": [ 4235.55126953125, 3313.9560546875, 8500.0 ], "wind_a": 0.0 }, "76519": { "creation_time": 1779555180309, "p": [ 4222.92529296875, 3289.18603515625, 8500.0 ], "wind_a": 0.0 }, "76520": { "creation_time": 1779555180309, "p": [ 4214.9306640625, 3262.49755859375, 8500.0 ], "wind_a": 0.0 }, "76521": { "creation_time": 1779555180309, "p": [ 4214.9306640625, 3233.443603515625, 8500.0 ], "wind_a": 0.0 }, "76522": { "creation_time": 1779555180309, "p": [ 4221.96337890625, 3206.356689453125, 8500.0 ], "wind_a": 0.0 }, "76523": { "creation_time": 1779555180309, "p": [ 4232.67822265625, 3180.794921875, 8500.0 ], "wind_a": 0.0 }, "76524": { "creation_time": 1779555180309, "p": [ 4247.76513671875, 3157.713134765625, 8500.0 ], "wind_a": 0.0 }, "76525": { "creation_time": 1779555180309, "p": [ 4268.50537109375, 3136.972900390625, 8500.0 ], "wind_a": 0.0 }, "76526": { "creation_time": 1779555180309, "p": [ 4291.7255859375, 3120.605224609375, 8500.0 ], "wind_a": 0.0 }, "76527": { "creation_time": 1779555180309, "p": [ 4312.3271484375, 3101.145751953125, 8500.0 ], "wind_a": 0.0 }, "76528": { "creation_time": 1779555180309, "p": [ 4334.07080078125, 3082.828369140625, 8500.0 ], "wind_a": 0.0 }, "76529": { "creation_time": 1779555180309, "p": [ 4357.9599609375, 3068.07568359375, 8500.0 ], "wind_a": 0.0 }, "76530": { "creation_time": 1779555180309, "p": [ 4382.85302734375, 3055.745849609375, 8500.0 ], "wind_a": 0.0 }, "76531": { "creation_time": 1779555180309, "p": [ 4408.74951171875, 3045.8388671875, 8500.0 ], "wind_a": 0.0 }, "76532": { "creation_time": 1779555180309, "p": [ 4434.31103515625, 3035.1240234375, 8500.0 ], "wind_a": 0.0 }, "76533": { "creation_time": 1779555180309, "p": [ 4459.873046875, 3024.4091796875, 8500.0 ], "wind_a": 0.0 }, "76534": { "creation_time": 1779555180309, "p": [ 4484.8916015625, 3012.3828125, 8500.0 ], "wind_a": 0.0 }, "76535": { "creation_time": 1779555180309, "p": [ 4511.10693359375, 3003.24609375, 8500.0 ], "wind_a": 0.0 }, "76536": { "creation_time": 1779555180309, "p": [ 4538.5654296875, 2997.110595703125, 8500.0 ], "wind_a": 0.0 }, "76537": { "creation_time": 1779555180309, "p": [ 4566.84912109375, 2992.96728515625, 8500.0 ], "wind_a": 0.0 }, "76538": { "creation_time": 1779555180309, "p": [ 4595.43017578125, 2991.8251953125, 8500.0 ], "wind_a": 0.0 }, "76539": { "creation_time": 1779555180309, "p": [ 4604.38134765625, 2992.96728515625, 8500.0 ], "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_3calkjhk/model_reopt.pt", "scale": [ 0.07999999821186066, 0.07999999821186066 ], "tags": { "date_last_modified": "20260614185644399", "reviewed": { "date": "20260604080934243" } }, "type": "seg", "uuid": "same_wrap001698_lasagna" }