{ "area_vx2": 531562.5, "base_shape_zyx": [ 18946, 8174, 8174 ], "bbox": [ [ 3268.254150390625, 2425.654296875, 9200.125 ], [ 3795.066650390625, 3037.56494140625, 9619.1884765625 ] ], "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": [ 13233.177734375, 10139.32421875, 37890.0 ], "final_anchor_h": 222.58996772766113, "final_anchor_w": 143.99999997019768, "final_shell_id": "shell_0004.tifxyz", "final_trim_bottom": 36, "final_trim_top": 4, "init_margin_grid_points": 80, "initial_seed": [ 13233.177734375, 10139.32421875, 37890.0 ], "initial_shell_id": "shell_0004.tifxyz", "initial_skipped_point_count": 0, "initial_skipped_reasons": {}, "initial_trim_bottom": 36, "initial_trim_top": 4, "initial_usable_point_count": 29, "mode": "corr-point-roi", "model_h": 8057.663726806641, "model_w": 8417.07534790039, "model_w_unit": "voxels", "output_radius_grid_points": 20, "parsed_point_count": 29, "projected_h_span_grid": 1.1532745361328125, "projected_h_span_vx": 57.663726806640625, "projected_points": [ { "collection_id": 1697, "direction_sign": -1, "grid_distance_to_anchor": 4.7110120158752995, "h": 222.16903686523438, "point_id": 63045, "row_index": 0, "w": 139.30783081054688 }, { "collection_id": 1697, "direction_sign": -1, "grid_distance_to_anchor": 4.337116766076513, "h": 222.16244506835938, "point_id": 63046, "row_index": 1, "w": 139.6840057373047 }, { "collection_id": 1697, "direction_sign": -1, "grid_distance_to_anchor": 3.959363227385986, "h": 222.14083862304688, "point_id": 63047, "row_index": 2, "w": 140.06619262695313 }, { "collection_id": 1697, "direction_sign": -1, "grid_distance_to_anchor": 3.5640323959445626, "h": 222.12486267089844, "point_id": 63048, "row_index": 3, "w": 140.46644592285156 }, { "collection_id": 1697, "direction_sign": -1, "grid_distance_to_anchor": 3.1769596003880194, "h": 222.1205596923828, "point_id": 63049, "row_index": 4, "w": 140.85791015625 }, { "collection_id": 1697, "direction_sign": -1, "grid_distance_to_anchor": 2.774451599474361, "h": 222.10809326171875, "point_id": 63050, "row_index": 5, "w": 141.26771545410156 }, { "collection_id": 1697, "direction_sign": -1, "grid_distance_to_anchor": 2.3751021238647967, "h": 222.09800720214844, "point_id": 63051, "row_index": 6, "w": 141.67640686035156 }, { "collection_id": 1697, "direction_sign": -1, "grid_distance_to_anchor": 1.9735017734723144, "h": 222.10191345214844, "point_id": 63052, "row_index": 7, "w": 142.08779907226563 }, { "collection_id": 1697, "direction_sign": -1, "grid_distance_to_anchor": 1.5583928894905337, "h": 222.13218688964844, "point_id": 63053, "row_index": 8, "w": 142.51036071777344 }, { "collection_id": 1697, "direction_sign": -1, "grid_distance_to_anchor": 1.2682119421720321, "h": 222.1512908935547, "point_id": 63054, "row_index": 9, "w": 142.81007385253906 }, { "collection_id": 1697, "direction_sign": -1, "grid_distance_to_anchor": 1.0496472021782832, "h": 222.23167419433594, "point_id": 63055, "row_index": 10, "w": 143.01339721679688 }, { "collection_id": 1697, "direction_sign": -1, "grid_distance_to_anchor": 0.7618188405928573, "h": 222.44186401367188, "point_id": 63056, "row_index": 11, "w": 143.25271606445313 }, { "collection_id": 1697, "direction_sign": 1, "grid_distance_to_anchor": 0.5477935317258952, "h": 222.46693420410156, "point_id": 63057, "row_index": 12, "w": 143.46620178222656 }, { "collection_id": 1697, "direction_sign": 1, "grid_distance_to_anchor": 0.31441159303197197, "h": 222.56224060058594, "point_id": 63058, "row_index": 13, "w": 143.6868133544922 }, { "collection_id": 1697, "direction_sign": 1, "grid_distance_to_anchor": 0.20703718811104646, "h": 222.70172119140625, "point_id": 63059, "row_index": 14, "w": 143.82571411132813 }, { "collection_id": 1697, "direction_sign": 1, "grid_distance_to_anchor": 0.2282168630542851, "h": 222.8115692138672, "point_id": 63060, "row_index": 15, "w": 143.94544982910156 }, { "collection_id": 1697, "direction_sign": 1, "grid_distance_to_anchor": 0.3597605018683133, "h": 222.9054412841797, "point_id": 63061, "row_index": 16, "w": 144.1729278564453 }, { "collection_id": 1697, "direction_sign": 1, "grid_distance_to_anchor": 0.6337018689692662, "h": 223.01942443847656, "point_id": 63062, "row_index": 17, "w": 144.4659881591797 }, { "collection_id": 1697, "direction_sign": 1, "grid_distance_to_anchor": 0.9315928338153726, "h": 223.0757293701172, "point_id": 63063, "row_index": 18, "w": 144.794921875 }, { "collection_id": 1697, "direction_sign": 1, "grid_distance_to_anchor": 1.1986997147168772, "h": 223.10975646972656, "point_id": 63064, "row_index": 19, "w": 145.08013916015625 }, { "collection_id": 1697, "direction_sign": 1, "grid_distance_to_anchor": 1.3579936079035275, "h": 223.138916015625, "point_id": 63065, "row_index": 20, "w": 145.24209594726563 }, { "collection_id": 1697, "direction_sign": 1, "grid_distance_to_anchor": 1.5798102987640221, "h": 223.12783813476563, "point_id": 63066, "row_index": 21, "w": 145.4854278564453 }, { "collection_id": 1697, "direction_sign": 1, "grid_distance_to_anchor": 1.9254290652116681, "h": 223.12205505371094, "point_id": 63067, "row_index": 22, "w": 145.85044860839844 }, { "collection_id": 1697, "direction_sign": 1, "grid_distance_to_anchor": 2.26152800405944, "h": 223.10824584960938, "point_id": 63068, "row_index": 23, "w": 146.2013397216797 }, { "collection_id": 1697, "direction_sign": 1, "grid_distance_to_anchor": 2.601246751631272, "h": 223.156982421875, "point_id": 63069, "row_index": 24, "w": 146.5386962890625 }, { "collection_id": 1697, "direction_sign": 1, "grid_distance_to_anchor": 2.891151429774001, "h": 223.1901397705078, "point_id": 63070, "row_index": 25, "w": 146.8281707763672 }, { "collection_id": 1697, "direction_sign": 1, "grid_distance_to_anchor": 3.1928898836620356, "h": 223.23483276367188, "point_id": 63071, "row_index": 26, "w": 147.12709045410156 }, { "collection_id": 1697, "direction_sign": 1, "grid_distance_to_anchor": 3.4641389520764663, "h": 223.23439025878906, "point_id": 63072, "row_index": 27, "w": 147.40367126464844 }, { "collection_id": 1697, "direction_sign": 1, "grid_distance_to_anchor": 3.7087737309196487, "h": 223.25128173828125, "point_id": 63073, "row_index": 28, "w": 147.6493377685547 } ], "projected_w_span_grid": 8.341506958007813, "projected_w_span_vx": 417.0753479003906, "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_1697/point_strip.lasagna.json", "mesh-h": 32, "mesh-step": 50, "mesh-w": 32, "model-h": 8057.663726806641, "model-init": "seed", "model-input": null, "model-output": "/tmp/fit_reopt_zwrzh7dx/model_reopt.pt", "model-w": 8417.07534790039, "model-w-unit": "voxels", "normal-mask-zero": 0, "out-dir": null, "progress": true, "pyramid-d": false, "seed": [ 13233.177734375, 10139.32421875, 37890.0 ], "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": { "1697": { "color": [ 0.0, 1.0, 0.27450981736183167 ], "metadata": { "winding_is_absolute": true }, "name": "same_wrap1287", "points": { "63045": { "creation_time": 1779507829330, "p": [ 13438.75390625, 11132.541015625, 37890.0 ], "wind_a": 0.0 }, "63046": { "creation_time": 1779507829336, "p": [ 13414.4892578125, 11062.591796875, 37890.0 ], "wind_a": 0.0 }, "63047": { "creation_time": 1779507829340, "p": [ 13386.994140625, 10993.9814453125, 37890.0 ], "wind_a": 0.0 }, "63048": { "creation_time": 1779507829344, "p": [ 13361.091796875, 10924.7099609375, 37890.0 ], "wind_a": 0.0 }, "63049": { "creation_time": 1779507829349, "p": [ 13335.232421875, 10855.421875, 37890.0 ], "wind_a": 0.0 }, "63050": { "creation_time": 1779507829353, "p": [ 13307.7373046875, 10786.810546875, 37890.0 ], "wind_a": 0.0 }, "63051": { "creation_time": 1779507829357, "p": [ 13278.861328125, 10718.771484375, 37890.0 ], "wind_a": 0.0 }, "63052": { "creation_time": 1779507829361, "p": [ 13246.28515625, 10652.2646484375, 37890.0 ], "wind_a": 0.0 }, "63053": { "creation_time": 1779507829365, "p": [ 13214.904296875, 10585.263671875, 37890.0 ], "wind_a": 0.0 }, "63054": { "creation_time": 1779507829369, "p": [ 13188.064453125, 10516.380859375, 37890.0 ], "wind_a": 0.0 }, "63055": { "creation_time": 1779507829373, "p": [ 13182.92578125, 10438.509765625, 37890.0 ], "wind_a": 0.0 }, "63056": { "creation_time": 1779507829377, "p": [ 13182.92578125, 10358.5087890625, 37890.0 ], "wind_a": 0.0 }, "63057": { "creation_time": 1779507829381, "p": [ 13189.20703125, 10281.111328125, 37890.0 ], "wind_a": 0.0 }, "63058": { "creation_time": 1779507829385, "p": [ 13205.767578125, 10207.970703125, 37890.0 ], "wind_a": 0.0 }, "63059": { "creation_time": 1779507829389, "p": [ 13233.177734375, 10139.32421875, 37890.0 ], "wind_a": 0.0 }, "63060": { "creation_time": 1779507829393, "p": [ 13269.724609375, 10074.462890625, 37890.0 ], "wind_a": 0.0 }, "63061": { "creation_time": 1779507829397, "p": [ 13325.0322265625, 10017.37109375, 37890.0 ], "wind_a": 0.0 }, "63062": { "creation_time": 1779507829401, "p": [ 13384.2763671875, 9967.263671875, 37890.0 ], "wind_a": 0.0 }, "63063": { "creation_time": 1779507829405, "p": [ 13443.521484375, 9917.1552734375, 37890.0 ], "wind_a": 0.0 }, "63064": { "creation_time": 1779507829409, "p": [ 13506.572265625, 9876.23828125, 37890.0 ], "wind_a": 0.0 }, "63065": { "creation_time": 1779507829413, "p": [ 13570.0390625, 9836.322265625, 37890.0 ], "wind_a": 0.0 }, "63066": { "creation_time": 1779507829417, "p": [ 13641.97265625, 9816.849609375, 37890.0 ], "wind_a": 0.0 }, "63067": { "creation_time": 1779507829421, "p": [ 13713.951171875, 9797.482421875, 37890.0 ], "wind_a": 0.0 }, "63068": { "creation_time": 1779507829425, "p": [ 13786.8349609375, 9780.302734375, 37890.0 ], "wind_a": 0.0 }, "63069": { "creation_time": 1779507829429, "p": [ 13859.201171875, 9761.873046875, 37890.0 ], "wind_a": 0.0 }, "63070": { "creation_time": 1779507829434, "p": [ 13933.5888671875, 9748.32421875, 37890.0 ], "wind_a": 0.0 }, "63071": { "creation_time": 1779507829438, "p": [ 14011.6962890625, 9743.755859375, 37890.0 ], "wind_a": 0.0 }, "63072": { "creation_time": 1779507829442, "p": [ 14087.912109375, 9752.892578125, 37890.0 ], "wind_a": 0.0 }, "63073": { "creation_time": 1779507829446, "p": [ 14142.2841796875, 9762.029296875, 37890.0 ], "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": [ 3308.29443359375, 2534.8310546875, 9472.5 ], "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": { "1697": { "color": [ 0.0, 1.0, 0.27450981736183167 ], "metadata": { "winding_is_absolute": true }, "name": "same_wrap1287", "points": { "63045": { "creation_time": 1779507829330, "p": [ 3359.6884765625, 2783.13525390625, 9472.5 ], "wind_a": 0.0 }, "63046": { "creation_time": 1779507829336, "p": [ 3353.622314453125, 2765.64794921875, 9472.5 ], "wind_a": 0.0 }, "63047": { "creation_time": 1779507829340, "p": [ 3346.74853515625, 2748.495361328125, 9472.5 ], "wind_a": 0.0 }, "63048": { "creation_time": 1779507829344, "p": [ 3340.27294921875, 2731.177490234375, 9472.5 ], "wind_a": 0.0 }, "63049": { "creation_time": 1779507829349, "p": [ 3333.80810546875, 2713.85546875, 9472.5 ], "wind_a": 0.0 }, "63050": { "creation_time": 1779507829353, "p": [ 3326.934326171875, 2696.70263671875, 9472.5 ], "wind_a": 0.0 }, "63051": { "creation_time": 1779507829357, "p": [ 3319.71533203125, 2679.69287109375, 9472.5 ], "wind_a": 0.0 }, "63052": { "creation_time": 1779507829361, "p": [ 3311.5712890625, 2663.066162109375, 9472.5 ], "wind_a": 0.0 }, "63053": { "creation_time": 1779507829365, "p": [ 3303.72607421875, 2646.31591796875, 9472.5 ], "wind_a": 0.0 }, "63054": { "creation_time": 1779507829369, "p": [ 3297.01611328125, 2629.09521484375, 9472.5 ], "wind_a": 0.0 }, "63055": { "creation_time": 1779507829373, "p": [ 3295.7314453125, 2609.62744140625, 9472.5 ], "wind_a": 0.0 }, "63056": { "creation_time": 1779507829377, "p": [ 3295.7314453125, 2589.627197265625, 9472.5 ], "wind_a": 0.0 }, "63057": { "creation_time": 1779507829381, "p": [ 3297.3017578125, 2570.27783203125, 9472.5 ], "wind_a": 0.0 }, "63058": { "creation_time": 1779507829385, "p": [ 3301.44189453125, 2551.99267578125, 9472.5 ], "wind_a": 0.0 }, "63059": { "creation_time": 1779507829389, "p": [ 3308.29443359375, 2534.8310546875, 9472.5 ], "wind_a": 0.0 }, "63060": { "creation_time": 1779507829393, "p": [ 3317.43115234375, 2518.61572265625, 9472.5 ], "wind_a": 0.0 }, "63061": { "creation_time": 1779507829397, "p": [ 3331.258056640625, 2504.3427734375, 9472.5 ], "wind_a": 0.0 }, "63062": { "creation_time": 1779507829401, "p": [ 3346.069091796875, 2491.81591796875, 9472.5 ], "wind_a": 0.0 }, "63063": { "creation_time": 1779507829405, "p": [ 3360.88037109375, 2479.288818359375, 9472.5 ], "wind_a": 0.0 }, "63064": { "creation_time": 1779507829409, "p": [ 3376.64306640625, 2469.0595703125, 9472.5 ], "wind_a": 0.0 }, "63065": { "creation_time": 1779507829413, "p": [ 3392.509765625, 2459.08056640625, 9472.5 ], "wind_a": 0.0 }, "63066": { "creation_time": 1779507829417, "p": [ 3410.4931640625, 2454.21240234375, 9472.5 ], "wind_a": 0.0 }, "63067": { "creation_time": 1779507829421, "p": [ 3428.48779296875, 2449.37060546875, 9472.5 ], "wind_a": 0.0 }, "63068": { "creation_time": 1779507829425, "p": [ 3446.708740234375, 2445.07568359375, 9472.5 ], "wind_a": 0.0 }, "63069": { "creation_time": 1779507829429, "p": [ 3464.80029296875, 2440.46826171875, 9472.5 ], "wind_a": 0.0 }, "63070": { "creation_time": 1779507829434, "p": [ 3483.397216796875, 2437.0810546875, 9472.5 ], "wind_a": 0.0 }, "63071": { "creation_time": 1779507829438, "p": [ 3502.924072265625, 2435.93896484375, 9472.5 ], "wind_a": 0.0 }, "63072": { "creation_time": 1779507829442, "p": [ 3521.97802734375, 2438.22314453125, 9472.5 ], "wind_a": 0.0 }, "63073": { "creation_time": 1779507829446, "p": [ 3535.571044921875, 2440.50732421875, 9472.5 ], "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_zwrzh7dx/model_reopt.pt", "scale": [ 0.07999999821186066, 0.07999999821186066 ], "tags": { "date_last_modified": "20260614185644294", "reviewed": { "date": "20260604080934222" } }, "type": "seg", "uuid": "same_wrap001287_lasagna" }