{ "area_vx2": 593437.5, "base_shape_zyx": [ 18946, 8174, 8174 ], "bbox": [ [ 2331.0830078125, 1749.73046875, 8748.875 ], [ 3011.771484375, 2007.6719970703125, 9349.8603515625 ] ], "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": [ 10507.0908203125, 7143.0712890625, 36210.0 ], "final_anchor_h": 200.0, "final_anchor_w": 299.0, "final_shell_id": "shell_0007.tifxyz", "final_trim_bottom": 65, "final_trim_top": 18, "init_margin_grid_points": 80, "initial_seed": [ 9664.232421875, 7286.6484375, 36210.0 ], "initial_shell_id": "shell_0007.tifxyz", "initial_skipped_point_count": 0, "initial_skipped_reasons": {}, "initial_trim_bottom": 65, "initial_trim_top": 18, "initial_usable_point_count": 21, "mode": "corr-point-roi", "model_h": 8790.182495117188, "model_w": 8419.978332519531, "model_w_unit": "voxels", "output_radius_grid_points": 20, "parsed_point_count": 21, "projected_h_span_grid": 15.80364990234375, "projected_h_span_vx": 790.1824951171875, "projected_points": [ { "collection_id": 773, "direction_sign": -1, "grid_distance_to_anchor": 0.2927574496424129, "h": 199.86387634277344, "point_id": 72143, "row_index": 0, "w": 299.2591857910156 }, { "collection_id": 773, "direction_sign": -1, "grid_distance_to_anchor": 0.5235161582094849, "h": 200.10227966308594, "point_id": 72144, "row_index": 1, "w": 298.486572265625 }, { "collection_id": 773, "direction_sign": -1, "grid_distance_to_anchor": 1.3020474412362115, "h": 200.49574279785156, "point_id": 72145, "row_index": 2, "w": 297.7960205078125 }, { "collection_id": 773, "direction_sign": -1, "grid_distance_to_anchor": 1.8702251652777422, "h": 200.95579528808594, "point_id": 72146, "row_index": 3, "w": 297.3924560546875 }, { "collection_id": 773, "direction_sign": -1, "grid_distance_to_anchor": 1.9955178757968528, "h": 200.53195190429688, "point_id": 72147, "row_index": 4, "w": 297.0766906738281 }, { "collection_id": 773, "direction_sign": -1, "grid_distance_to_anchor": 2.2857859205033093, "h": 200.4045867919922, "point_id": 72148, "row_index": 5, "w": 296.75030517578125 }, { "collection_id": 773, "direction_sign": -1, "grid_distance_to_anchor": 2.7025663165095097, "h": 201.12701416015625, "point_id": 72149, "row_index": 6, "w": 296.54364013671875 }, { "collection_id": 773, "direction_sign": -1, "grid_distance_to_anchor": 2.556827222529356, "h": 200.66903686523438, "point_id": 72150, "row_index": 7, "w": 296.5322570800781 }, { "collection_id": 773, "direction_sign": -1, "grid_distance_to_anchor": 2.49644066951118, "h": 201.08786010742188, "point_id": 72151, "row_index": 8, "w": 296.7530517578125 }, { "collection_id": 773, "direction_sign": -1, "grid_distance_to_anchor": 2.088076498912845, "h": 200.70425415039063, "point_id": 72152, "row_index": 9, "w": 297.0342712402344 }, { "collection_id": 773, "direction_sign": 1, "grid_distance_to_anchor": 16.154744366501646, "h": 215.6675262451172, "point_id": 72153, "row_index": 10, "w": 302.93756103515625 }, { "collection_id": 773, "direction_sign": 1, "grid_distance_to_anchor": 1.784719032060662, "h": 201.04005432128906, "point_id": 72154, "row_index": 11, "w": 300.4503479003906 }, { "collection_id": 773, "direction_sign": 1, "grid_distance_to_anchor": 2.4293833801774802, "h": 202.424072265625, "point_id": 72155, "row_index": 12, "w": 299.1605529785156 }, { "collection_id": 773, "direction_sign": -1, "grid_distance_to_anchor": 1.333570662641102, "h": 200.57492065429688, "point_id": 72156, "row_index": 13, "w": 297.7967224121094 }, { "collection_id": 773, "direction_sign": -1, "grid_distance_to_anchor": 1.7468666101302837, "h": 200.92800903320313, "point_id": 72157, "row_index": 14, "w": 297.52001953125 }, { "collection_id": 773, "direction_sign": -1, "grid_distance_to_anchor": 2.550479924287633, "h": 200.6874542236328, "point_id": 72158, "row_index": 15, "w": 296.5439147949219 }, { "collection_id": 773, "direction_sign": -1, "grid_distance_to_anchor": 2.9556422205739126, "h": 200.86947631835938, "point_id": 72159, "row_index": 16, "w": 296.1751403808594 }, { "collection_id": 773, "direction_sign": -1, "grid_distance_to_anchor": 3.265604394445308, "h": 201.05690002441406, "point_id": 72160, "row_index": 17, "w": 295.91015625 }, { "collection_id": 773, "direction_sign": -1, "grid_distance_to_anchor": 3.7224371718103826, "h": 201.06080627441406, "point_id": 72161, "row_index": 18, "w": 295.4319152832031 }, { "collection_id": 773, "direction_sign": -1, "grid_distance_to_anchor": 4.186769328344176, "h": 200.53627014160156, "point_id": 72162, "row_index": 19, "w": 294.84771728515625 }, { "collection_id": 773, "direction_sign": -1, "grid_distance_to_anchor": 4.498689330024272, "h": 200.57333374023438, "point_id": 72163, "row_index": 20, "w": 294.5379943847656 } ], "projected_w_span_grid": 8.399566650390625, "projected_w_span_vx": 419.97833251953125, "projection_mode": "normal-line", "skipped_point_count": 0, "skipped_points": [], "skipped_reasons": {}, "usable_point_count": 21, "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_773/point_strip.lasagna.json", "mesh-h": 32, "mesh-step": 50, "mesh-w": 32, "model-h": 8790.182495117188, "model-init": "seed", "model-input": null, "model-output": "/tmp/fit_reopt_vdqa73fm/model_reopt.pt", "model-w": 8419.978332519531, "model-w-unit": "voxels", "normal-mask-zero": 0, "out-dir": null, "progress": true, "pyramid-d": false, "seed": [ 10507.0908203125, 7143.0712890625, 36210.0 ], "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": { "773": { "color": [ 0.0, 1.0, 1.0 ], "metadata": { "winding_is_absolute": true }, "name": "same_wrap1541", "points": { "72143": { "creation_time": 1779553694186, "p": [ 10825.154296875, 7244.314453125, 36210.0 ], "wind_a": 0.0 }, "72144": { "creation_time": 1779553694186, "p": [ 10716.5791015625, 7216.7333984375, 36210.0 ], "wind_a": 0.0 }, "72145": { "creation_time": 1779553694186, "p": [ 10611.95703125, 7179.607421875, 36210.0 ], "wind_a": 0.0 }, "72146": { "creation_time": 1779553694186, "p": [ 10507.0908203125, 7143.0712890625, 36210.0 ], "wind_a": 0.0 }, "72147": { "creation_time": 1779553694186, "p": [ 10398.2734375, 7116.0732421875, 36210.0 ], "wind_a": 0.0 }, "72148": { "creation_time": 1779553694186, "p": [ 10286.6611328125, 7095.82421875, 36210.0 ], "wind_a": 0.0 }, "72149": { "creation_time": 1779553694186, "p": [ 10169.45703125, 7089.0751953125, 36210.0 ], "wind_a": 0.0 }, "72150": { "creation_time": 1779553694186, "p": [ 10049.45703125, 7089.0751953125, 36210.0 ], "wind_a": 0.0 }, "72151": { "creation_time": 1779553694186, "p": [ 9935.048828125, 7102.57421875, 36210.0 ], "wind_a": 0.0 }, "72152": { "creation_time": 1779553694186, "p": [ 9829.02734375, 7136.322265625, 36210.0 ], "wind_a": 0.0 }, "72153": { "creation_time": 1779553694186, "p": [ 9733.46875, 7195.3271484375, 36210.0 ], "wind_a": 0.0 }, "72154": { "creation_time": 1779553694186, "p": [ 9664.232421875, 7286.6484375, 36210.0 ], "wind_a": 0.0 }, "72155": { "creation_time": 1779553694186, "p": [ 9610.2353515625, 7384.2822265625, 36210.0 ], "wind_a": 0.0 }, "72156": { "creation_time": 1779553694186, "p": [ 9550.5, 7479.5390625, 36210.0 ], "wind_a": 0.0 }, "72157": { "creation_time": 1779553694186, "p": [ 9499.0546875, 7578.23046875, 36210.0 ], "wind_a": 0.0 }, "72158": { "creation_time": 1779553694186, "p": [ 9447.611328125, 7676.9208984375, 36210.0 ], "wind_a": 0.0 }, "72159": { "creation_time": 1779553694186, "p": [ 9391.39453125, 7773.634765625, 36210.0 ], "wind_a": 0.0 }, "72160": { "creation_time": 1779553694186, "p": [ 9340.25390625, 7872.4521484375, 36210.0 ], "wind_a": 0.0 }, "72161": { "creation_time": 1779553694186, "p": [ 9299.755859375, 7975.677734375, 36210.0 ], "wind_a": 0.0 }, "72162": { "creation_time": 1779553694186, "p": [ 9272.7578125, 8084.4951171875, 36210.0 ], "wind_a": 0.0 }, "72163": { "creation_time": 1779553694186, "p": [ 9239.009765625, 8182.50244140625, 36210.0 ], "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": [ 2433.3671875, 1798.831787109375, 9052.5 ], "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": { "773": { "color": [ 0.0, 1.0, 1.0 ], "metadata": { "winding_is_absolute": true }, "name": "same_wrap1541", "points": { "72143": { "creation_time": 1779553694186, "p": [ 2706.28857421875, 1811.07861328125, 9052.5 ], "wind_a": 0.0 }, "72144": { "creation_time": 1779553694186, "p": [ 2679.144775390625, 1804.183349609375, 9052.5 ], "wind_a": 0.0 }, "72145": { "creation_time": 1779553694186, "p": [ 2652.9892578125, 1794.90185546875, 9052.5 ], "wind_a": 0.0 }, "72146": { "creation_time": 1779553694186, "p": [ 2626.772705078125, 1785.767822265625, 9052.5 ], "wind_a": 0.0 }, "72147": { "creation_time": 1779553694186, "p": [ 2599.568359375, 1779.018310546875, 9052.5 ], "wind_a": 0.0 }, "72148": { "creation_time": 1779553694186, "p": [ 2571.665283203125, 1773.9560546875, 9052.5 ], "wind_a": 0.0 }, "72149": { "creation_time": 1779553694186, "p": [ 2542.3642578125, 1772.268798828125, 9052.5 ], "wind_a": 0.0 }, "72150": { "creation_time": 1779553694186, "p": [ 2512.3642578125, 1772.268798828125, 9052.5 ], "wind_a": 0.0 }, "72151": { "creation_time": 1779553694186, "p": [ 2483.76220703125, 1775.6435546875, 9052.5 ], "wind_a": 0.0 }, "72152": { "creation_time": 1779553694186, "p": [ 2457.2568359375, 1784.08056640625, 9052.5 ], "wind_a": 0.0 }, "72153": { "creation_time": 1779553694186, "p": [ 2433.3671875, 1798.831787109375, 9052.5 ], "wind_a": 0.0 }, "72154": { "creation_time": 1779553694186, "p": [ 2416.05810546875, 1821.662109375, 9052.5 ], "wind_a": 0.0 }, "72155": { "creation_time": 1779553694186, "p": [ 2402.558837890625, 1846.070556640625, 9052.5 ], "wind_a": 0.0 }, "72156": { "creation_time": 1779553694186, "p": [ 2387.625, 1869.884765625, 9052.5 ], "wind_a": 0.0 }, "72157": { "creation_time": 1779553694186, "p": [ 2374.763671875, 1894.5576171875, 9052.5 ], "wind_a": 0.0 }, "72158": { "creation_time": 1779553694186, "p": [ 2361.90283203125, 1919.230224609375, 9052.5 ], "wind_a": 0.0 }, "72159": { "creation_time": 1779553694186, "p": [ 2347.8486328125, 1943.40869140625, 9052.5 ], "wind_a": 0.0 }, "72160": { "creation_time": 1779553694186, "p": [ 2335.0634765625, 1968.113037109375, 9052.5 ], "wind_a": 0.0 }, "72161": { "creation_time": 1779553694186, "p": [ 2324.93896484375, 1993.91943359375, 9052.5 ], "wind_a": 0.0 }, "72162": { "creation_time": 1779553694186, "p": [ 2318.189453125, 2021.123779296875, 9052.5 ], "wind_a": 0.0 }, "72163": { "creation_time": 1779553694186, "p": [ 2309.75244140625, 2045.6256103515625, 9052.5 ], "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_vdqa73fm/model_reopt.pt", "scale": [ 0.07999999821186066, 0.07999999821186066 ], "tags": { "date_last_modified": "20260614185644361", "reviewed": { "date": "20260604080934236" } }, "type": "seg", "uuid": "same_wrap001541_lasagna" }