{ "area_vx2": 499218.75, "base_shape_zyx": [ 18946, 8174, 8174 ], "bbox": [ [ 4496.7783203125, 3624.297119140625, 10194.0205078125 ], [ 5259.76904296875, 4277.14404296875, 10740.4326171875 ] ], "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": [ 19660.625, 15776.6083984375, 41881.640625 ], "final_anchor_h": 232.39941722154617, "final_anchor_w": 42.39941722154617, "final_shell_id": "shell_0007.tifxyz", "final_trim_bottom": 21, "final_trim_top": 20, "init_margin_grid_points": 80, "initial_seed": [ 19660.625, 15776.6083984375, 41881.640625 ], "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": 25, "mode": "corr-point-roi", "model_h": 8025.309753417969, "model_w": 8480.612182617188, "model_w_unit": "voxels", "output_radius_grid_points": 20, "parsed_point_count": 25, "projected_h_span_grid": 0.506195068359375, "projected_h_span_vx": 25.30975341796875, "projected_points": [ { "collection_id": 2308, "direction_sign": -1, "grid_distance_to_anchor": 5.17968895187462, "h": 232.12930297851563, "point_id": 8665, "row_index": 0, "w": 37.226776123046875 }, { "collection_id": 2308, "direction_sign": -1, "grid_distance_to_anchor": 4.742512438507029, "h": 232.2220916748047, "point_id": 8666, "row_index": 1, "w": 37.660221099853516 }, { "collection_id": 2308, "direction_sign": -1, "grid_distance_to_anchor": 4.35060262399411, "h": 232.2767333984375, "point_id": 8667, "row_index": 2, "w": 38.05054473876953 }, { "collection_id": 2308, "direction_sign": -1, "grid_distance_to_anchor": 3.9008671391089, "h": 232.30731201171875, "point_id": 8668, "row_index": 3, "w": 38.499637603759766 }, { "collection_id": 2308, "direction_sign": -1, "grid_distance_to_anchor": 3.3555755972905263, "h": 232.25375366210938, "point_id": 8669, "row_index": 4, "w": 39.04700469970703 }, { "collection_id": 2308, "direction_sign": -1, "grid_distance_to_anchor": 3.0021148114062184, "h": 232.2548065185547, "point_id": 8670, "row_index": 5, "w": 39.400787353515625 }, { "collection_id": 2308, "direction_sign": -1, "grid_distance_to_anchor": 2.617525908124336, "h": 232.2681121826172, "point_id": 8671, "row_index": 6, "w": 39.785186767578125 }, { "collection_id": 2308, "direction_sign": -1, "grid_distance_to_anchor": 2.136507799382827, "h": 232.2948760986328, "point_id": 8672, "row_index": 7, "w": 40.26546859741211 }, { "collection_id": 2308, "direction_sign": -1, "grid_distance_to_anchor": 1.6538785723470635, "h": 232.34242248535156, "point_id": 8673, "row_index": 8, "w": 40.74652099609375 }, { "collection_id": 2308, "direction_sign": -1, "grid_distance_to_anchor": 1.3050340615728717, "h": 232.3623504638672, "point_id": 8674, "row_index": 9, "w": 41.09490966796875 }, { "collection_id": 2308, "direction_sign": -1, "grid_distance_to_anchor": 0.9000265533335259, "h": 232.35113525390625, "point_id": 8675, "row_index": 10, "w": 41.50068664550781 }, { "collection_id": 2308, "direction_sign": -1, "grid_distance_to_anchor": 0.4333603920610324, "h": 232.3545684814453, "point_id": 8676, "row_index": 11, "w": 41.9683837890625 }, { "collection_id": 2308, "direction_sign": -1, "grid_distance_to_anchor": 0.027895974327878714, "h": 232.38308715820313, "point_id": 8677, "row_index": 12, "w": 42.376800537109375 }, { "collection_id": 2308, "direction_sign": -1, "grid_distance_to_anchor": 0.3912393283146092, "h": 232.41864013671875, "point_id": 8678, "row_index": 13, "w": 42.790184020996094 }, { "collection_id": 2308, "direction_sign": -1, "grid_distance_to_anchor": 0.7954120576167693, "h": 232.45465087890625, "point_id": 8679, "row_index": 14, "w": 43.192909240722656 }, { "collection_id": 2308, "direction_sign": -1, "grid_distance_to_anchor": 1.1642004222311577, "h": 232.44351196289063, "point_id": 8680, "row_index": 15, "w": 43.562782287597656 }, { "collection_id": 2308, "direction_sign": -1, "grid_distance_to_anchor": 1.5410202498342722, "h": 232.46253967285156, "point_id": 8681, "row_index": 16, "w": 43.939144134521484 }, { "collection_id": 2308, "direction_sign": -1, "grid_distance_to_anchor": 1.965267433169947, "h": 232.5277099609375, "point_id": 8682, "row_index": 17, "w": 44.36049270629883 }, { "collection_id": 2308, "direction_sign": -1, "grid_distance_to_anchor": 2.3685644238811, "h": 232.59059143066406, "point_id": 8683, "row_index": 18, "w": 44.76025390625 }, { "collection_id": 2308, "direction_sign": -1, "grid_distance_to_anchor": 2.7964230897995352, "h": 232.58444213867188, "point_id": 8684, "row_index": 19, "w": 45.18971252441406 }, { "collection_id": 2308, "direction_sign": -1, "grid_distance_to_anchor": 3.187837450132808, "h": 232.5645751953125, "point_id": 8685, "row_index": 20, "w": 45.58297348022461 }, { "collection_id": 2308, "direction_sign": -1, "grid_distance_to_anchor": 3.6131609168219474, "h": 232.5907745361328, "point_id": 8686, "row_index": 21, "w": 46.00750732421875 }, { "collection_id": 2308, "direction_sign": -1, "grid_distance_to_anchor": 4.012465549065406, "h": 232.615234375, "point_id": 8687, "row_index": 22, "w": 46.40607452392578 }, { "collection_id": 2308, "direction_sign": -1, "grid_distance_to_anchor": 4.338188860445923, "h": 232.6226043701172, "point_id": 8688, "row_index": 23, "w": 46.73186111450195 }, { "collection_id": 2308, "direction_sign": -1, "grid_distance_to_anchor": 4.445875053596325, "h": 232.635498046875, "point_id": 8689, "row_index": 24, "w": 46.839019775390625 } ], "projected_w_span_grid": 9.61224365234375, "projected_w_span_vx": 480.6121826171875, "projection_mode": "normal-line", "skipped_point_count": 0, "skipped_points": [], "skipped_reasons": {}, "usable_point_count": 25, "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_2308/point_strip.lasagna.json", "mesh-h": 32, "mesh-step": 50, "mesh-w": 32, "model-h": 8025.309753417969, "model-init": "seed", "model-input": null, "model-output": "/tmp/fit_reopt_ug5l5n7a/model_reopt.pt", "model-w": 8480.612182617188, "model-w-unit": "voxels", "normal-mask-zero": 0, "out-dir": null, "progress": true, "pyramid-d": false, "seed": [ 19660.625, 15776.6083984375, 41881.640625 ], "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": { "2308": { "color": [ 0.7058823704719543, 1.0, 0.3137255012989044 ], "metadata": { "winding_is_absolute": true }, "name": "same_wrap1111", "points": { "8665": { "creation_time": 8665, "p": [ 20318.296875, 16426.763671875, 41881.640625 ], "wind_a": 0.0 }, "8666": { "creation_time": 8666, "p": [ 20269.701171875, 16366.8935546875, 41881.640625 ], "wind_a": 0.0 }, "8667": { "creation_time": 8667, "p": [ 20222.662109375, 16308.5791015625, 41881.640625 ], "wind_a": 0.0 }, "8668": { "creation_time": 8668, "p": [ 20171.71875, 16251.8818359375, 41881.640625 ], "wind_a": 0.0 }, "8669": { "creation_time": 8669, "p": [ 20116.396484375, 16194.796875, 41881.640625 ], "wind_a": 0.0 }, "8670": { "creation_time": 8670, "p": [ 20061.384765625, 16139.78515625, 41881.640625 ], "wind_a": 0.0 }, "8671": { "creation_time": 8671, "p": [ 20006.373046875, 16084.7734375, 41881.640625 ], "wind_a": 0.0 }, "8672": { "creation_time": 8672, "p": [ 19952.462890625, 16027.1044921875, 41881.640625 ], "wind_a": 0.0 }, "8673": { "creation_time": 8673, "p": [ 19896.349609375, 15974.75, 41881.640625 ], "wind_a": 0.0 }, "8674": { "creation_time": 8674, "p": [ 19838.681640625, 15920.8388671875, 41881.640625 ], "wind_a": 0.0 }, "8675": { "creation_time": 8675, "p": [ 19781.466796875, 15871.142578125, 41881.640625 ], "wind_a": 0.0 }, "8676": { "creation_time": 8676, "p": [ 19721.595703125, 15822.546875, 41881.640625 ], "wind_a": 0.0 }, "8677": { "creation_time": 8677, "p": [ 19660.625, 15776.6083984375, 41881.640625 ], "wind_a": 0.0 }, "8678": { "creation_time": 8678, "p": [ 19600.75390625, 15728.0126953125, 41881.640625 ], "wind_a": 0.0 }, "8679": { "creation_time": 8679, "p": [ 19539.564453125, 15682.6015625, 41881.640625 ], "wind_a": 0.0 }, "8680": { "creation_time": 8680, "p": [ 19477.708984375, 15638.7939453125, 41881.640625 ], "wind_a": 0.0 }, "8681": { "creation_time": 8681, "p": [ 19416.92578125, 15592.400390625, 41881.640625 ], "wind_a": 0.0 }, "8682": { "creation_time": 8682, "p": [ 19356.8671875, 15544.259765625, 41881.640625 ], "wind_a": 0.0 }, "8683": { "creation_time": 8683, "p": [ 19298.552734375, 15497.220703125, 41881.640625 ], "wind_a": 0.0 }, "8684": { "creation_time": 8684, "p": [ 19236.728515625, 15453.33984375, 41881.640625 ], "wind_a": 0.0 }, "8685": { "creation_time": 8685, "p": [ 19177.064453125, 15409.55859375, 41881.640625 ], "wind_a": 0.0 }, "8686": { "creation_time": 8686, "p": [ 19114.9921875, 15366.2783203125, 41881.640625 ], "wind_a": 0.0 }, "8687": { "creation_time": 8687, "p": [ 19052.919921875, 15322.998046875, 41881.640625 ], "wind_a": 0.0 }, "8688": { "creation_time": 8688, "p": [ 18990.84765625, 15279.716796875, 41881.640625 ], "wind_a": 0.0 }, "8689": { "creation_time": 8689, "p": [ 18972.791015625, 15265.419921875, 41881.640625 ], "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": [ 4915.15625, 3944.152099609375, 10470.41015625 ], "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": { "2308": { "color": [ 0.7058823704719543, 1.0, 0.3137255012989044 ], "metadata": { "winding_is_absolute": true }, "name": "same_wrap1111", "points": { "8665": { "creation_time": 8665, "p": [ 5079.57421875, 4106.69091796875, 10470.41015625 ], "wind_a": 0.0 }, "8666": { "creation_time": 8666, "p": [ 5067.42529296875, 4091.723388671875, 10470.41015625 ], "wind_a": 0.0 }, "8667": { "creation_time": 8667, "p": [ 5055.66552734375, 4077.144775390625, 10470.41015625 ], "wind_a": 0.0 }, "8668": { "creation_time": 8668, "p": [ 5042.9296875, 4062.970458984375, 10470.41015625 ], "wind_a": 0.0 }, "8669": { "creation_time": 8669, "p": [ 5029.09912109375, 4048.69921875, 10470.41015625 ], "wind_a": 0.0 }, "8670": { "creation_time": 8670, "p": [ 5015.34619140625, 4034.9462890625, 10470.41015625 ], "wind_a": 0.0 }, "8671": { "creation_time": 8671, "p": [ 5001.59326171875, 4021.193359375, 10470.41015625 ], "wind_a": 0.0 }, "8672": { "creation_time": 8672, "p": [ 4988.11572265625, 4006.776123046875, 10470.41015625 ], "wind_a": 0.0 }, "8673": { "creation_time": 8673, "p": [ 4974.08740234375, 3993.6875, 10470.41015625 ], "wind_a": 0.0 }, "8674": { "creation_time": 8674, "p": [ 4959.67041015625, 3980.209716796875, 10470.41015625 ], "wind_a": 0.0 }, "8675": { "creation_time": 8675, "p": [ 4945.36669921875, 3967.78564453125, 10470.41015625 ], "wind_a": 0.0 }, "8676": { "creation_time": 8676, "p": [ 4930.39892578125, 3955.63671875, 10470.41015625 ], "wind_a": 0.0 }, "8677": { "creation_time": 8677, "p": [ 4915.15625, 3944.152099609375, 10470.41015625 ], "wind_a": 0.0 }, "8678": { "creation_time": 8678, "p": [ 4900.1884765625, 3932.003173828125, 10470.41015625 ], "wind_a": 0.0 }, "8679": { "creation_time": 8679, "p": [ 4884.89111328125, 3920.650390625, 10470.41015625 ], "wind_a": 0.0 }, "8680": { "creation_time": 8680, "p": [ 4869.42724609375, 3909.698486328125, 10470.41015625 ], "wind_a": 0.0 }, "8681": { "creation_time": 8681, "p": [ 4854.2314453125, 3898.10009765625, 10470.41015625 ], "wind_a": 0.0 }, "8682": { "creation_time": 8682, "p": [ 4839.216796875, 3886.06494140625, 10470.41015625 ], "wind_a": 0.0 }, "8683": { "creation_time": 8683, "p": [ 4824.63818359375, 3874.30517578125, 10470.41015625 ], "wind_a": 0.0 }, "8684": { "creation_time": 8684, "p": [ 4809.18212890625, 3863.3349609375, 10470.41015625 ], "wind_a": 0.0 }, "8685": { "creation_time": 8685, "p": [ 4794.26611328125, 3852.3896484375, 10470.41015625 ], "wind_a": 0.0 }, "8686": { "creation_time": 8686, "p": [ 4778.748046875, 3841.569580078125, 10470.41015625 ], "wind_a": 0.0 }, "8687": { "creation_time": 8687, "p": [ 4763.22998046875, 3830.74951171875, 10470.41015625 ], "wind_a": 0.0 }, "8688": { "creation_time": 8688, "p": [ 4747.7119140625, 3819.92919921875, 10470.41015625 ], "wind_a": 0.0 }, "8689": { "creation_time": 8689, "p": [ 4743.19775390625, 3816.35498046875, 10470.41015625 ], "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_ug5l5n7a/model_reopt.pt", "scale": [ 0.07999999821186066, 0.07999999821186066 ], "tags": { "date_last_modified": "20260614185644263", "reviewed": { "date": "20260604080934215" } }, "type": "seg", "uuid": "same_wrap001111_lasagna" }