{ "area_vx2": 542187.5, "base_shape_zyx": [ 18946, 8174, 8174 ], "bbox": [ [ 5950.61962890625, 4068.2880859375, 11859.5546875 ], [ 6389.87939453125, 4812.19775390625, 12497.234375 ] ], "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": [ 25214.25390625, 17573.560546875, 48771.5859375 ], "final_anchor_h": 286.04365795105696, "final_anchor_w": 54.95928578823805, "final_shell_id": "shell_0001.tifxyz", "final_trim_bottom": 30, "final_trim_top": 0, "init_margin_grid_points": 80, "initial_seed": [ 25160.9140625, 17631.466796875, 48771.5859375 ], "initial_shell_id": "shell_0001.tifxyz", "initial_skipped_point_count": 0, "initial_skipped_reasons": {}, "initial_trim_bottom": 30, "initial_trim_top": 0, "initial_usable_point_count": 26, "mode": "corr-point-roi", "model_h": 8138.270568847656, "model_w": 8375.09765625, "model_w_unit": "voxels", "output_radius_grid_points": 20, "parsed_point_count": 26, "projected_h_span_grid": 2.765411376953125, "projected_h_span_vx": 138.27056884765625, "projected_points": [ { "collection_id": 1583, "direction_sign": 1, "grid_distance_to_anchor": 4.0001646953283, "h": 285.8423156738281, "point_id": 108226, "row_index": 0, "w": 50.96419143676758 }, { "collection_id": 1583, "direction_sign": 1, "grid_distance_to_anchor": 3.6439117189916943, "h": 285.86517333984375, "point_id": 108227, "row_index": 1, "w": 51.31974792480469 }, { "collection_id": 1583, "direction_sign": 1, "grid_distance_to_anchor": 3.279935672073556, "h": 285.8990173339844, "point_id": 108228, "row_index": 2, "w": 51.68254089355469 }, { "collection_id": 1583, "direction_sign": 1, "grid_distance_to_anchor": 2.9244264318558764, "h": 285.9326171875, "point_id": 108229, "row_index": 3, "w": 52.03696823120117 }, { "collection_id": 1583, "direction_sign": 1, "grid_distance_to_anchor": 2.577896360110327, "h": 285.9598693847656, "point_id": 108230, "row_index": 4, "w": 52.38275146484375 }, { "collection_id": 1583, "direction_sign": 1, "grid_distance_to_anchor": 2.2411385259736187, "h": 286.0080871582031, "point_id": 108231, "row_index": 5, "w": 52.71842956542969 }, { "collection_id": 1583, "direction_sign": 1, "grid_distance_to_anchor": 1.8751391077667308, "h": 286.00408935546875, "point_id": 108232, "row_index": 6, "w": 53.084564208984375 }, { "collection_id": 1583, "direction_sign": 1, "grid_distance_to_anchor": 1.662048432173242, "h": 286.62548828125, "point_id": 108233, "row_index": 7, "w": 53.40240478515625 }, { "collection_id": 1583, "direction_sign": -1, "grid_distance_to_anchor": 1.8324286477620892, "h": 284.84686279296875, "point_id": 108234, "row_index": 8, "w": 53.57167053222656 }, { "collection_id": 1583, "direction_sign": -1, "grid_distance_to_anchor": 1.3381422821699465, "h": 285.8223876953125, "point_id": 108235, "row_index": 9, "w": 53.639564514160156 }, { "collection_id": 1583, "direction_sign": -1, "grid_distance_to_anchor": 1.184688872204701, "h": 285.7355041503906, "point_id": 108236, "row_index": 10, "w": 53.81537628173828 }, { "collection_id": 1583, "direction_sign": -1, "grid_distance_to_anchor": 0.9864464764417016, "h": 285.76995849609375, "point_id": 108237, "row_index": 11, "w": 54.01156997680664 }, { "collection_id": 1583, "direction_sign": -1, "grid_distance_to_anchor": 0.836504539816213, "h": 285.8186950683594, "point_id": 108238, "row_index": 12, "w": 54.15359878540039 }, { "collection_id": 1583, "direction_sign": -1, "grid_distance_to_anchor": 0.5455280926209899, "h": 285.9311218261719, "point_id": 108239, "row_index": 13, "w": 54.42549133300781 }, { "collection_id": 1583, "direction_sign": -1, "grid_distance_to_anchor": 0.1537230617633598, "h": 286.0572814941406, "point_id": 108240, "row_index": 14, "w": 54.80616760253906 }, { "collection_id": 1583, "direction_sign": -1, "grid_distance_to_anchor": 0.25521910197160314, "h": 286.18603515625, "point_id": 108241, "row_index": 15, "w": 55.17110061645508 }, { "collection_id": 1583, "direction_sign": -1, "grid_distance_to_anchor": 0.6427673862878125, "h": 286.32476806640625, "point_id": 108242, "row_index": 16, "w": 55.537322998046875 }, { "collection_id": 1583, "direction_sign": -1, "grid_distance_to_anchor": 1.0315963014298521, "h": 286.46990966796875, "point_id": 108243, "row_index": 17, "w": 55.89870071411133 }, { "collection_id": 1583, "direction_sign": -1, "grid_distance_to_anchor": 1.4136039501443165, "h": 286.6094665527344, "point_id": 108244, "row_index": 18, "w": 56.25471496582031 }, { "collection_id": 1583, "direction_sign": -1, "grid_distance_to_anchor": 1.7898258228756603, "h": 286.74310302734375, "point_id": 108245, "row_index": 19, "w": 56.60678482055664 }, { "collection_id": 1583, "direction_sign": -1, "grid_distance_to_anchor": 2.1722889186109686, "h": 286.8873596191406, "point_id": 108246, "row_index": 20, "w": 56.961036682128906 }, { "collection_id": 1583, "direction_sign": -1, "grid_distance_to_anchor": 2.5654093216180556, "h": 287.0461120605469, "point_id": 108247, "row_index": 21, "w": 57.32072830200195 }, { "collection_id": 1583, "direction_sign": 1, "grid_distance_to_anchor": 2.948927314478062, "h": 287.2102355957031, "point_id": 108248, "row_index": 22, "w": 57.66765594482422 }, { "collection_id": 1583, "direction_sign": 1, "grid_distance_to_anchor": 3.3322223614747295, "h": 287.37847900390625, "point_id": 108249, "row_index": 23, "w": 58.012474060058594 }, { "collection_id": 1583, "direction_sign": 1, "grid_distance_to_anchor": 3.7094989731767227, "h": 287.5514831542969, "point_id": 108250, "row_index": 24, "w": 58.3485107421875 }, { "collection_id": 1583, "direction_sign": 1, "grid_distance_to_anchor": 3.8416943266698236, "h": 287.6122741699219, "point_id": 108251, "row_index": 25, "w": 58.46614456176758 } ], "projected_w_span_grid": 7.501953125, "projected_w_span_vx": 375.09765625, "projection_mode": "normal-line", "skipped_point_count": 0, "skipped_points": [], "skipped_reasons": {}, "usable_point_count": 26, "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_1583/point_strip.lasagna.json", "mesh-h": 32, "mesh-step": 50, "mesh-w": 32, "model-h": 8138.270568847656, "model-init": "seed", "model-input": null, "model-output": "/tmp/fit_reopt_3bhhp7ni/model_reopt.pt", "model-w": 8375.09765625, "model-w-unit": "voxels", "normal-mask-zero": 0, "out-dir": null, "progress": true, "pyramid-d": false, "seed": [ 25214.25390625, 17573.560546875, 48771.5859375 ], "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": { "1583": { "color": [ 0.0, 1.0, 1.0 ], "metadata": { "winding_is_absolute": true }, "name": "same_wrap2422", "points": { "108226": { "creation_time": 1779668274185, "p": [ 24752.8046875, 16902.05859375, 48771.5859375 ], "wind_a": 0.0 }, "108227": { "creation_time": 1779668274185, "p": [ 24818.740234375, 16936.013671875, 48771.5859375 ], "wind_a": 0.0 }, "108228": { "creation_time": 1779668274185, "p": [ 24886.3125, 16966.013671875, 48771.5859375 ], "wind_a": 0.0 }, "108229": { "creation_time": 1779668274185, "p": [ 24954.9609375, 16993.423828125, 48771.5859375 ], "wind_a": 0.0 }, "108230": { "creation_time": 1779668274185, "p": [ 25023.60546875, 17020.833984375, 48771.5859375 ], "wind_a": 0.0 }, "108231": { "creation_time": 1779668274185, "p": [ 25091.845703125, 17049.2265625, 48771.5859375 ], "wind_a": 0.0 }, "108232": { "creation_time": 1779668274185, "p": [ 25159.0078125, 17080.22265625, 48771.5859375 ], "wind_a": 0.0 }, "108233": { "creation_time": 1779668274185, "p": [ 25223.8671875, 17116.76953125, 48771.5859375 ], "wind_a": 0.0 }, "108234": { "creation_time": 1779668274185, "p": [ 25282.734375, 17167.341796875, 48771.5859375 ], "wind_a": 0.0 }, "108235": { "creation_time": 1779668274185, "p": [ 25314.712890625, 17234.095703125, 48771.5859375 ], "wind_a": 0.0 }, "108236": { "creation_time": 1779668274185, "p": [ 25328.021484375, 17304.46875, 48771.5859375 ], "wind_a": 0.0 }, "108237": { "creation_time": 1779668274185, "p": [ 25325.8125, 17379.76953125, 48771.5859375 ], "wind_a": 0.0 }, "108238": { "creation_time": 1779668274185, "p": [ 25304.77734375, 17451.056640625, 48771.5859375 ], "wind_a": 0.0 }, "108239": { "creation_time": 1779668274185, "p": [ 25264.361328125, 17514.31640625, 48771.5859375 ], "wind_a": 0.0 }, "108240": { "creation_time": 1779668274185, "p": [ 25214.25390625, 17573.560546875, 48771.5859375 ], "wind_a": 0.0 }, "108241": { "creation_time": 1779668274185, "p": [ 25160.9140625, 17631.466796875, 48771.5859375 ], "wind_a": 0.0 }, "108242": { "creation_time": 1779668274185, "p": [ 25104.34765625, 17688.03515625, 48771.5859375 ], "wind_a": 0.0 }, "108243": { "creation_time": 1779668274185, "p": [ 25049.748046875, 17745.419921875, 48771.5859375 ], "wind_a": 0.0 }, "108244": { "creation_time": 1779668274185, "p": [ 24997.671875, 17803.849609375, 48771.5859375 ], "wind_a": 0.0 }, "108245": { "creation_time": 1779668274185, "p": [ 24947.5625, 17863.09375, 48771.5859375 ], "wind_a": 0.0 }, "108246": { "creation_time": 1779668274185, "p": [ 24894.224609375, 17921.0, 48771.5859375 ], "wind_a": 0.0 }, "108247": { "creation_time": 1779668274185, "p": [ 24837.65625, 17977.568359375, 48771.5859375 ], "wind_a": 0.0 }, "108248": { "creation_time": 1779668274185, "p": [ 24779.556640625, 18030.44140625, 48771.5859375 ], "wind_a": 0.0 }, "108249": { "creation_time": 1779668274185, "p": [ 24720.50390625, 18081.015625, 48771.5859375 ], "wind_a": 0.0 }, "108250": { "creation_time": 1779668274185, "p": [ 24659.921875, 18127.892578125, 48771.5859375 ], "wind_a": 0.0 }, "108251": { "creation_time": 1779668274185, "p": [ 24638.59765625, 18144.650390625, 48771.5859375 ], "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": [ 6316.09033203125, 4378.5791015625, 12192.896484375 ], "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": { "1583": { "color": [ 0.0, 1.0, 1.0 ], "metadata": { "winding_is_absolute": true }, "name": "same_wrap2422", "points": { "108226": { "creation_time": 1779668274185, "p": [ 6188.201171875, 4225.5146484375, 12192.896484375 ], "wind_a": 0.0 }, "108227": { "creation_time": 1779668274185, "p": [ 6204.68505859375, 4234.00341796875, 12192.896484375 ], "wind_a": 0.0 }, "108228": { "creation_time": 1779668274185, "p": [ 6221.578125, 4241.50341796875, 12192.896484375 ], "wind_a": 0.0 }, "108229": { "creation_time": 1779668274185, "p": [ 6238.740234375, 4248.35595703125, 12192.896484375 ], "wind_a": 0.0 }, "108230": { "creation_time": 1779668274185, "p": [ 6255.9013671875, 4255.20849609375, 12192.896484375 ], "wind_a": 0.0 }, "108231": { "creation_time": 1779668274185, "p": [ 6272.96142578125, 4262.306640625, 12192.896484375 ], "wind_a": 0.0 }, "108232": { "creation_time": 1779668274185, "p": [ 6289.751953125, 4270.0556640625, 12192.896484375 ], "wind_a": 0.0 }, "108233": { "creation_time": 1779668274185, "p": [ 6305.966796875, 4279.1923828125, 12192.896484375 ], "wind_a": 0.0 }, "108234": { "creation_time": 1779668274185, "p": [ 6320.68359375, 4291.83544921875, 12192.896484375 ], "wind_a": 0.0 }, "108235": { "creation_time": 1779668274185, "p": [ 6328.67822265625, 4308.52392578125, 12192.896484375 ], "wind_a": 0.0 }, "108236": { "creation_time": 1779668274185, "p": [ 6332.00537109375, 4326.1171875, 12192.896484375 ], "wind_a": 0.0 }, "108237": { "creation_time": 1779668274185, "p": [ 6331.453125, 4344.9423828125, 12192.896484375 ], "wind_a": 0.0 }, "108238": { "creation_time": 1779668274185, "p": [ 6326.1943359375, 4362.76416015625, 12192.896484375 ], "wind_a": 0.0 }, "108239": { "creation_time": 1779668274185, "p": [ 6316.09033203125, 4378.5791015625, 12192.896484375 ], "wind_a": 0.0 }, "108240": { "creation_time": 1779668274185, "p": [ 6303.5634765625, 4393.39013671875, 12192.896484375 ], "wind_a": 0.0 }, "108241": { "creation_time": 1779668274185, "p": [ 6290.228515625, 4407.86669921875, 12192.896484375 ], "wind_a": 0.0 }, "108242": { "creation_time": 1779668274185, "p": [ 6276.0869140625, 4422.0087890625, 12192.896484375 ], "wind_a": 0.0 }, "108243": { "creation_time": 1779668274185, "p": [ 6262.43701171875, 4436.35498046875, 12192.896484375 ], "wind_a": 0.0 }, "108244": { "creation_time": 1779668274185, "p": [ 6249.41796875, 4450.96240234375, 12192.896484375 ], "wind_a": 0.0 }, "108245": { "creation_time": 1779668274185, "p": [ 6236.890625, 4465.7734375, 12192.896484375 ], "wind_a": 0.0 }, "108246": { "creation_time": 1779668274185, "p": [ 6223.55615234375, 4480.25, 12192.896484375 ], "wind_a": 0.0 }, "108247": { "creation_time": 1779668274185, "p": [ 6209.4140625, 4494.39208984375, 12192.896484375 ], "wind_a": 0.0 }, "108248": { "creation_time": 1779668274185, "p": [ 6194.88916015625, 4507.6103515625, 12192.896484375 ], "wind_a": 0.0 }, "108249": { "creation_time": 1779668274185, "p": [ 6180.1259765625, 4520.25390625, 12192.896484375 ], "wind_a": 0.0 }, "108250": { "creation_time": 1779668274185, "p": [ 6164.98046875, 4531.97314453125, 12192.896484375 ], "wind_a": 0.0 }, "108251": { "creation_time": 1779668274185, "p": [ 6159.6494140625, 4536.16259765625, 12192.896484375 ], "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_3bhhp7ni/model_reopt.pt", "scale": [ 0.07999999821186066, 0.07999999821186066 ], "tags": { "date_last_modified": "20260614185644526", "reviewed": { "date": "20260604080934271" } }, "type": "seg", "uuid": "same_wrap002422_lasagna" }