init circuit_data1

.gitattributes

@@ -58,3 +58,6 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 # Video files - compressed
 *.mp4 filter=lfs diff=lfs merge=lfs -text
 *.webm filter=lfs diff=lfs merge=lfs -text
+# 3D files and database
+*.db filter=lfs diff=lfs merge=lfs -text
+*.ply filter=lfs diff=lfs merge=lfs -text

.gitignore

@@ -0,0 +1 @@
+**/wandb/

circuit_data1/colmap/database.db

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+oid sha256:8f62031784350a7d4a97f59e4933b78bbc7e87e9fc6dd068ebc6e19fc612a78c
+size 12713984

circuit_data1/colmap/project.ini

@@ -0,0 +1,209 @@
+log_to_stderr=true
+log_level=0
+random_seed=0
+database_path=/home/codaero/Projects/Microscopic-3D-Reconstruction/microscope_scripts/outputs/robot_data3/database.db
+image_path=/home/codaero/Projects/Microscopic-3D-Reconstruction/microscope_scripts/outputs/robot_data3/focus_stacked
+[ImageReader]
+single_camera=false
+single_camera_per_folder=false
+single_camera_per_image=false
+existing_camera_id=-1
+default_focal_length_factor=1.2
+mask_path=
+camera_model=OPENCV
+camera_params=
+camera_mask_path=
+[SiftExtraction]
+use_gpu=true
+estimate_affine_shape=false
+upright=false
+domain_size_pooling=false
+num_threads=-1
+max_image_size=3200
+max_num_features=8192
+first_octave=-1
+num_octaves=4
+octave_resolution=3
+max_num_orientations=2
+dsp_num_scales=10
+peak_threshold=0.0015
+edge_threshold=10
+dsp_min_scale=0.16667000000000001
+dsp_max_scale=3
+gpu_index=-1
+[SiftMatching]
+use_gpu=true
+cross_check=true
+guided_matching=false
+num_threads=-1
+max_num_matches=32768
+max_ratio=0.80000000000000004
+max_distance=0.69999999999999996
+gpu_index=-1
+[TwoViewGeometry]
+multiple_models=false
+compute_relative_pose=false
+min_num_inliers=15
+max_num_trials=10000
+max_error=4
+confidence=0.999
+min_inlier_ratio=0.25
+[SequentialMatching]
+quadratic_overlap=true
+loop_detection=false
+overlap=2
+loop_detection_period=10
+loop_detection_num_images=50
+loop_detection_num_nearest_neighbors=1
+loop_detection_num_checks=256
+loop_detection_num_images_after_verification=0
+loop_detection_max_num_features=-1
+vocab_tree_path=
+[SpatialMatching]
+is_gps=true
+ignore_z=true
+max_num_neighbors=50
+max_distance=100
+[BundleAdjustment]
+refine_focal_length=true
+refine_principal_point=false
+refine_extra_params=true
+refine_extrinsics=true
+max_num_iterations=100
+max_linear_solver_iterations=200
+function_tolerance=0
+gradient_tolerance=0
+parameter_tolerance=0
+[Mapper]
+ignore_watermarks=false
+multiple_models=true
+extract_colors=true
+ba_refine_focal_length=true
+ba_refine_principal_point=false
+ba_refine_extra_params=true
+fix_existing_images=false
+tri_ignore_two_view_tracks=true
+min_num_matches=15
+max_num_models=50
+max_model_overlap=20
+min_model_size=10
+init_image_id1=-1
+init_image_id2=-1
+init_num_trials=200
+num_threads=-1
+ba_min_num_residuals_for_multi_threading=50000
+ba_local_num_images=6
+ba_local_max_num_iterations=25
+ba_global_images_freq=500
+ba_global_points_freq=250000
+ba_global_max_num_iterations=50
+ba_global_max_refinements=5
+ba_local_max_refinements=2
+snapshot_images_freq=0
+init_min_num_inliers=100
+init_max_reg_trials=2
+abs_pose_min_num_inliers=30
+max_reg_trials=3
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+tri_complete_max_transitivity=5
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+ba_local_max_refinement_change=0.001
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+abs_pose_max_error=12
+abs_pose_min_inlier_ratio=0.25
+filter_max_reproj_error=4
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+local_ba_min_tri_angle=6
+tri_create_max_angle_error=2
+tri_continue_max_angle_error=2
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+tri_complete_max_reproj_error=4
+tri_re_max_angle_error=5
+tri_re_min_ratio=0.20000000000000001
+tri_min_angle=1.5
+snapshot_path=
+[PatchMatchStereo]
+geom_consistency=true
+filter=true
+allow_missing_files=false
+write_consistency_graph=false
+max_image_size=2000
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+window_step=1
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+depth_max=-1
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+sigma_color=0.20000000298023224
+ncc_sigma=0.60000002384185791
+min_triangulation_angle=1
+incident_angle_sigma=0.89999997615814209
+geom_consistency_regularizer=0.30000001192092896
+geom_consistency_max_cost=3
+filter_min_ncc=0.10000000149011612
+filter_min_triangulation_angle=3
+filter_geom_consistency_max_cost=1
+cache_size=32
+gpu_index=-1
+[StereoFusion]
+use_cache=false
+num_threads=-1
+max_image_size=-1
+min_num_pixels=5
+max_num_pixels=10000
+max_traversal_depth=100
+check_num_images=50
+max_reproj_error=2
+max_depth_error=0.0099999997764825821
+max_normal_error=10
+cache_size=32
+mask_path=
+[Render]
+adapt_refresh_rate=true
+image_connections=false
+min_track_len=3
+refresh_rate=1
+projection_type=0
+max_error=2
+[ExhaustiveMatching]
+block_size=50
+[VocabTreeMatching]
+num_images=100
+num_nearest_neighbors=5
+num_checks=256
+num_images_after_verification=0
+max_num_features=-1
+vocab_tree_path=
+match_list_path=
+[TransitiveMatching]
+batch_size=1000
+num_iterations=3
+[ImagePairsMatching]
+block_size=1225
+[PoissonMeshing]
+depth=13
+num_threads=-1
+point_weight=1
+color=32
+trim=10
+[DelaunayMeshing]
+num_threads=-1
+max_proj_dist=20
+max_depth_dist=0.050000000000000003
+visibility_sigma=3
+distance_sigma_factor=1
+quality_regularization=1
+max_side_length_factor=25
+max_side_length_percentile=95

circuit_data1/colmap/sparse/0/cameras.bin

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+oid sha256:d8930314599ecb6a77bc189e3322e21b81c19c6d57cd89cc20e5ae5379a27e80
+size 800

circuit_data1/colmap/sparse/0/images.bin

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+size 1958075

circuit_data1/colmap/sparse/0/points3D.bin

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+version https://git-lfs.github.com/spec/v1
+oid sha256:2ffbd39d229c0a0363433d404bb6b5d29503f97d293c335e1ebe765ec6839914
+size 160036

circuit_data1/colmap/sparse/project.ini

@@ -0,0 +1,209 @@
+log_to_stderr=true
+random_seed=0
+log_level=0
+database_path=/home/codaero/Projects/Microscopic-3D-Reconstruction/microscope_scripts/outputs/robot_data3/database.db
+image_path=/home/codaero/Projects/Microscopic-3D-Reconstruction/microscope_scripts/outputs/robot_data3/focus_stacked
+[ImageReader]
+single_camera=false
+single_camera_per_folder=false
+single_camera_per_image=false
+existing_camera_id=-1
+default_focal_length_factor=1.2
+mask_path=
+camera_model=SIMPLE_RADIAL
+camera_params=
+camera_mask_path=
+[SiftExtraction]
+use_gpu=true
+estimate_affine_shape=true
+upright=false
+domain_size_pooling=false
+num_threads=-1
+max_image_size=2400
+max_num_features=8192
+first_octave=-1
+num_octaves=4
+octave_resolution=3
+max_num_orientations=2
+dsp_num_scales=10
+peak_threshold=0.0066666666666666671
+edge_threshold=10
+dsp_min_scale=0.16666666666666666
+dsp_max_scale=3
+gpu_index=-1
+[SiftMatching]
+use_gpu=true
+cross_check=true
+guided_matching=true
+num_threads=-1
+max_num_matches=32768
+max_ratio=0.80000000000000004
+max_distance=0.69999999999999996
+gpu_index=-1
+[TwoViewGeometry]
+multiple_models=false
+compute_relative_pose=false
+min_num_inliers=15
+max_num_trials=10000
+max_error=4
+confidence=0.999
+min_inlier_ratio=0.25
+[SequentialMatching]
+quadratic_overlap=true
+loop_detection=false
+overlap=10
+loop_detection_period=10
+loop_detection_num_images=50
+loop_detection_num_nearest_neighbors=1
+loop_detection_num_checks=256
+loop_detection_num_images_after_verification=0
+loop_detection_max_num_features=-1
+vocab_tree_path=
+[SpatialMatching]
+is_gps=true
+ignore_z=true
+max_num_neighbors=50
+max_distance=100
+[BundleAdjustment]
+refine_focal_length=true
+refine_principal_point=false
+refine_extra_params=true
+refine_extrinsics=true
+max_num_iterations=100
+max_linear_solver_iterations=200
+function_tolerance=0
+gradient_tolerance=0
+parameter_tolerance=0
+[Mapper]
+ignore_watermarks=false
+multiple_models=true
+extract_colors=true
+ba_refine_focal_length=true
+ba_refine_principal_point=false
+ba_refine_extra_params=true
+fix_existing_images=false
+tri_ignore_two_view_tracks=true
+min_num_matches=15
+max_num_models=50
+max_model_overlap=20
+min_model_size=10
+init_image_id1=-1
+init_image_id2=-1
+init_num_trials=200
+num_threads=-1
+ba_min_num_residuals_for_multi_threading=50000
+ba_local_num_images=6
+ba_local_max_num_iterations=30
+ba_global_images_freq=500
+ba_global_points_freq=250000
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+ba_global_max_refinements=5
+ba_local_max_refinements=3
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+init_min_num_inliers=100
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+tri_complete_max_transitivity=5
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+init_min_tri_angle=16
+abs_pose_max_error=12
+abs_pose_min_inlier_ratio=0.25
+filter_max_reproj_error=4
+filter_min_tri_angle=1.5
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+tri_complete_max_reproj_error=4
+tri_re_max_angle_error=5
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+tri_min_angle=1.5
+snapshot_path=
+[PatchMatchStereo]
+geom_consistency=true
+filter=true
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+max_image_size=2400
+window_radius=5
+window_step=1
+num_samples=15
+num_iterations=5
+filter_min_num_consistent=2
+depth_min=-1
+depth_max=-1
+sigma_spatial=-1
+sigma_color=0.20000000298023224
+ncc_sigma=0.60000002384185791
+min_triangulation_angle=1
+incident_angle_sigma=0.89999997615814209
+geom_consistency_regularizer=0.30000001192092896
+geom_consistency_max_cost=3
+filter_min_ncc=0.10000000149011612
+filter_min_triangulation_angle=3
+filter_geom_consistency_max_cost=1
+cache_size=32
+gpu_index=-1
+[StereoFusion]
+use_cache=false
+num_threads=-1
+max_image_size=2400
+min_num_pixels=5
+max_num_pixels=10000
+max_traversal_depth=100
+check_num_images=50
+max_reproj_error=2
+max_depth_error=0.0099999997764825821
+max_normal_error=10
+cache_size=32
+mask_path=
+[Render]
+adapt_refresh_rate=true
+image_connections=false
+min_track_len=3
+refresh_rate=1
+projection_type=0
+max_error=2
+[ExhaustiveMatching]
+block_size=50
+[VocabTreeMatching]
+num_images=100
+num_nearest_neighbors=5
+num_checks=256
+num_images_after_verification=0
+max_num_features=-1
+vocab_tree_path=
+match_list_path=
+[TransitiveMatching]
+batch_size=1000
+num_iterations=3
+[ImagePairsMatching]
+block_size=1225
+[PoissonMeshing]
+depth=13
+num_threads=-1
+point_weight=1
+color=32
+trim=10
+[DelaunayMeshing]
+num_threads=-1
+max_proj_dist=20
+max_depth_dist=0.050000000000000003
+visibility_sigma=3
+distance_sigma_factor=1
+quality_regularization=1
+max_side_length_factor=25
+max_side_length_percentile=95

circuit_data1/outputs/splatfacto/2026-03-10_070926/config.yml

@@ -0,0 +1,256 @@
+!!python/object:nerfstudio.engine.trainer.TrainerConfig
+_target: !!python/name:nerfstudio.engine.trainer.Trainer ''
+data: null
+experiment_name: robot_data3
+gradient_accumulation_steps: {}
+load_checkpoint: null
+load_config: null
+load_dir: null
+load_scheduler: true
+load_step: null
+log_gradients: false
+logging: !!python/object:nerfstudio.configs.base_config.LoggingConfig
+  local_writer: !!python/object:nerfstudio.configs.base_config.LocalWriterConfig
+    _target: !!python/name:nerfstudio.utils.writer.LocalWriter ''
+    enable: true
+    max_log_size: 10
+    stats_to_track: !!python/tuple
+    - !!python/object/apply:nerfstudio.utils.writer.EventName
+      - Train Iter (time)
+    - !!python/object/apply:nerfstudio.utils.writer.EventName
+      - Train Rays / Sec
+    - !!python/object/apply:nerfstudio.utils.writer.EventName
+      - Test PSNR
+    - !!python/object/apply:nerfstudio.utils.writer.EventName
+      - Vis Rays / Sec
+    - !!python/object/apply:nerfstudio.utils.writer.EventName
+      - Test Rays / Sec
+    - !!python/object/apply:nerfstudio.utils.writer.EventName
+      - ETA (time)
+  max_buffer_size: 20
+  profiler: basic
+  relative_log_dir: !!python/object/apply:pathlib.PosixPath []
+  steps_per_log: 10
+machine: !!python/object:nerfstudio.configs.base_config.MachineConfig
+  device_type: cuda
+  dist_url: auto
+  machine_rank: 0
+  num_devices: 1
+  num_machines: 1
+  seed: 42
+max_num_iterations: 30000
+method_name: splatfacto
+mixed_precision: false
+optimizers:
+  bilateral_grid:
+    optimizer: !!python/object:nerfstudio.engine.optimizers.AdamOptimizerConfig
+      _target: &id001 !!python/name:torch.optim.adam.Adam ''
+      eps: 1.0e-15
+      lr: 0.002
+      max_norm: null
+      weight_decay: 0
+    scheduler: !!python/object:nerfstudio.engine.schedulers.ExponentialDecaySchedulerConfig
+      _target: &id002 !!python/name:nerfstudio.engine.schedulers.ExponentialDecayScheduler ''
+      lr_final: 0.0001
+      lr_pre_warmup: 0
+      max_steps: 30000
+      ramp: cosine
+      warmup_steps: 1000
+  camera_opt:
+    optimizer: !!python/object:nerfstudio.engine.optimizers.AdamOptimizerConfig
+      _target: *id001
+      eps: 1.0e-15
+      lr: 0.0001
+      max_norm: null
+      weight_decay: 0
+    scheduler: !!python/object:nerfstudio.engine.schedulers.ExponentialDecaySchedulerConfig
+      _target: *id002
+      lr_final: 5.0e-07
+      lr_pre_warmup: 0
+      max_steps: 30000
+      ramp: cosine
+      warmup_steps: 1000
+  features_dc:
+    optimizer: !!python/object:nerfstudio.engine.optimizers.AdamOptimizerConfig
+      _target: *id001
+      eps: 1.0e-15
+      lr: 0.0025
+      max_norm: null
+      weight_decay: 0
+    scheduler: null
+  features_rest:
+    optimizer: !!python/object:nerfstudio.engine.optimizers.AdamOptimizerConfig
+      _target: *id001
+      eps: 1.0e-15
+      lr: 0.000125
+      max_norm: null
+      weight_decay: 0
+    scheduler: null
+  means:
+    optimizer: !!python/object:nerfstudio.engine.optimizers.AdamOptimizerConfig
+      _target: *id001
+      eps: 1.0e-15
+      lr: 0.00016
+      max_norm: null
+      weight_decay: 0
+    scheduler: !!python/object:nerfstudio.engine.schedulers.ExponentialDecaySchedulerConfig
+      _target: *id002
+      lr_final: 1.6e-06
+      lr_pre_warmup: 1.0e-08
+      max_steps: 30000
+      ramp: cosine
+      warmup_steps: 0
+  opacities:
+    optimizer: !!python/object:nerfstudio.engine.optimizers.AdamOptimizerConfig
+      _target: *id001
+      eps: 1.0e-15
+      lr: 0.05
+      max_norm: null
+      weight_decay: 0
+    scheduler: null
+  quats:
+    optimizer: !!python/object:nerfstudio.engine.optimizers.AdamOptimizerConfig
+      _target: *id001
+      eps: 1.0e-15
+      lr: 0.001
+      max_norm: null
+      weight_decay: 0
+    scheduler: null
+  scales:
+    optimizer: !!python/object:nerfstudio.engine.optimizers.AdamOptimizerConfig
+      _target: *id001
+      eps: 1.0e-15
+      lr: 0.005
+      max_norm: null
+      weight_decay: 0
+    scheduler: null
+output_dir: !!python/object/apply:pathlib.PosixPath
+- outputs
+pipeline: !!python/object:nerfstudio.pipelines.base_pipeline.VanillaPipelineConfig
+  _target: !!python/name:nerfstudio.pipelines.base_pipeline.VanillaPipeline ''
+  datamanager: !!python/object:nerfstudio.data.datamanagers.full_images_datamanager.FullImageDatamanagerConfig
+    _target: !!python/name:nerfstudio.data.datamanagers.full_images_datamanager.FullImageDatamanager ''
+    cache_compressed_images: false
+    cache_images: gpu
+    cache_images_type: uint8
+    camera_res_scale_factor: 1.0
+    data: null
+    dataloader_num_workers: 4
+    dataparser: !!python/object:nerfstudio.data.dataparsers.colmap_dataparser.ColmapDataParserConfig
+      _target: !!python/name:nerfstudio.data.dataparsers.colmap_dataparser.ColmapDataParser ''
+      assume_colmap_world_coordinate_convention: true
+      auto_scale_poses: true
+      center_method: poses
+      colmap_path: !!python/object/apply:pathlib.PosixPath
+      - colmap
+      - sparse
+      - '0'
+      data: !!python/object/apply:pathlib.PosixPath
+      - data
+      - robot_data3
+      depth_unit_scale_factor: 0.001
+      depths_path: null
+      downscale_factor: 1
+      downscale_rounding_mode: floor
+      eval_interval: 8
+      eval_mode: interval
+      images_path: !!python/object/apply:pathlib.PosixPath
+      - images
+      load_3D_points: true
+      masks_path: null
+      max_2D_matches_per_3D_point: 0
+      orientation_method: up
+      scale_factor: 1.0
+      scene_scale: 1.0
+      tiling_factor: 1
+      train_split_fraction: 0.9
+    eval_num_images_to_sample_from: -1
+    eval_num_times_to_repeat_images: -1
+    fps_reset_every: 100
+    images_on_gpu: false
+    masks_on_gpu: false
+    max_thread_workers: null
+    prefetch_factor: 4
+    train_cameras_sampling_seed: 42
+    train_cameras_sampling_strategy: random
+  model: !!python/object:nerfstudio.models.splatfacto.SplatfactoModelConfig
+    _target: !!python/name:nerfstudio.models.splatfacto.SplatfactoModel ''
+    background_color: random
+    camera_optimizer: !!python/object:nerfstudio.cameras.camera_optimizers.CameraOptimizerConfig
+      _target: !!python/name:nerfstudio.cameras.camera_optimizers.CameraOptimizer ''
+      mode: 'off'
+      optimizer: null
+      rot_l2_penalty: 0.001
+      scheduler: null
+      trans_l2_penalty: 0.01
+    collider_params:
+      far_plane: 6.0
+      near_plane: 2.0
+    color_corrected_metrics: false
+    cull_alpha_thresh: 0.1
+    cull_scale_thresh: 0.5
+    cull_screen_size: 0.15
+    densify_grad_thresh: 0.0008
+    densify_size_thresh: 0.01
+    enable_collider: true
+    eval_num_rays_per_chunk: 4096
+    grid_shape: !!python/tuple
+    - 16
+    - 16
+    - 8
+    loss_coefficients:
+      rgb_loss_coarse: 1.0
+      rgb_loss_fine: 1.0
+    max_gauss_ratio: 10.0
+    max_gs_num: 1000000
+    mcmc_opacity_reg: 0.01
+    mcmc_scale_reg: 0.01
+    n_split_samples: 2
+    noise_lr: 500000.0
+    num_downscales: 2
+    num_random: 50000
+    output_depth_during_training: false
+    prompt: null
+    random_init: false
+    random_scale: 10.0
+    rasterize_mode: classic
+    refine_every: 100
+    reset_alpha_every: 30
+    resolution_schedule: 3000
+    sh_degree: 3
+    sh_degree_interval: 1000
+    split_screen_size: 0.05
+    ssim_lambda: 0.2
+    stop_screen_size_at: 4000
+    stop_split_at: 15000
+    strategy: default
+    use_absgrad: true
+    use_bilateral_grid: false
+    use_scale_regularization: false
+    warmup_length: 500
+project_name: nerfstudio-project
+prompt: null
+relative_model_dir: !!python/object/apply:pathlib.PosixPath
+- nerfstudio_models
+save_only_latest_checkpoint: true
+start_paused: false
+steps_per_eval_all_images: 1000
+steps_per_eval_batch: 0
+steps_per_eval_image: 100
+steps_per_save: 2000
+timestamp: 2026-03-10_070926
+use_grad_scaler: false
+viewer: !!python/object:nerfstudio.configs.base_config.ViewerConfig
+  camera_frustum_scale: 0.1
+  default_composite_depth: true
+  image_format: jpeg
+  jpeg_quality: 75
+  make_share_url: false
+  max_num_display_images: 512
+  num_rays_per_chunk: 32768
+  quit_on_train_completion: false
+  relative_log_filename: viewer_log_filename.txt
+  websocket_host: 0.0.0.0
+  websocket_port: null
+  websocket_port_default: 7007
+vis: viewer+wandb

circuit_data1/outputs/splatfacto/2026-03-10_070926/dataparser_transforms.json

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+{
+    "transform": [
+        [
+            0.9784600734710693,
+            -0.20636433362960815,
+            0.005449836142361164,
+            -0.4741067588329315
+        ],
+        [
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+            0.05221235379576683,
+            0.9986211061477661,
+            -0.11240027844905853
+        ],
+        [
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+            0.05221235379576683,
+            0.5911481380462646
+        ]
+    ],
+    "scale": 0.22240158700717413
+}

circuit_data1/outputs/splatfacto/2026-03-10_070926/nerfstudio_models/step-000029999.ckpt

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circuit_data1/outputs/splatfacto/2026-03-10_070926/splat/splat.ply

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