diff --git a/outputs/main_paper/ablation/.hydra/config.yaml b/outputs/main_paper/ablation/.hydra/config.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..983b322766a3a8e0c89d34ee53b2dbd17da02a03
--- /dev/null
+++ b/outputs/main_paper/ablation/.hydra/config.yaml
@@ -0,0 +1,235 @@
+focus_stack:
+  dataset_dir: ${dataset_dir}
+  scan_prefix: scan
+  scan_dirs: null
+  output_dir: ${output_dir}
+  experiment_name: ${experiment_name}
+  find_sharpest_image: true
+  sharpness_score: tenengrad
+  sharpness_selection_mode: window
+  sharpness_window_weights: uniform
+  sharpness_gaussian_sigma: null
+  output_paths:
+    output_dir: ${..output_dir}/${..experiment_name}/focus_stack
+    images_subdir: focus_stacked_images
+    masks_subdir: focus_stacked_masks
+    depthmaps_subdir: depthmaps
+    sharpness_scores_subdir: sharpness_scores
+    poses_filename: poses.json
+    intrinsics_filename: intrinsics.json
+  focus_stack_params:
+    focal_stack_size: 7
+    full_resolution_align: true
+    global_align: true
+    align_keep_size: true
+    no_contrast: true
+  low_pass_output: true
+  low_pass_kernel_size: 5
+  hydra:
+    job:
+      chdir: false
+    run:
+      dir: ${output_dir}/${experiment_name}
+    output_subdir: .hydra
+  random_seed: ${random_seed}
+masking:
+  output_dir: ${output_dir}
+  experiment_name: ${experiment_name}
+  random_seed: ${random_seed}
+  input_paths:
+    images_dir: ${...output_dir}/${...experiment_name}/focus_stack/focus_stacked_images
+    valid_regions_dir: ${...output_dir}/${...experiment_name}/focus_stack/focus_stacked_masks
+  output_paths:
+    output_dir: ${..output_dir}/${..experiment_name}/masking
+    masks_subdir: masks
+  bootstrap:
+    bootstrap_stem: scan00
+    focus_mask_border_padding: 8
+    edge_blur_kernel_size: 5
+    canny_threshold1: 25.0
+    canny_threshold2: 150.0
+    point_sampling_scale: 0.9
+    point_prompt_count: 80
+    firstpass_shrink_scale: 0.9
+    points_refine_kernel_size: 9
+    points_refine_dilate_iterations: 1
+  sam2:
+    model_id: facebook/sam2.1-hiera-large
+    device: cuda
+    offload_video_to_cpu: true
+  visualization:
+    overlay_alpha: 0.4
+    overlay_color:
+    - 255
+    - 0
+    - 0
+  hydra:
+    job:
+      chdir: false
+    run:
+      dir: ${output_dir}/${experiment_name}
+    output_subdir: .hydra
+colmap:
+  random_seed: ${random_seed}
+  run:
+    colmap_feat_extract_match: true
+    colmap_reconstruct: true
+  output_dir: ${output_dir}
+  experiment_name: ${experiment_name}
+  feat_extract_match:
+    input_paths:
+      images_dir: ${...output_dir}/${...experiment_name}/focus_stack/focus_stacked_images
+      masks_dir: ${...output_dir}/${...experiment_name}/masking/masks
+    output_paths:
+      output_dir: ${...output_dir}/${...experiment_name}
+      database_filename: database.db
+    extraction:
+      device: cpu
+      camera_model: OPENCV
+      num_threads: 1
+      max_num_features: 8192
+      estimate_affine_shape: true
+    matching:
+      use_gpu: false
+      num_threads: 1
+      guided_matching: true
+  reconstruction:
+    mode: automatic
+    load_prior_poses: true
+    load_prior_intrinsics: true
+    refine_intrinsics: true
+    input_paths:
+      poses_json: ${...output_dir}/${...experiment_name}/poses.json
+      prior_intrinsics_filepath: ${...output_dir}/${...experiment_name}/intrinsics.json
+      images_dir: ${...feat_extract_match.input_paths.images_dir}
+      database_filepath: ${...feat_extract_match.output_paths.output_dir}/${...feat_extract_match.output_paths.database_filename}
+    output_paths:
+      output_dir: ${...output_dir}/${...experiment_name}
+      model_dirname: sparse_model
+    mapping_params:
+      min_focal_length_ratio: 0.1
+      max_focal_length_ratio: 10.0
+      max_extra_param: .inf
+      ba_local_max_num_iterations: 30
+      ba_local_max_refinements: 3
+      ba_global_max_num_iterations: 75
+      ba_use_gpu: true
+      num_threads: 1
+  hydra:
+    job:
+      chdir: false
+    run:
+      dir: ${output_dir}/${experiment_name}
+    output_subdir: .hydra
+gs_3d:
+  random_seed: ${random_seed}
+  strategy:
+    _target_: gsplat.strategy.DefaultStrategy
+    verbose: true
+    prune_opa: 0.1
+    grow_grad2d: 0.0004
+    grow_scale3d: 0.01
+    prune_scale3d: 0.1
+    refine_start_iter: 500
+    refine_stop_iter: 15000
+    reset_every: 3000
+    refine_every: 100
+    absgrad: false
+    revised_opacity: false
+    key_for_gradient: means2d
+  disable_viewer: true
+  ckpt: null
+  compression: null
+  render_traj_path: interp
+  render_traj_trim: 5
+  output_dir: ${output_dir}
+  experiment_name: ${experiment_name}
+  input_paths:
+    model_dir: ${..output_dir}/${..experiment_name}/sparse_model
+    images_dir: ${..output_dir}/${..experiment_name}/masking/masked_images
+    masks_dir: ${..output_dir}/${..experiment_name}/masking/masks
+    valid_region_masks_dir: ${..output_dir}/${..experiment_name}/focus_stack/focus_stacked_masks
+  output_paths:
+    splat_dir: ${..output_dir}/${..experiment_name}/gs_3d
+  data_factor: 1
+  test_every: 8
+  patch_size: null
+  global_scale: 1.0
+  normalize_world_space: true
+  camera_model: pinhole
+  port: 8080
+  batch_size: 1
+  steps_scaler: 1.0
+  max_steps: 30000
+  eval_steps:
+  - 7000
+  - 30000
+  save_steps:
+  - 7000
+  - 30000
+  save_ply: true
+  ply_steps:
+  - 7000
+  - 30000
+  disable_video: true
+  init_type: sfm
+  init_num_pts: 100000
+  init_extent: 3.0
+  sh_degree: 3
+  sh_degree_interval: 1000
+  init_opa: 0.1
+  init_scale: 1.0
+  ssim_lambda: 0.2
+  near_plane: 0.01
+  far_plane: 10000000000.0
+  packed: false
+  sparse_grad: false
+  visible_adam: false
+  antialiased: false
+  random_bkgd: false
+  means_lr: 0.00016
+  scales_lr: 0.005
+  opacities_lr: 0.05
+  quats_lr: 0.001
+  sh0_lr: 0.0025
+  shN_lr: 0.000125
+  opacity_reg: 0.0
+  scale_reg: 0.0
+  pose_opt: false
+  pose_opt_lr: 1.0e-05
+  pose_opt_reg: 1.0e-06
+  pose_noise: 0.0
+  app_opt: false
+  app_embed_dim: 16
+  app_opt_lr: 0.001
+  app_opt_reg: 1.0e-06
+  use_bilateral_grid: false
+  bilateral_grid_shape:
+  - 16
+  - 16
+  - 8
+  depth_loss: false
+  depth_lambda: 0.01
+  bg_alpha_loss: true
+  bg_alpha_lambda: 0.5
+  tb_every: 100
+  tb_save_image: false
+  lpips_net: alex
+  with_ut: false
+  with_eval3d: false
+  use_fused_bilagrid: false
+  hydra:
+    job:
+      chdir: false
+    run:
+      dir: outputs/hydra/${now:%Y-%m-%d_%H-%M-%S}
+    output_subdir: .hydra
+output_dir: outputs/main_paper
+experiment_name: ablation
+random_seed: 0
+dataset_dir: data/ablation
+run:
+  focus_stack: true
+  masking: true
+  colmap: true
+  gs_3d: true
diff --git a/outputs/main_paper/ablation/.hydra/hydra.yaml b/outputs/main_paper/ablation/.hydra/hydra.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..c051165d067cc210d68a21f10b074ba67e0d1b76
--- /dev/null
+++ b/outputs/main_paper/ablation/.hydra/hydra.yaml
@@ -0,0 +1,162 @@
+hydra:
+  run:
+    dir: ${output_dir}/${experiment_name}
+  sweep:
+    dir: multirun/${now:%Y-%m-%d}/${now:%H-%M-%S}
+    subdir: ${hydra.job.num}
+  launcher:
+    _target_: hydra._internal.core_plugins.basic_launcher.BasicLauncher
+  sweeper:
+    _target_: hydra._internal.core_plugins.basic_sweeper.BasicSweeper
+    max_batch_size: null
+    params: null
+  help:
+    app_name: ${hydra.job.name}
+    header: '${hydra.help.app_name} is powered by Hydra.
+
+      '
+    footer: 'Powered by Hydra (https://hydra.cc)
+
+      Use --hydra-help to view Hydra specific help
+
+      '
+    template: '${hydra.help.header}
+
+      == Configuration groups ==
+
+      Compose your configuration from those groups (group=option)
+
+
+      $APP_CONFIG_GROUPS
+
+
+      == Config ==
+
+      Override anything in the config (foo.bar=value)
+
+
+      $CONFIG
+
+
+      ${hydra.help.footer}
+
+      '
+  hydra_help:
+    template: 'Hydra (${hydra.runtime.version})
+
+      See https://hydra.cc for more info.
+
+
+      == Flags ==
+
+      $FLAGS_HELP
+
+
+      == Configuration groups ==
+
+      Compose your configuration from those groups (For example, append hydra/job_logging=disabled
+      to command line)
+
+
+      $HYDRA_CONFIG_GROUPS
+
+
+      Use ''--cfg hydra'' to Show the Hydra config.
+
+      '
+    hydra_help: ???
+  hydra_logging:
+    version: 1
+    formatters:
+      simple:
+        format: '[%(asctime)s][HYDRA] %(message)s'
+    handlers:
+      console:
+        class: logging.StreamHandler
+        formatter: simple
+        stream: ext://sys.stdout
+    root:
+      level: INFO
+      handlers:
+      - console
+    loggers:
+      logging_example:
+        level: DEBUG
+    disable_existing_loggers: false
+  job_logging:
+    version: 1
+    formatters:
+      simple:
+        format: '[%(asctime)s][%(name)s][%(levelname)s] - %(message)s'
+    handlers:
+      console:
+        class: logging.StreamHandler
+        formatter: simple
+        stream: ext://sys.stdout
+      file:
+        class: logging.FileHandler
+        formatter: simple
+        filename: ${hydra.runtime.output_dir}/${hydra.job.name}.log
+    root:
+      level: INFO
+      handlers:
+      - console
+      - file
+    disable_existing_loggers: false
+  env: {}
+  mode: RUN
+  searchpath: []
+  callbacks: {}
+  output_subdir: .hydra
+  overrides:
+    hydra:
+    - hydra.mode=RUN
+    task:
+    - +experiment=main_paper
+    - experiment_name=ablation
+    - dataset_dir=data/ablation
+  job:
+    name: run_pipeline
+    chdir: false
+    override_dirname: +experiment=main_paper,dataset_dir=data/ablation,experiment_name=ablation
+    id: ???
+    num: ???
+    config_name: pipeline
+    env_set: {}
+    env_copy: []
+    config:
+      override_dirname:
+        kv_sep: '='
+        item_sep: ','
+        exclude_keys: []
+  runtime:
+    version: 1.3.2
+    version_base: '1.3'
+    cwd: /storage/scratch1/8/razarcon3/Microscopic-3D-Reconstruction/reconstruction
+    config_sources:
+    - path: hydra.conf
+      schema: pkg
+      provider: hydra
+    - path: /storage/scratch1/8/razarcon3/Microscopic-3D-Reconstruction/reconstruction/configs
+      schema: file
+      provider: main
+    - path: ''
+      schema: structured
+      provider: schema
+    output_dir: /storage/scratch1/8/razarcon3/Microscopic-3D-Reconstruction/reconstruction/outputs/main_paper/ablation
+    choices:
+      experiment: main_paper
+      gs_3d: default
+      colmap: default
+      masking: default
+      focus_stack: default
+      hydra/env: default
+      hydra/callbacks: null
+      hydra/job_logging: default
+      hydra/hydra_logging: default
+      hydra/hydra_help: default
+      hydra/help: default
+      hydra/sweeper: basic
+      hydra/launcher: basic
+      hydra/output: default
+  verbose: false
diff --git a/outputs/main_paper/ablation/.hydra/overrides.yaml b/outputs/main_paper/ablation/.hydra/overrides.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..0090382d2909e539fddaae9642a18991515e7250
--- /dev/null
+++ b/outputs/main_paper/ablation/.hydra/overrides.yaml
@@ -0,0 +1,3 @@
+- +experiment=main_paper
+- experiment_name=ablation
+- dataset_dir=data/ablation
diff --git a/outputs/main_paper/ablation/database.db b/outputs/main_paper/ablation/database.db
new file mode 100644
index 0000000000000000000000000000000000000000..b01a15697161c2a007c979e8fdf6d1400df22f8e
--- /dev/null
+++ b/outputs/main_paper/ablation/database.db
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:1ef2a78e20d52b7f30327919fc3d6dd738616ce1a1781ef907a919e0c3463e91
+size 235671552
diff --git a/outputs/main_paper/ablation/focus_stack/depthmaps/scan00.png b/outputs/main_paper/ablation/focus_stack/depthmaps/scan00.png
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+size 153653
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+  "scan131.png": [
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+      0.8261265195918598,
+      0.7236284727497565
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+      -0.8316363072858964,
+      -0.01091926096324569,
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+      0.04180204323379948
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+    [
+      0.0772496880695947,
+      -0.9923604860180621,
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+      0.4122220040641221
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+    [
+      0.0,
+      0.0,
+      0.0,
+      1.0
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+  "scan132.png": [
+    [
+      -0.356787252663707,
+      -0.14515777374536074,
+      0.9228391393184268,
+      0.7143411163498747
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+    [
+      -0.9323282300269533,
+      -0.00693437817723599,
+      -0.361546657976676,
+      0.021140098255186104
+    ],
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+      0.05888062356575864,
+      -0.989384220169589,
+      -0.1328605925318781,
+      0.4160503541193135
+    ],
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+      0.0,
+      0.0,
+      0.0,
+      1.0
+    ]
+  ],
+  "scan133.png": [
+    [
+      -0.3460972873567526,
+      -0.34631969603117224,
+      0.8719399840729712,
+      0.7202833952782102
+    ],
+    [
+      -0.928456553172432,
+      -0.007154914421907361,
+      -0.3713720992088417,
+      0.02205494611828683
+    ],
+    [
+      0.13485212847954586,
+      -0.9380892683217794,
+      -0.3190664948001349,
+      0.435742883260066
+    ],
+    [
+      0.0,
+      0.0,
+      0.0,
+      1.0
+    ]
+  ],
+  "scan134.png": [
+    [
+      -0.6597450432886888,
+      0.522229255954008,
+      0.5403823480478703,
+      0.7522622805776122
+    ],
+    [
+      -0.6406982220998201,
+      -0.015081201929518912,
+      -0.767644674016886,
+      0.0640429991252904
+    ],
+    [
+      -0.3927368916388378,
+      -0.8526717783379978,
+      0.34454110403808047,
+      0.3639057660545062
+    ],
+    [
+      0.0,
+      0.0,
+      0.0,
+      1.0
+    ]
+  ]
+}
\ No newline at end of file
diff --git a/outputs/main_paper/ablation/run_pipeline.log b/outputs/main_paper/ablation/run_pipeline.log
new file mode 100644
index 0000000000000000000000000000000000000000..d7319c72f266d6f521e9f7c57a2c2c6558a3ff5c
--- /dev/null
+++ b/outputs/main_paper/ablation/run_pipeline.log
@@ -0,0 +1,5 @@
+[2026-05-27 02:11:35,832][httpx][INFO] - HTTP Request: HEAD https://huggingface.co/facebook/sam2.1-hiera-large/resolve/main/sam2.1_hiera_large.pt "HTTP/1.1 302 Found"
+[2026-05-27 02:11:45,209][httpx][INFO] - HTTP Request: HEAD https://huggingface.co/facebook/sam2.1-hiera-large/resolve/main/sam2.1_hiera_large.pt "HTTP/1.1 302 Found"
+[2026-05-27 02:11:46,726][root][INFO] - For numpy array image, we assume (HxWxC) format
+[2026-05-27 02:11:47,881][root][INFO] - Computing image embeddings for the provided image...
+[2026-05-27 02:11:50,154][root][INFO] - Image embeddings computed.
diff --git a/outputs/main_paper/ablation/sparse_model/cameras.bin b/outputs/main_paper/ablation/sparse_model/cameras.bin
new file mode 100644
index 0000000000000000000000000000000000000000..9ebb96a325a82e9a34643bcf108eeb9b7331b8fe
--- /dev/null
+++ b/outputs/main_paper/ablation/sparse_model/cameras.bin
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:1a45b9840e376ac70339a355aebd969fbceed58b4948e24585b8c40e92cada78
+size 96
diff --git a/outputs/main_paper/ablation/sparse_model/cameras.txt b/outputs/main_paper/ablation/sparse_model/cameras.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d4141b339c7233c5970459813c65d7f13c552088
--- /dev/null
+++ b/outputs/main_paper/ablation/sparse_model/cameras.txt
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:59a59c9eb3990ec919e27977e0facb6191128bf9b8cb5f3c28634278258b27b5
+size 296
diff --git a/outputs/main_paper/ablation/sparse_model/frames.bin b/outputs/main_paper/ablation/sparse_model/frames.bin
new file mode 100644
index 0000000000000000000000000000000000000000..73d340a3d5b3066747b75ca1c7cf47081e3dc97a
--- /dev/null
+++ b/outputs/main_paper/ablation/sparse_model/frames.bin
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:db01082fec69b819f4defff1f7a9ac5debf8838de3fda54877102f9d1e150c9b
+size 8828
diff --git a/outputs/main_paper/ablation/sparse_model/frames.txt b/outputs/main_paper/ablation/sparse_model/frames.txt
new file mode 100644
index 0000000000000000000000000000000000000000..01cad39520de1f6ebbb991e14d5e6b2681fd4b8c
--- /dev/null
+++ b/outputs/main_paper/ablation/sparse_model/frames.txt
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:89c02ce727b13c952005116b43a38db136edc0ae170a1cacd6ff4c3b7dd9aba8
+size 16879
diff --git a/outputs/main_paper/ablation/sparse_model/images.bin b/outputs/main_paper/ablation/sparse_model/images.bin
new file mode 100644
index 0000000000000000000000000000000000000000..bf77cca5e6439fbb5f3c3fd380becd3d8d630c9a
--- /dev/null
+++ b/outputs/main_paper/ablation/sparse_model/images.bin
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:1e86945962789cf941276d7520be520c46d8570ae996fb209ca86696b616f8b2
+size 36852520
diff --git a/outputs/main_paper/ablation/sparse_model/images.txt b/outputs/main_paper/ablation/sparse_model/images.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9616ef671b7f75f086b56f173b64e146edbc3ba1
--- /dev/null
+++ b/outputs/main_paper/ablation/sparse_model/images.txt
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:cf028f732f6502493fa064cf75760eeb5c73a390852a39cd28ff0d91d4f6e4bd
+size 60438190
diff --git a/outputs/main_paper/ablation/sparse_model/points3D.bin b/outputs/main_paper/ablation/sparse_model/points3D.bin
new file mode 100644
index 0000000000000000000000000000000000000000..7d301806042a34d7079295b507020a9ba4434727
--- /dev/null
+++ b/outputs/main_paper/ablation/sparse_model/points3D.bin
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:761b8926215fee5d5ea4c7bcfad406d1a8553896e0a8965dd78167293c8a5c19
+size 1228143
diff --git a/outputs/main_paper/ablation/sparse_model/points3D.txt b/outputs/main_paper/ablation/sparse_model/points3D.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9c7c9d96e4e492dc4ee1edf2f35e0a4e0b113708
--- /dev/null
+++ b/outputs/main_paper/ablation/sparse_model/points3D.txt
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:4848339f3254614909fb240a397f24548e2cd26eb80532745e048b33d451cb26
+size 1806099
diff --git a/outputs/main_paper/ablation/sparse_model/rigs.bin b/outputs/main_paper/ablation/sparse_model/rigs.bin
new file mode 100644
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--- /dev/null
+++ b/outputs/main_paper/ablation/sparse_model/rigs.bin
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:73e4d5f0da0a84a5711b46ae716a149f1532832f95bb09b4b01e73cf2c5afbe9
+size 24
diff --git a/outputs/main_paper/ablation/sparse_model/rigs.txt b/outputs/main_paper/ablation/sparse_model/rigs.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f5a80293086199eaafc48e225055030960a80714
--- /dev/null
+++ b/outputs/main_paper/ablation/sparse_model/rigs.txt
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:8472bec629acf5f8204018b1b34b699709d2b4d203898facf500c0edec35ca68
+size 218
diff --git a/outputs/main_paper/ablation/sparse_model/sparse_pointcloud.ply b/outputs/main_paper/ablation/sparse_model/sparse_pointcloud.ply
new file mode 100644
index 0000000000000000000000000000000000000000..e6ec7e441ccb0a56a38cefc2f4559eb3a531cb4f
--- /dev/null
+++ b/outputs/main_paper/ablation/sparse_model/sparse_pointcloud.ply
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:18306ed6b0a26d052f9fb97d9c5917787add138730a25855875de7e81b0aa78f
+size 215654
diff --git a/outputs/main_paper/dark_rock_20260526_204204/.hydra/config.yaml b/outputs/main_paper/dark_rock_20260526_204204/.hydra/config.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..0eaa97eda1c84bd107cc400b6331bda821936ad4
--- /dev/null
+++ b/outputs/main_paper/dark_rock_20260526_204204/.hydra/config.yaml
@@ -0,0 +1,235 @@
+focus_stack:
+  dataset_dir: ${dataset_dir}
+  scan_prefix: scan
+  scan_dirs: null
+  output_dir: ${output_dir}
+  experiment_name: ${experiment_name}
+  find_sharpest_image: true
+  sharpness_score: tenengrad
+  sharpness_selection_mode: window
+  sharpness_window_weights: uniform
+  sharpness_gaussian_sigma: null
+  output_paths:
+    output_dir: ${..output_dir}/${..experiment_name}/focus_stack
+    images_subdir: focus_stacked_images
+    masks_subdir: focus_stacked_masks
+    depthmaps_subdir: depthmaps
+    sharpness_scores_subdir: sharpness_scores
+    poses_filename: poses.json
+    intrinsics_filename: intrinsics.json
+  focus_stack_params:
+    focal_stack_size: 7
+    full_resolution_align: true
+    global_align: true
+    align_keep_size: true
+    no_contrast: true
+  low_pass_output: true
+  low_pass_kernel_size: 5
+  hydra:
+    job:
+      chdir: false
+    run:
+      dir: ${output_dir}/${experiment_name}
+    output_subdir: .hydra
+  random_seed: ${random_seed}
+masking:
+  output_dir: ${output_dir}
+  experiment_name: ${experiment_name}
+  random_seed: ${random_seed}
+  input_paths:
+    images_dir: ${...output_dir}/${...experiment_name}/focus_stack/focus_stacked_images
+    valid_regions_dir: ${...output_dir}/${...experiment_name}/focus_stack/focus_stacked_masks
+  output_paths:
+    output_dir: ${..output_dir}/${..experiment_name}/masking
+    masks_subdir: masks
+  bootstrap:
+    bootstrap_stem: scan00
+    focus_mask_border_padding: 8
+    edge_blur_kernel_size: 5
+    canny_threshold1: 25.0
+    canny_threshold2: 150.0
+    point_sampling_scale: 0.9
+    point_prompt_count: 80
+    firstpass_shrink_scale: 0.9
+    points_refine_kernel_size: 9
+    points_refine_dilate_iterations: 1
+  sam2:
+    model_id: facebook/sam2.1-hiera-large
+    device: cuda
+    offload_video_to_cpu: true
+  visualization:
+    overlay_alpha: 0.4
+    overlay_color:
+    - 255
+    - 0
+    - 0
+  hydra:
+    job:
+      chdir: false
+    run:
+      dir: ${output_dir}/${experiment_name}
+    output_subdir: .hydra
+colmap:
+  random_seed: ${random_seed}
+  run:
+    colmap_feat_extract_match: true
+    colmap_reconstruct: true
+  output_dir: ${output_dir}
+  experiment_name: ${experiment_name}
+  feat_extract_match:
+    input_paths:
+      images_dir: ${...output_dir}/${...experiment_name}/focus_stack/focus_stacked_images
+      masks_dir: ${...output_dir}/${...experiment_name}/masking/masks
+    output_paths:
+      output_dir: ${...output_dir}/${...experiment_name}
+      database_filename: database.db
+    extraction:
+      device: cpu
+      camera_model: OPENCV
+      num_threads: 1
+      max_num_features: 8192
+      estimate_affine_shape: true
+    matching:
+      use_gpu: false
+      num_threads: 1
+      guided_matching: true
+  reconstruction:
+    mode: automatic
+    load_prior_poses: true
+    load_prior_intrinsics: true
+    refine_intrinsics: true
+    input_paths:
+      poses_json: ${...output_dir}/${...experiment_name}/poses.json
+      prior_intrinsics_filepath: ${...output_dir}/${...experiment_name}/intrinsics.json
+      images_dir: ${...feat_extract_match.input_paths.images_dir}
+      database_filepath: ${...feat_extract_match.output_paths.output_dir}/${...feat_extract_match.output_paths.database_filename}
+    output_paths:
+      output_dir: ${...output_dir}/${...experiment_name}
+      model_dirname: sparse_model
+    mapping_params:
+      min_focal_length_ratio: 0.1
+      max_focal_length_ratio: 10.0
+      max_extra_param: .inf
+      ba_local_max_num_iterations: 30
+      ba_local_max_refinements: 3
+      ba_global_max_num_iterations: 75
+      ba_use_gpu: true
+      num_threads: 1
+  hydra:
+    job:
+      chdir: false
+    run:
+      dir: ${output_dir}/${experiment_name}
+    output_subdir: .hydra
+gs_3d:
+  random_seed: ${random_seed}
+  strategy:
+    _target_: gsplat.strategy.DefaultStrategy
+    verbose: true
+    prune_opa: 0.1
+    grow_grad2d: 0.0004
+    grow_scale3d: 0.01
+    prune_scale3d: 0.1
+    refine_start_iter: 500
+    refine_stop_iter: 15000
+    reset_every: 3000
+    refine_every: 100
+    absgrad: false
+    revised_opacity: false
+    key_for_gradient: means2d
+  disable_viewer: true
+  ckpt: null
+  compression: null
+  render_traj_path: interp
+  render_traj_trim: 5
+  output_dir: ${output_dir}
+  experiment_name: ${experiment_name}
+  input_paths:
+    model_dir: ${..output_dir}/${..experiment_name}/sparse_model
+    images_dir: ${..output_dir}/${..experiment_name}/masking/masked_images
+    masks_dir: ${..output_dir}/${..experiment_name}/masking/masks
+    valid_region_masks_dir: ${..output_dir}/${..experiment_name}/focus_stack/focus_stacked_masks
+  output_paths:
+    splat_dir: ${..output_dir}/${..experiment_name}/gs_3d
+  data_factor: 1
+  test_every: 8
+  patch_size: null
+  global_scale: 1.0
+  normalize_world_space: true
+  camera_model: pinhole
+  port: 8080
+  batch_size: 1
+  steps_scaler: 1.0
+  max_steps: 30000
+  eval_steps:
+  - 7000
+  - 30000
+  save_steps:
+  - 7000
+  - 30000
+  save_ply: true
+  ply_steps:
+  - 7000
+  - 30000
+  disable_video: true
+  init_type: sfm
+  init_num_pts: 100000
+  init_extent: 3.0
+  sh_degree: 3
+  sh_degree_interval: 1000
+  init_opa: 0.1
+  init_scale: 1.0
+  ssim_lambda: 0.2
+  near_plane: 0.01
+  far_plane: 10000000000.0
+  packed: false
+  sparse_grad: false
+  visible_adam: false
+  antialiased: false
+  random_bkgd: false
+  means_lr: 0.00016
+  scales_lr: 0.005
+  opacities_lr: 0.05
+  quats_lr: 0.001
+  sh0_lr: 0.0025
+  shN_lr: 0.000125
+  opacity_reg: 0.0
+  scale_reg: 0.0
+  pose_opt: false
+  pose_opt_lr: 1.0e-05
+  pose_opt_reg: 1.0e-06
+  pose_noise: 0.0
+  app_opt: false
+  app_embed_dim: 16
+  app_opt_lr: 0.001
+  app_opt_reg: 1.0e-06
+  use_bilateral_grid: false
+  bilateral_grid_shape:
+  - 16
+  - 16
+  - 8
+  depth_loss: false
+  depth_lambda: 0.01
+  bg_alpha_loss: true
+  bg_alpha_lambda: 0.5
+  tb_every: 100
+  tb_save_image: false
+  lpips_net: alex
+  with_ut: false
+  with_eval3d: false
+  use_fused_bilagrid: false
+  hydra:
+    job:
+      chdir: false
+    run:
+      dir: outputs/hydra/${now:%Y-%m-%d_%H-%M-%S}
+    output_subdir: .hydra
+output_dir: outputs/main_paper
+experiment_name: dark_rock_20260526_204204
+random_seed: 0
+dataset_dir: data/dark_rock_20260526_204204
+run:
+  focus_stack: true
+  masking: true
+  colmap: true
+  gs_3d: true
diff --git a/outputs/main_paper/dark_rock_20260526_204204/.hydra/hydra.yaml b/outputs/main_paper/dark_rock_20260526_204204/.hydra/hydra.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..3add581289132e84e394da856df6aa12e6bde5ae
--- /dev/null
+++ b/outputs/main_paper/dark_rock_20260526_204204/.hydra/hydra.yaml
@@ -0,0 +1,162 @@
+hydra:
+  run:
+    dir: ${output_dir}/${experiment_name}
+  sweep:
+    dir: multirun/${now:%Y-%m-%d}/${now:%H-%M-%S}
+    subdir: ${hydra.job.num}
+  launcher:
+    _target_: hydra._internal.core_plugins.basic_launcher.BasicLauncher
+  sweeper:
+    _target_: hydra._internal.core_plugins.basic_sweeper.BasicSweeper
+    max_batch_size: null
+    params: null
+  help:
+    app_name: ${hydra.job.name}
+    header: '${hydra.help.app_name} is powered by Hydra.
+
+      '
+    footer: 'Powered by Hydra (https://hydra.cc)
+
+      Use --hydra-help to view Hydra specific help
+
+      '
+    template: '${hydra.help.header}
+
+      == Configuration groups ==
+
+      Compose your configuration from those groups (group=option)
+
+
+      $APP_CONFIG_GROUPS
+
+
+      == Config ==
+
+      Override anything in the config (foo.bar=value)
+
+
+      $CONFIG
+
+
+      ${hydra.help.footer}
+
+      '
+  hydra_help:
+    template: 'Hydra (${hydra.runtime.version})
+
+      See https://hydra.cc for more info.
+
+
+      == Flags ==
+
+      $FLAGS_HELP
+
+
+      == Configuration groups ==
+
+      Compose your configuration from those groups (For example, append hydra/job_logging=disabled
+      to command line)
+
+
+      $HYDRA_CONFIG_GROUPS
+
+
+      Use ''--cfg hydra'' to Show the Hydra config.
+
+      '
+    hydra_help: ???
+  hydra_logging:
+    version: 1
+    formatters:
+      simple:
+        format: '[%(asctime)s][HYDRA] %(message)s'
+    handlers:
+      console:
+        class: logging.StreamHandler
+        formatter: simple
+        stream: ext://sys.stdout
+    root:
+      level: INFO
+      handlers:
+      - console
+    loggers:
+      logging_example:
+        level: DEBUG
+    disable_existing_loggers: false
+  job_logging:
+    version: 1
+    formatters:
+      simple:
+        format: '[%(asctime)s][%(name)s][%(levelname)s] - %(message)s'
+    handlers:
+      console:
+        class: logging.StreamHandler
+        formatter: simple
+        stream: ext://sys.stdout
+      file:
+        class: logging.FileHandler
+        formatter: simple
+        filename: ${hydra.runtime.output_dir}/${hydra.job.name}.log
+    root:
+      level: INFO
+      handlers:
+      - console
+      - file
+    disable_existing_loggers: false
+  env: {}
+  mode: RUN
+  searchpath: []
+  callbacks: {}
+  output_subdir: .hydra
+  overrides:
+    hydra:
+    - hydra.mode=RUN
+    task:
+    - +experiment=main_paper
+    - experiment_name=dark_rock_20260526_204204
+    - dataset_dir=data/dark_rock_20260526_204204
+  job:
+    name: run_pipeline
+    chdir: false
+    override_dirname: +experiment=main_paper,dataset_dir=data/dark_rock_20260526_204204,experiment_name=dark_rock_20260526_204204
+    id: ???
+    num: ???
+    config_name: pipeline
+    env_set: {}
+    env_copy: []
+    config:
+      override_dirname:
+        kv_sep: '='
+        item_sep: ','
+        exclude_keys: []
+  runtime:
+    version: 1.3.2
+    version_base: '1.3'
+    cwd: /storage/scratch1/8/razarcon3/Microscopic-3D-Reconstruction/reconstruction
+    config_sources:
+    - path: hydra.conf
+      schema: pkg
+      provider: hydra
+    - path: /storage/scratch1/8/razarcon3/Microscopic-3D-Reconstruction/reconstruction/configs
+      schema: file
+      provider: main
+    - path: ''
+      schema: structured
+      provider: schema
+    output_dir: /storage/scratch1/8/razarcon3/Microscopic-3D-Reconstruction/reconstruction/outputs/main_paper/dark_rock_20260526_204204
+    choices:
+      experiment: main_paper
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\ No newline at end of file
diff --git a/outputs/main_paper/dark_rock_20260526_204204/run_pipeline.log b/outputs/main_paper/dark_rock_20260526_204204/run_pipeline.log
new file mode 100644
index 0000000000000000000000000000000000000000..3488d08425fef8d8536c2e7afff307fa2c13987e
--- /dev/null
+++ b/outputs/main_paper/dark_rock_20260526_204204/run_pipeline.log
@@ -0,0 +1,5 @@
+[2026-05-27 02:39:14,018][httpx][INFO] - HTTP Request: HEAD https://huggingface.co/facebook/sam2.1-hiera-large/resolve/main/sam2.1_hiera_large.pt "HTTP/1.1 302 Found"
+[2026-05-27 02:39:17,952][httpx][INFO] - HTTP Request: HEAD https://huggingface.co/facebook/sam2.1-hiera-large/resolve/main/sam2.1_hiera_large.pt "HTTP/1.1 302 Found"
+[2026-05-27 02:39:19,428][root][INFO] - For numpy array image, we assume (HxWxC) format
+[2026-05-27 02:39:19,677][root][INFO] - Computing image embeddings for the provided image...
+[2026-05-27 02:39:21,793][root][INFO] - Image embeddings computed.
diff --git a/outputs/main_paper/dark_rock_20260526_204204/sparse_model/cameras.bin b/outputs/main_paper/dark_rock_20260526_204204/sparse_model/cameras.bin
new file mode 100644
index 0000000000000000000000000000000000000000..c17b597d38d926e797b75cb638bda5aaa57f8638
--- /dev/null
+++ b/outputs/main_paper/dark_rock_20260526_204204/sparse_model/cameras.bin
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:ef01e9358e34d92a2643d4ff7c21e5c01943af4b868fe1c209a2748e5e90ebf8
+size 96
diff --git a/outputs/main_paper/dark_rock_20260526_204204/sparse_model/cameras.txt b/outputs/main_paper/dark_rock_20260526_204204/sparse_model/cameras.txt
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index 0000000000000000000000000000000000000000..2c8376a116ff1453c14e796adb2280f1274c8c34
--- /dev/null
+++ b/outputs/main_paper/dark_rock_20260526_204204/sparse_model/cameras.txt
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:cd2a978b4a3e9c016cd6bda67f2f37231ea1c7d549c7c8c9a0d7a541a27af60b
+size 298
diff --git a/outputs/main_paper/dark_rock_20260526_204204/sparse_model/frames.bin b/outputs/main_paper/dark_rock_20260526_204204/sparse_model/frames.bin
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index 0000000000000000000000000000000000000000..637cbe7b40573fdbe03ca11e6de10e8d96efe6ff
--- /dev/null
+++ b/outputs/main_paper/dark_rock_20260526_204204/sparse_model/frames.bin
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:8a45b75a4db56d37f62a38bf7514d6e67e0e03744395b666b6b17b04138da5fe
+size 8828
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index 0000000000000000000000000000000000000000..0c62140fe79703412e4c77b92a7ed63516caa08b
--- /dev/null
+++ b/outputs/main_paper/dark_rock_20260526_204204/sparse_model/frames.txt
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
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+size 16873
diff --git a/outputs/main_paper/dark_rock_20260526_204204/sparse_model/images.bin b/outputs/main_paper/dark_rock_20260526_204204/sparse_model/images.bin
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--- /dev/null
+++ b/outputs/main_paper/dark_rock_20260526_204204/sparse_model/images.bin
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
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--- /dev/null
+++ b/outputs/main_paper/dark_rock_20260526_204204/sparse_model/images.txt
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
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diff --git a/outputs/main_paper/dark_rock_20260526_204204/sparse_model/points3D.bin b/outputs/main_paper/dark_rock_20260526_204204/sparse_model/points3D.bin
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index 0000000000000000000000000000000000000000..8e421778e82b93748fef05df659a9857759e3889
--- /dev/null
+++ b/outputs/main_paper/dark_rock_20260526_204204/sparse_model/points3D.bin
@@ -0,0 +1,3 @@
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+size 9270999
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--- /dev/null
+++ b/outputs/main_paper/dark_rock_20260526_204204/sparse_model/points3D.txt
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
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+size 12132229
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--- /dev/null
+++ b/outputs/main_paper/dark_rock_20260526_204204/sparse_model/rigs.bin
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
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+size 24
diff --git a/outputs/main_paper/dark_rock_20260526_204204/sparse_model/rigs.txt b/outputs/main_paper/dark_rock_20260526_204204/sparse_model/rigs.txt
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--- /dev/null
+++ b/outputs/main_paper/dark_rock_20260526_204204/sparse_model/rigs.txt
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+version https://git-lfs.github.com/spec/v1
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+size 218
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--- /dev/null
+++ b/outputs/main_paper/dark_rock_20260526_204204/sparse_model/sparse_pointcloud.ply
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
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diff --git a/outputs/main_paper/lego_20260526_195340/.hydra/config.yaml b/outputs/main_paper/lego_20260526_195340/.hydra/config.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..420252e19277d30ef08ba3a93ed0da1cf0470659
--- /dev/null
+++ b/outputs/main_paper/lego_20260526_195340/.hydra/config.yaml
@@ -0,0 +1,235 @@
+focus_stack:
+  dataset_dir: ${dataset_dir}
+  scan_prefix: scan
+  scan_dirs: null
+  output_dir: ${output_dir}
+  experiment_name: ${experiment_name}
+  find_sharpest_image: true
+  sharpness_score: tenengrad
+  sharpness_selection_mode: window
+  sharpness_window_weights: uniform
+  sharpness_gaussian_sigma: null
+  output_paths:
+    output_dir: ${..output_dir}/${..experiment_name}/focus_stack
+    images_subdir: focus_stacked_images
+    masks_subdir: focus_stacked_masks
+    depthmaps_subdir: depthmaps
+    sharpness_scores_subdir: sharpness_scores
+    poses_filename: poses.json
+    intrinsics_filename: intrinsics.json
+  focus_stack_params:
+    focal_stack_size: 7
+    full_resolution_align: true
+    global_align: true
+    align_keep_size: true
+    no_contrast: true
+  low_pass_output: true
+  low_pass_kernel_size: 5
+  hydra:
+    job:
+      chdir: false
+    run:
+      dir: ${output_dir}/${experiment_name}
+    output_subdir: .hydra
+  random_seed: ${random_seed}
+masking:
+  output_dir: ${output_dir}
+  experiment_name: ${experiment_name}
+  random_seed: ${random_seed}
+  input_paths:
+    images_dir: ${...output_dir}/${...experiment_name}/focus_stack/focus_stacked_images
+    valid_regions_dir: ${...output_dir}/${...experiment_name}/focus_stack/focus_stacked_masks
+  output_paths:
+    output_dir: ${..output_dir}/${..experiment_name}/masking
+    masks_subdir: masks
+  bootstrap:
+    bootstrap_stem: scan00
+    focus_mask_border_padding: 8
+    edge_blur_kernel_size: 5
+    canny_threshold1: 25.0
+    canny_threshold2: 150.0
+    point_sampling_scale: 0.9
+    point_prompt_count: 80
+    firstpass_shrink_scale: 0.9
+    points_refine_kernel_size: 9
+    points_refine_dilate_iterations: 1
+  sam2:
+    model_id: facebook/sam2.1-hiera-large
+    device: cuda
+    offload_video_to_cpu: true
+  visualization:
+    overlay_alpha: 0.4
+    overlay_color:
+    - 255
+    - 0
+    - 0
+  hydra:
+    job:
+      chdir: false
+    run:
+      dir: ${output_dir}/${experiment_name}
+    output_subdir: .hydra
+colmap:
+  random_seed: ${random_seed}
+  run:
+    colmap_feat_extract_match: true
+    colmap_reconstruct: true
+  output_dir: ${output_dir}
+  experiment_name: ${experiment_name}
+  feat_extract_match:
+    input_paths:
+      images_dir: ${...output_dir}/${...experiment_name}/focus_stack/focus_stacked_images
+      masks_dir: ${...output_dir}/${...experiment_name}/masking/masks
+    output_paths:
+      output_dir: ${...output_dir}/${...experiment_name}
+      database_filename: database.db
+    extraction:
+      device: cpu
+      camera_model: OPENCV
+      num_threads: 1
+      max_num_features: 8192
+      estimate_affine_shape: true
+    matching:
+      use_gpu: false
+      num_threads: 1
+      guided_matching: true
+  reconstruction:
+    mode: automatic
+    load_prior_poses: true
+    load_prior_intrinsics: true
+    refine_intrinsics: true
+    input_paths:
+      poses_json: ${...output_dir}/${...experiment_name}/poses.json
+      prior_intrinsics_filepath: ${...output_dir}/${...experiment_name}/intrinsics.json
+      images_dir: ${...feat_extract_match.input_paths.images_dir}
+      database_filepath: ${...feat_extract_match.output_paths.output_dir}/${...feat_extract_match.output_paths.database_filename}
+    output_paths:
+      output_dir: ${...output_dir}/${...experiment_name}
+      model_dirname: sparse_model
+    mapping_params:
+      min_focal_length_ratio: 0.1
+      max_focal_length_ratio: 10.0
+      max_extra_param: .inf
+      ba_local_max_num_iterations: 30
+      ba_local_max_refinements: 3
+      ba_global_max_num_iterations: 75
+      ba_use_gpu: true
+      num_threads: 1
+  hydra:
+    job:
+      chdir: false
+    run:
+      dir: ${output_dir}/${experiment_name}
+    output_subdir: .hydra
+gs_3d:
+  random_seed: ${random_seed}
+  strategy:
+    _target_: gsplat.strategy.DefaultStrategy
+    verbose: true
+    prune_opa: 0.1
+    grow_grad2d: 0.0004
+    grow_scale3d: 0.01
+    prune_scale3d: 0.1
+    refine_start_iter: 500
+    refine_stop_iter: 15000
+    reset_every: 3000
+    refine_every: 100
+    absgrad: false
+    revised_opacity: false
+    key_for_gradient: means2d
+  disable_viewer: true
+  ckpt: null
+  compression: null
+  render_traj_path: interp
+  render_traj_trim: 5
+  output_dir: ${output_dir}
+  experiment_name: ${experiment_name}
+  input_paths:
+    model_dir: ${..output_dir}/${..experiment_name}/sparse_model
+    images_dir: ${..output_dir}/${..experiment_name}/masking/masked_images
+    masks_dir: ${..output_dir}/${..experiment_name}/masking/masks
+    valid_region_masks_dir: ${..output_dir}/${..experiment_name}/focus_stack/focus_stacked_masks
+  output_paths:
+    splat_dir: ${..output_dir}/${..experiment_name}/gs_3d
+  data_factor: 1
+  test_every: 8
+  patch_size: null
+  global_scale: 1.0
+  normalize_world_space: true
+  camera_model: pinhole
+  port: 8080
+  batch_size: 1
+  steps_scaler: 1.0
+  max_steps: 30000
+  eval_steps:
+  - 7000
+  - 30000
+  save_steps:
+  - 7000
+  - 30000
+  save_ply: true
+  ply_steps:
+  - 7000
+  - 30000
+  disable_video: true
+  init_type: sfm
+  init_num_pts: 100000
+  init_extent: 3.0
+  sh_degree: 3
+  sh_degree_interval: 1000
+  init_opa: 0.1
+  init_scale: 1.0
+  ssim_lambda: 0.2
+  near_plane: 0.01
+  far_plane: 10000000000.0
+  packed: false
+  sparse_grad: false
+  visible_adam: false
+  antialiased: false
+  random_bkgd: false
+  means_lr: 0.00016
+  scales_lr: 0.005
+  opacities_lr: 0.05
+  quats_lr: 0.001
+  sh0_lr: 0.0025
+  shN_lr: 0.000125
+  opacity_reg: 0.0
+  scale_reg: 0.0
+  pose_opt: false
+  pose_opt_lr: 1.0e-05
+  pose_opt_reg: 1.0e-06
+  pose_noise: 0.0
+  app_opt: false
+  app_embed_dim: 16
+  app_opt_lr: 0.001
+  app_opt_reg: 1.0e-06
+  use_bilateral_grid: false
+  bilateral_grid_shape:
+  - 16
+  - 16
+  - 8
+  depth_loss: false
+  depth_lambda: 0.01
+  bg_alpha_loss: true
+  bg_alpha_lambda: 0.5
+  tb_every: 100
+  tb_save_image: false
+  lpips_net: alex
+  with_ut: false
+  with_eval3d: false
+  use_fused_bilagrid: false
+  hydra:
+    job:
+      chdir: false
+    run:
+      dir: outputs/hydra/${now:%Y-%m-%d_%H-%M-%S}
+    output_subdir: .hydra
+output_dir: outputs/main_paper
+experiment_name: lego_20260526_195340
+random_seed: 0
+dataset_dir: data/lego_20260526_195340
+run:
+  focus_stack: true
+  masking: true
+  colmap: true
+  gs_3d: true
diff --git a/outputs/main_paper/lego_20260526_195340/.hydra/hydra.yaml b/outputs/main_paper/lego_20260526_195340/.hydra/hydra.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..5aedabde25a49e4973654679265ffe0ec54e0d6d
--- /dev/null
+++ b/outputs/main_paper/lego_20260526_195340/.hydra/hydra.yaml
@@ -0,0 +1,162 @@
+hydra:
+  run:
+    dir: ${output_dir}/${experiment_name}
+  sweep:
+    dir: multirun/${now:%Y-%m-%d}/${now:%H-%M-%S}
+    subdir: ${hydra.job.num}
+  launcher:
+    _target_: hydra._internal.core_plugins.basic_launcher.BasicLauncher
+  sweeper:
+    _target_: hydra._internal.core_plugins.basic_sweeper.BasicSweeper
+    max_batch_size: null
+    params: null
+  help:
+    app_name: ${hydra.job.name}
+    header: '${hydra.help.app_name} is powered by Hydra.
+
+      '
+    footer: 'Powered by Hydra (https://hydra.cc)
+
+      Use --hydra-help to view Hydra specific help
+
+      '
+    template: '${hydra.help.header}
+
+      == Configuration groups ==
+
+      Compose your configuration from those groups (group=option)
+
+
+      $APP_CONFIG_GROUPS
+
+
+      == Config ==
+
+      Override anything in the config (foo.bar=value)
+
+
+      $CONFIG
+
+
+      ${hydra.help.footer}
+
+      '
+  hydra_help:
+    template: 'Hydra (${hydra.runtime.version})
+
+      See https://hydra.cc for more info.
+
+
+      == Flags ==
+
+      $FLAGS_HELP
+
+
+      == Configuration groups ==
+
+      Compose your configuration from those groups (For example, append hydra/job_logging=disabled
+      to command line)
+
+
+      $HYDRA_CONFIG_GROUPS
+
+
+      Use ''--cfg hydra'' to Show the Hydra config.
+
+      '
+    hydra_help: ???
+  hydra_logging:
+    version: 1
+    formatters:
+      simple:
+        format: '[%(asctime)s][HYDRA] %(message)s'
+    handlers:
+      console:
+        class: logging.StreamHandler
+        formatter: simple
+        stream: ext://sys.stdout
+    root:
+      level: INFO
+      handlers:
+      - console
+    loggers:
+      logging_example:
+        level: DEBUG
+    disable_existing_loggers: false
+  job_logging:
+    version: 1
+    formatters:
+      simple:
+        format: '[%(asctime)s][%(name)s][%(levelname)s] - %(message)s'
+    handlers:
+      console:
+        class: logging.StreamHandler
+        formatter: simple
+        stream: ext://sys.stdout
+      file:
+        class: logging.FileHandler
+        formatter: simple
+        filename: ${hydra.runtime.output_dir}/${hydra.job.name}.log
+    root:
+      level: INFO
+      handlers:
+      - console
+      - file
+    disable_existing_loggers: false
+  env: {}
+  mode: RUN
+  searchpath: []
+  callbacks: {}
+  output_subdir: .hydra
+  overrides:
+    hydra:
+    - hydra.mode=RUN
+    task:
+    - +experiment=main_paper
+    - experiment_name=lego_20260526_195340
+    - dataset_dir=data/lego_20260526_195340
+  job:
+    name: run_pipeline
+    chdir: false
+    override_dirname: +experiment=main_paper,dataset_dir=data/lego_20260526_195340,experiment_name=lego_20260526_195340
+    id: ???
+    num: ???
+    config_name: pipeline
+    env_set: {}
+    env_copy: []
+    config:
+      override_dirname:
+        kv_sep: '='
+        item_sep: ','
+        exclude_keys: []
+  runtime:
+    version: 1.3.2
+    version_base: '1.3'
+    cwd: /storage/scratch1/8/razarcon3/Microscopic-3D-Reconstruction/reconstruction
+    config_sources:
+    - path: hydra.conf
+      schema: pkg
+      provider: hydra
+    - path: /storage/scratch1/8/razarcon3/Microscopic-3D-Reconstruction/reconstruction/configs
+      schema: file
+      provider: main
+    - path: ''
+      schema: structured
+      provider: schema
+    output_dir: /storage/scratch1/8/razarcon3/Microscopic-3D-Reconstruction/reconstruction/outputs/main_paper/lego_20260526_195340
+    choices:
+      experiment: main_paper
+      gs_3d: default
+      colmap: default
+      masking: default
+      focus_stack: default
+      hydra/env: default
+      hydra/callbacks: null
+      hydra/job_logging: default
+      hydra/hydra_logging: default
+      hydra/hydra_help: default
+      hydra/help: default
+      hydra/sweeper: basic
+      hydra/launcher: basic
+      hydra/output: default
+  verbose: false
diff --git a/outputs/main_paper/lego_20260526_195340/.hydra/overrides.yaml b/outputs/main_paper/lego_20260526_195340/.hydra/overrides.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..c43d5383b4207164800cc3412ad43a24ea06de48
--- /dev/null
+++ b/outputs/main_paper/lego_20260526_195340/.hydra/overrides.yaml
@@ -0,0 +1,3 @@
+- +experiment=main_paper
+- experiment_name=lego_20260526_195340
+- dataset_dir=data/lego_20260526_195340
diff --git a/outputs/main_paper/lego_20260526_195340/database.db b/outputs/main_paper/lego_20260526_195340/database.db
new file mode 100644
index 0000000000000000000000000000000000000000..2531e4ff01598c5497544242861dde60edef44b7
--- /dev/null
+++ b/outputs/main_paper/lego_20260526_195340/database.db
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:4d59f9365b55b8e8116ab46dc9815bd558276499cf648e2c4156414a96bffe37
+size 16060416
diff --git a/outputs/main_paper/lego_20260526_195340/focus_stack/depthmaps/scan00.png b/outputs/main_paper/lego_20260526_195340/focus_stack/depthmaps/scan00.png
new file mode 100644
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--- /dev/null
+++ b/outputs/main_paper/lego_20260526_195340/focus_stack/depthmaps/scan00.png
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:7190799439b8a9dc759fbb10ec47ac83b2ac2a9f1f4e75fe4e53bb0012682fd5
+size 179222
diff --git a/outputs/main_paper/lego_20260526_195340/focus_stack/depthmaps/scan01.png b/outputs/main_paper/lego_20260526_195340/focus_stack/depthmaps/scan01.png
new file mode 100644
index 0000000000000000000000000000000000000000..d1334f00ccb3aff5d148b8a247dab832d787e870
--- /dev/null
+++ b/outputs/main_paper/lego_20260526_195340/focus_stack/depthmaps/scan01.png
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diff --git a/outputs/main_paper/lego_20260526_195340/run_pipeline.log b/outputs/main_paper/lego_20260526_195340/run_pipeline.log
new file mode 100644
index 0000000000000000000000000000000000000000..eb422e83926fdca8091163a172dcdb6b615994c1
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+++ b/outputs/main_paper/lego_20260526_195340/run_pipeline.log
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+[2026-05-27 02:02:38,805][httpx][INFO] - HTTP Request: HEAD https://huggingface.co/facebook/sam2.1-hiera-large/resolve/main/sam2.1_hiera_large.pt "HTTP/1.1 302 Found"
+[2026-05-27 02:02:50,749][httpx][INFO] - HTTP Request: HEAD https://huggingface.co/facebook/sam2.1-hiera-large/resolve/main/sam2.1_hiera_large.pt "HTTP/1.1 302 Found"
+[2026-05-27 02:02:52,240][root][INFO] - For numpy array image, we assume (HxWxC) format
+[2026-05-27 02:02:53,342][root][INFO] - Computing image embeddings for the provided image...
+[2026-05-27 02:03:03,792][root][INFO] - Image embeddings computed.
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diff --git a/outputs/main_paper/lego_20260526_195340/sparse_model/points3D.txt b/outputs/main_paper/lego_20260526_195340/sparse_model/points3D.txt
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@@ -0,0 +1,3 @@
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diff --git a/outputs/main_paper/lego_20260526_195340/sparse_model/rigs.bin b/outputs/main_paper/lego_20260526_195340/sparse_model/rigs.bin
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@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
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diff --git a/outputs/main_paper/lego_20260526_195340/sparse_model/rigs.txt b/outputs/main_paper/lego_20260526_195340/sparse_model/rigs.txt
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+version https://git-lfs.github.com/spec/v1
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diff --git a/outputs/main_paper/lego_20260526_195340/sparse_model/sparse_pointcloud.ply b/outputs/main_paper/lego_20260526_195340/sparse_model/sparse_pointcloud.ply
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--- /dev/null
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@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
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diff --git a/outputs/main_paper/nezuko_20260526_151752/.hydra/config.yaml b/outputs/main_paper/nezuko_20260526_151752/.hydra/config.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..60d168e3de19176dd011ac81ba2f0655f5708e82
--- /dev/null
+++ b/outputs/main_paper/nezuko_20260526_151752/.hydra/config.yaml
@@ -0,0 +1,235 @@
+focus_stack:
+  dataset_dir: ${dataset_dir}
+  scan_prefix: scan
+  scan_dirs: null
+  output_dir: ${output_dir}
+  experiment_name: ${experiment_name}
+  find_sharpest_image: true
+  sharpness_score: tenengrad
+  sharpness_selection_mode: window
+  sharpness_window_weights: uniform
+  sharpness_gaussian_sigma: null
+  output_paths:
+    output_dir: ${..output_dir}/${..experiment_name}/focus_stack
+    images_subdir: focus_stacked_images
+    masks_subdir: focus_stacked_masks
+    depthmaps_subdir: depthmaps
+    sharpness_scores_subdir: sharpness_scores
+    poses_filename: poses.json
+    intrinsics_filename: intrinsics.json
+  focus_stack_params:
+    focal_stack_size: 7
+    full_resolution_align: true
+    global_align: true
+    align_keep_size: true
+    no_contrast: true
+  low_pass_output: true
+  low_pass_kernel_size: 5
+  hydra:
+    job:
+      chdir: false
+    run:
+      dir: ${output_dir}/${experiment_name}
+    output_subdir: .hydra
+  random_seed: ${random_seed}
+masking:
+  output_dir: ${output_dir}
+  experiment_name: ${experiment_name}
+  random_seed: ${random_seed}
+  input_paths:
+    images_dir: ${...output_dir}/${...experiment_name}/focus_stack/focus_stacked_images
+    valid_regions_dir: ${...output_dir}/${...experiment_name}/focus_stack/focus_stacked_masks
+  output_paths:
+    output_dir: ${..output_dir}/${..experiment_name}/masking
+    masks_subdir: masks
+  bootstrap:
+    bootstrap_stem: scan00
+    focus_mask_border_padding: 8
+    edge_blur_kernel_size: 5
+    canny_threshold1: 25.0
+    canny_threshold2: 150.0
+    point_sampling_scale: 0.9
+    point_prompt_count: 80
+    firstpass_shrink_scale: 0.9
+    points_refine_kernel_size: 9
+    points_refine_dilate_iterations: 1
+  sam2:
+    model_id: facebook/sam2.1-hiera-large
+    device: cuda
+    offload_video_to_cpu: true
+  visualization:
+    overlay_alpha: 0.4
+    overlay_color:
+    - 255
+    - 0
+    - 0
+  hydra:
+    job:
+      chdir: false
+    run:
+      dir: ${output_dir}/${experiment_name}
+    output_subdir: .hydra
+colmap:
+  random_seed: ${random_seed}
+  run:
+    colmap_feat_extract_match: true
+    colmap_reconstruct: true
+  output_dir: ${output_dir}
+  experiment_name: ${experiment_name}
+  feat_extract_match:
+    input_paths:
+      images_dir: ${...output_dir}/${...experiment_name}/focus_stack/focus_stacked_images
+      masks_dir: ${...output_dir}/${...experiment_name}/masking/masks
+    output_paths:
+      output_dir: ${...output_dir}/${...experiment_name}
+      database_filename: database.db
+    extraction:
+      device: cpu
+      camera_model: OPENCV
+      num_threads: 1
+      max_num_features: 8192
+      estimate_affine_shape: true
+    matching:
+      use_gpu: false
+      num_threads: 1
+      guided_matching: true
+  reconstruction:
+    mode: automatic
+    load_prior_poses: true
+    load_prior_intrinsics: true
+    refine_intrinsics: true
+    input_paths:
+      poses_json: ${...output_dir}/${...experiment_name}/poses.json
+      prior_intrinsics_filepath: ${...output_dir}/${...experiment_name}/intrinsics.json
+      images_dir: ${...feat_extract_match.input_paths.images_dir}
+      database_filepath: ${...feat_extract_match.output_paths.output_dir}/${...feat_extract_match.output_paths.database_filename}
+    output_paths:
+      output_dir: ${...output_dir}/${...experiment_name}
+      model_dirname: sparse_model
+    mapping_params:
+      min_focal_length_ratio: 0.1
+      max_focal_length_ratio: 10.0
+      max_extra_param: .inf
+      ba_local_max_num_iterations: 30
+      ba_local_max_refinements: 3
+      ba_global_max_num_iterations: 75
+      ba_use_gpu: true
+      num_threads: 1
+  hydra:
+    job:
+      chdir: false
+    run:
+      dir: ${output_dir}/${experiment_name}
+    output_subdir: .hydra
+gs_3d:
+  random_seed: ${random_seed}
+  strategy:
+    _target_: gsplat.strategy.DefaultStrategy
+    verbose: true
+    prune_opa: 0.1
+    grow_grad2d: 0.0004
+    grow_scale3d: 0.01
+    prune_scale3d: 0.1
+    refine_start_iter: 500
+    refine_stop_iter: 15000
+    reset_every: 3000
+    refine_every: 100
+    absgrad: false
+    revised_opacity: false
+    key_for_gradient: means2d
+  disable_viewer: true
+  ckpt: null
+  compression: null
+  render_traj_path: interp
+  render_traj_trim: 5
+  output_dir: ${output_dir}
+  experiment_name: ${experiment_name}
+  input_paths:
+    model_dir: ${..output_dir}/${..experiment_name}/sparse_model
+    images_dir: ${..output_dir}/${..experiment_name}/masking/masked_images
+    masks_dir: ${..output_dir}/${..experiment_name}/masking/masks
+    valid_region_masks_dir: ${..output_dir}/${..experiment_name}/focus_stack/focus_stacked_masks
+  output_paths:
+    splat_dir: ${..output_dir}/${..experiment_name}/gs_3d
+  data_factor: 1
+  test_every: 8
+  patch_size: null
+  global_scale: 1.0
+  normalize_world_space: true
+  camera_model: pinhole
+  port: 8080
+  batch_size: 1
+  steps_scaler: 1.0
+  max_steps: 30000
+  eval_steps:
+  - 7000
+  - 30000
+  save_steps:
+  - 7000
+  - 30000
+  save_ply: true
+  ply_steps:
+  - 7000
+  - 30000
+  disable_video: true
+  init_type: sfm
+  init_num_pts: 100000
+  init_extent: 3.0
+  sh_degree: 3
+  sh_degree_interval: 1000
+  init_opa: 0.1
+  init_scale: 1.0
+  ssim_lambda: 0.2
+  near_plane: 0.01
+  far_plane: 10000000000.0
+  packed: false
+  sparse_grad: false
+  visible_adam: false
+  antialiased: false
+  random_bkgd: false
+  means_lr: 0.00016
+  scales_lr: 0.005
+  opacities_lr: 0.05
+  quats_lr: 0.001
+  sh0_lr: 0.0025
+  shN_lr: 0.000125
+  opacity_reg: 0.0
+  scale_reg: 0.0
+  pose_opt: false
+  pose_opt_lr: 1.0e-05
+  pose_opt_reg: 1.0e-06
+  pose_noise: 0.0
+  app_opt: false
+  app_embed_dim: 16
+  app_opt_lr: 0.001
+  app_opt_reg: 1.0e-06
+  use_bilateral_grid: false
+  bilateral_grid_shape:
+  - 16
+  - 16
+  - 8
+  depth_loss: false
+  depth_lambda: 0.01
+  bg_alpha_loss: true
+  bg_alpha_lambda: 0.5
+  tb_every: 100
+  tb_save_image: false
+  lpips_net: alex
+  with_ut: false
+  with_eval3d: false
+  use_fused_bilagrid: false
+  hydra:
+    job:
+      chdir: false
+    run:
+      dir: outputs/hydra/${now:%Y-%m-%d_%H-%M-%S}
+    output_subdir: .hydra
+output_dir: outputs/main_paper
+experiment_name: nezuko_20260526_151752
+random_seed: 0
+dataset_dir: data/nezuko_20260526_151752
+run:
+  focus_stack: true
+  masking: true
+  colmap: true
+  gs_3d: true
diff --git a/outputs/main_paper/nezuko_20260526_151752/.hydra/hydra.yaml b/outputs/main_paper/nezuko_20260526_151752/.hydra/hydra.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..de3d39d600045f38a08675e52a47821451cd8807
--- /dev/null
+++ b/outputs/main_paper/nezuko_20260526_151752/.hydra/hydra.yaml
@@ -0,0 +1,162 @@
+hydra:
+  run:
+    dir: ${output_dir}/${experiment_name}
+  sweep:
+    dir: multirun/${now:%Y-%m-%d}/${now:%H-%M-%S}
+    subdir: ${hydra.job.num}
+  launcher:
+    _target_: hydra._internal.core_plugins.basic_launcher.BasicLauncher
+  sweeper:
+    _target_: hydra._internal.core_plugins.basic_sweeper.BasicSweeper
+    max_batch_size: null
+    params: null
+  help:
+    app_name: ${hydra.job.name}
+    header: '${hydra.help.app_name} is powered by Hydra.
+
+      '
+    footer: 'Powered by Hydra (https://hydra.cc)
+
+      Use --hydra-help to view Hydra specific help
+
+      '
+    template: '${hydra.help.header}
+
+      == Configuration groups ==
+
+      Compose your configuration from those groups (group=option)
+
+
+      $APP_CONFIG_GROUPS
+
+
+      == Config ==
+
+      Override anything in the config (foo.bar=value)
+
+
+      $CONFIG
+
+
+      ${hydra.help.footer}
+
+      '
+  hydra_help:
+    template: 'Hydra (${hydra.runtime.version})
+
+      See https://hydra.cc for more info.
+
+
+      == Flags ==
+
+      $FLAGS_HELP
+
+
+      == Configuration groups ==
+
+      Compose your configuration from those groups (For example, append hydra/job_logging=disabled
+      to command line)
+
+
+      $HYDRA_CONFIG_GROUPS
+
+
+      Use ''--cfg hydra'' to Show the Hydra config.
+
+      '
+    hydra_help: ???
+  hydra_logging:
+    version: 1
+    formatters:
+      simple:
+        format: '[%(asctime)s][HYDRA] %(message)s'
+    handlers:
+      console:
+        class: logging.StreamHandler
+        formatter: simple
+        stream: ext://sys.stdout
+    root:
+      level: INFO
+      handlers:
+      - console
+    loggers:
+      logging_example:
+        level: DEBUG
+    disable_existing_loggers: false
+  job_logging:
+    version: 1
+    formatters:
+      simple:
+        format: '[%(asctime)s][%(name)s][%(levelname)s] - %(message)s'
+    handlers:
+      console:
+        class: logging.StreamHandler
+        formatter: simple
+        stream: ext://sys.stdout
+      file:
+        class: logging.FileHandler
+        formatter: simple
+        filename: ${hydra.runtime.output_dir}/${hydra.job.name}.log
+    root:
+      level: INFO
+      handlers:
+      - console
+      - file
+    disable_existing_loggers: false
+  env: {}
+  mode: RUN
+  searchpath: []
+  callbacks: {}
+  output_subdir: .hydra
+  overrides:
+    hydra:
+    - hydra.mode=RUN
+    task:
+    - +experiment=main_paper
+    - experiment_name=nezuko_20260526_151752
+    - dataset_dir=data/nezuko_20260526_151752
+  job:
+    name: run_pipeline
+    chdir: false
+    override_dirname: +experiment=main_paper,dataset_dir=data/nezuko_20260526_151752,experiment_name=nezuko_20260526_151752
+    id: ???
+    num: ???
+    config_name: pipeline
+    env_set: {}
+    env_copy: []
+    config:
+      override_dirname:
+        kv_sep: '='
+        item_sep: ','
+        exclude_keys: []
+  runtime:
+    version: 1.3.2
+    version_base: '1.3'
+    cwd: /storage/scratch1/8/razarcon3/Microscopic-3D-Reconstruction/reconstruction
+    config_sources:
+    - path: hydra.conf
+      schema: pkg
+      provider: hydra
+    - path: /storage/scratch1/8/razarcon3/Microscopic-3D-Reconstruction/reconstruction/configs
+      schema: file
+      provider: main
+    - path: ''
+      schema: structured
+      provider: schema
+    output_dir: /storage/scratch1/8/razarcon3/Microscopic-3D-Reconstruction/reconstruction/outputs/main_paper/nezuko_20260526_151752
+    choices:
+      experiment: main_paper
+      gs_3d: default
+      colmap: default
+      masking: default
+      focus_stack: default
+      hydra/env: default
+      hydra/callbacks: null
+      hydra/job_logging: default
+      hydra/hydra_logging: default
+      hydra/hydra_help: default
+      hydra/help: default
+      hydra/sweeper: basic
+      hydra/launcher: basic
+      hydra/output: default
+  verbose: false
diff --git a/outputs/main_paper/nezuko_20260526_151752/.hydra/overrides.yaml b/outputs/main_paper/nezuko_20260526_151752/.hydra/overrides.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..7c294b45970d4796507bc287706d7963432bbc01
--- /dev/null
+++ b/outputs/main_paper/nezuko_20260526_151752/.hydra/overrides.yaml
@@ -0,0 +1,3 @@
+- +experiment=main_paper
+- experiment_name=nezuko_20260526_151752
+- dataset_dir=data/nezuko_20260526_151752
diff --git a/outputs/main_paper/nezuko_20260526_151752/database.db b/outputs/main_paper/nezuko_20260526_151752/database.db
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+version https://git-lfs.github.com/spec/v1
+oid sha256:9869a20e14b062272097309dc25192eb62f31e7c1ae8c69032ac49e8ebe11fcf
+size 130490368
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diff --git a/outputs/main_paper/nezuko_20260526_151752/run_pipeline.log b/outputs/main_paper/nezuko_20260526_151752/run_pipeline.log
new file mode 100644
index 0000000000000000000000000000000000000000..4fd0f13696d2460a46120926e08b797450af0616
--- /dev/null
+++ b/outputs/main_paper/nezuko_20260526_151752/run_pipeline.log
@@ -0,0 +1,6 @@
+[2026-05-26 23:45:06,819][httpx][INFO] - HTTP Request: HEAD https://huggingface.co/facebook/sam2.1-hiera-large/resolve/main/sam2.1_hiera_large.pt "HTTP/1.1 302 Found"
+[2026-05-26 23:45:10,080][httpx][INFO] - HTTP Request: HEAD https://huggingface.co/facebook/sam2.1-hiera-large/resolve/main/sam2.1_hiera_large.pt "HTTP/1.1 302 Found"
+[2026-05-26 23:45:10,081][huggingface_hub.utils._http][WARNING] - Warning: You are sending unauthenticated requests to the HF Hub. Please set a HF_TOKEN to enable higher rate limits and faster downloads.
+[2026-05-26 23:45:11,520][root][INFO] - For numpy array image, we assume (HxWxC) format
+[2026-05-26 23:45:12,018][root][INFO] - Computing image embeddings for the provided image...
+[2026-05-26 23:45:13,256][root][INFO] - Image embeddings computed.
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new file mode 100644
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new file mode 100644
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diff --git a/outputs/main_paper/nezuko_20260526_151752/sparse_model/frames.bin b/outputs/main_paper/nezuko_20260526_151752/sparse_model/frames.bin
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+version https://git-lfs.github.com/spec/v1
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+++ b/outputs/main_paper/nezuko_20260526_151752/sparse_model/points3D.bin
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
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+size 2137778
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@@ -0,0 +1,3 @@
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diff --git a/outputs/main_paper/pinecone_20260513_205949/.hydra/config.yaml b/outputs/main_paper/pinecone_20260513_205949/.hydra/config.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..778b40ed7a81c4cd77d6077f78f22bc43da6ed63
--- /dev/null
+++ b/outputs/main_paper/pinecone_20260513_205949/.hydra/config.yaml
@@ -0,0 +1,235 @@
+focus_stack:
+  dataset_dir: ${dataset_dir}
+  scan_prefix: scan
+  scan_dirs: null
+  output_dir: ${output_dir}
+  experiment_name: ${experiment_name}
+  find_sharpest_image: true
+  sharpness_score: tenengrad
+  sharpness_selection_mode: window
+  sharpness_window_weights: uniform
+  sharpness_gaussian_sigma: null
+  output_paths:
+    output_dir: ${..output_dir}/${..experiment_name}/focus_stack
+    images_subdir: focus_stacked_images
+    masks_subdir: focus_stacked_masks
+    depthmaps_subdir: depthmaps
+    sharpness_scores_subdir: sharpness_scores
+    poses_filename: poses.json
+    intrinsics_filename: intrinsics.json
+  focus_stack_params:
+    focal_stack_size: 7
+    full_resolution_align: true
+    global_align: true
+    align_keep_size: true
+    no_contrast: true
+  low_pass_output: true
+  low_pass_kernel_size: 5
+  hydra:
+    job:
+      chdir: false
+    run:
+      dir: ${output_dir}/${experiment_name}
+    output_subdir: .hydra
+  random_seed: ${random_seed}
+masking:
+  output_dir: ${output_dir}
+  experiment_name: ${experiment_name}
+  random_seed: ${random_seed}
+  input_paths:
+    images_dir: ${...output_dir}/${...experiment_name}/focus_stack/focus_stacked_images
+    valid_regions_dir: ${...output_dir}/${...experiment_name}/focus_stack/focus_stacked_masks
+  output_paths:
+    output_dir: ${..output_dir}/${..experiment_name}/masking
+    masks_subdir: masks
+  bootstrap:
+    bootstrap_stem: scan00
+    focus_mask_border_padding: 8
+    edge_blur_kernel_size: 5
+    canny_threshold1: 25.0
+    canny_threshold2: 150.0
+    point_sampling_scale: 0.9
+    point_prompt_count: 80
+    firstpass_shrink_scale: 0.9
+    points_refine_kernel_size: 9
+    points_refine_dilate_iterations: 1
+  sam2:
+    model_id: facebook/sam2.1-hiera-large
+    device: cuda
+    offload_video_to_cpu: true
+  visualization:
+    overlay_alpha: 0.4
+    overlay_color:
+    - 255
+    - 0
+    - 0
+  hydra:
+    job:
+      chdir: false
+    run:
+      dir: ${output_dir}/${experiment_name}
+    output_subdir: .hydra
+colmap:
+  random_seed: ${random_seed}
+  run:
+    colmap_feat_extract_match: true
+    colmap_reconstruct: true
+  output_dir: ${output_dir}
+  experiment_name: ${experiment_name}
+  feat_extract_match:
+    input_paths:
+      images_dir: ${...output_dir}/${...experiment_name}/focus_stack/focus_stacked_images
+      masks_dir: ${...output_dir}/${...experiment_name}/masking/masks
+    output_paths:
+      output_dir: ${...output_dir}/${...experiment_name}
+      database_filename: database.db
+    extraction:
+      device: cpu
+      camera_model: OPENCV
+      num_threads: 1
+      max_num_features: 8192
+      estimate_affine_shape: true
+    matching:
+      use_gpu: false
+      num_threads: 1
+      guided_matching: true
+  reconstruction:
+    mode: automatic
+    load_prior_poses: true
+    load_prior_intrinsics: true
+    refine_intrinsics: true
+    input_paths:
+      poses_json: ${...output_dir}/${...experiment_name}/poses.json
+      prior_intrinsics_filepath: ${...output_dir}/${...experiment_name}/intrinsics.json
+      images_dir: ${...feat_extract_match.input_paths.images_dir}
+      database_filepath: ${...feat_extract_match.output_paths.output_dir}/${...feat_extract_match.output_paths.database_filename}
+    output_paths:
+      output_dir: ${...output_dir}/${...experiment_name}
+      model_dirname: sparse_model
+    mapping_params:
+      min_focal_length_ratio: 0.1
+      max_focal_length_ratio: 10.0
+      max_extra_param: .inf
+      ba_local_max_num_iterations: 30
+      ba_local_max_refinements: 3
+      ba_global_max_num_iterations: 75
+      ba_use_gpu: true
+      num_threads: 1
+  hydra:
+    job:
+      chdir: false
+    run:
+      dir: ${output_dir}/${experiment_name}
+    output_subdir: .hydra
+gs_3d:
+  random_seed: ${random_seed}
+  strategy:
+    _target_: gsplat.strategy.DefaultStrategy
+    verbose: true
+    prune_opa: 0.1
+    grow_grad2d: 0.0004
+    grow_scale3d: 0.01
+    prune_scale3d: 0.1
+    refine_start_iter: 500
+    refine_stop_iter: 15000
+    reset_every: 3000
+    refine_every: 100
+    absgrad: false
+    revised_opacity: false
+    key_for_gradient: means2d
+  disable_viewer: true
+  ckpt: null
+  compression: null
+  render_traj_path: interp
+  render_traj_trim: 5
+  output_dir: ${output_dir}
+  experiment_name: ${experiment_name}
+  input_paths:
+    model_dir: ${..output_dir}/${..experiment_name}/sparse_model
+    images_dir: ${..output_dir}/${..experiment_name}/masking/masked_images
+    masks_dir: ${..output_dir}/${..experiment_name}/masking/masks
+    valid_region_masks_dir: ${..output_dir}/${..experiment_name}/focus_stack/focus_stacked_masks
+  output_paths:
+    splat_dir: ${..output_dir}/${..experiment_name}/gs_3d
+  data_factor: 1
+  test_every: 8
+  patch_size: null
+  global_scale: 1.0
+  normalize_world_space: true
+  camera_model: pinhole
+  port: 8080
+  batch_size: 1
+  steps_scaler: 1.0
+  max_steps: 30000
+  eval_steps:
+  - 7000
+  - 30000
+  save_steps:
+  - 7000
+  - 30000
+  save_ply: true
+  ply_steps:
+  - 7000
+  - 30000
+  disable_video: true
+  init_type: sfm
+  init_num_pts: 100000
+  init_extent: 3.0
+  sh_degree: 3
+  sh_degree_interval: 1000
+  init_opa: 0.1
+  init_scale: 1.0
+  ssim_lambda: 0.2
+  near_plane: 0.01
+  far_plane: 10000000000.0
+  packed: false
+  sparse_grad: false
+  visible_adam: false
+  antialiased: false
+  random_bkgd: false
+  means_lr: 0.00016
+  scales_lr: 0.005
+  opacities_lr: 0.05
+  quats_lr: 0.001
+  sh0_lr: 0.0025
+  shN_lr: 0.000125
+  opacity_reg: 0.0
+  scale_reg: 0.0
+  pose_opt: false
+  pose_opt_lr: 1.0e-05
+  pose_opt_reg: 1.0e-06
+  pose_noise: 0.0
+  app_opt: false
+  app_embed_dim: 16
+  app_opt_lr: 0.001
+  app_opt_reg: 1.0e-06
+  use_bilateral_grid: false
+  bilateral_grid_shape:
+  - 16
+  - 16
+  - 8
+  depth_loss: false
+  depth_lambda: 0.01
+  bg_alpha_loss: true
+  bg_alpha_lambda: 0.5
+  tb_every: 100
+  tb_save_image: false
+  lpips_net: alex
+  with_ut: false
+  with_eval3d: false
+  use_fused_bilagrid: false
+  hydra:
+    job:
+      chdir: false
+    run:
+      dir: outputs/hydra/${now:%Y-%m-%d_%H-%M-%S}
+    output_subdir: .hydra
+output_dir: outputs/main_paper
+experiment_name: pinecone_20260513_205949
+random_seed: 0
+dataset_dir: data/pinecone_20260513_205949
+run:
+  focus_stack: true
+  masking: true
+  colmap: true
+  gs_3d: true
diff --git a/outputs/main_paper/pinecone_20260513_205949/.hydra/hydra.yaml b/outputs/main_paper/pinecone_20260513_205949/.hydra/hydra.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..fb47e3bb2c21d08b1d909c69619798da675d83ba
--- /dev/null
+++ b/outputs/main_paper/pinecone_20260513_205949/.hydra/hydra.yaml
@@ -0,0 +1,162 @@
+hydra:
+  run:
+    dir: ${output_dir}/${experiment_name}
+  sweep:
+    dir: multirun/${now:%Y-%m-%d}/${now:%H-%M-%S}
+    subdir: ${hydra.job.num}
+  launcher:
+    _target_: hydra._internal.core_plugins.basic_launcher.BasicLauncher
+  sweeper:
+    _target_: hydra._internal.core_plugins.basic_sweeper.BasicSweeper
+    max_batch_size: null
+    params: null
+  help:
+    app_name: ${hydra.job.name}
+    header: '${hydra.help.app_name} is powered by Hydra.
+
+      '
+    footer: 'Powered by Hydra (https://hydra.cc)
+
+      Use --hydra-help to view Hydra specific help
+
+      '
+    template: '${hydra.help.header}
+
+      == Configuration groups ==
+
+      Compose your configuration from those groups (group=option)
+
+
+      $APP_CONFIG_GROUPS
+
+
+      == Config ==
+
+      Override anything in the config (foo.bar=value)
+
+
+      $CONFIG
+
+
+      ${hydra.help.footer}
+
+      '
+  hydra_help:
+    template: 'Hydra (${hydra.runtime.version})
+
+      See https://hydra.cc for more info.
+
+
+      == Flags ==
+
+      $FLAGS_HELP
+
+
+      == Configuration groups ==
+
+      Compose your configuration from those groups (For example, append hydra/job_logging=disabled
+      to command line)
+
+
+      $HYDRA_CONFIG_GROUPS
+
+
+      Use ''--cfg hydra'' to Show the Hydra config.
+
+      '
+    hydra_help: ???
+  hydra_logging:
+    version: 1
+    formatters:
+      simple:
+        format: '[%(asctime)s][HYDRA] %(message)s'
+    handlers:
+      console:
+        class: logging.StreamHandler
+        formatter: simple
+        stream: ext://sys.stdout
+    root:
+      level: INFO
+      handlers:
+      - console
+    loggers:
+      logging_example:
+        level: DEBUG
+    disable_existing_loggers: false
+  job_logging:
+    version: 1
+    formatters:
+      simple:
+        format: '[%(asctime)s][%(name)s][%(levelname)s] - %(message)s'
+    handlers:
+      console:
+        class: logging.StreamHandler
+        formatter: simple
+        stream: ext://sys.stdout
+      file:
+        class: logging.FileHandler
+        formatter: simple
+        filename: ${hydra.runtime.output_dir}/${hydra.job.name}.log
+    root:
+      level: INFO
+      handlers:
+      - console
+      - file
+    disable_existing_loggers: false
+  env: {}
+  mode: RUN
+  searchpath: []
+  callbacks: {}
+  output_subdir: .hydra
+  overrides:
+    hydra:
+    - hydra.mode=RUN
+    task:
+    - +experiment=main_paper
+    - experiment_name=pinecone_20260513_205949
+    - dataset_dir=data/pinecone_20260513_205949
+  job:
+    name: run_pipeline
+    chdir: false
+    override_dirname: +experiment=main_paper,dataset_dir=data/pinecone_20260513_205949,experiment_name=pinecone_20260513_205949
+    id: ???
+    num: ???
+    config_name: pipeline
+    env_set: {}
+    env_copy: []
+    config:
+      override_dirname:
+        kv_sep: '='
+        item_sep: ','
+        exclude_keys: []
+  runtime:
+    version: 1.3.2
+    version_base: '1.3'
+    cwd: /storage/scratch1/8/razarcon3/Microscopic-3D-Reconstruction/reconstruction
+    config_sources:
+    - path: hydra.conf
+      schema: pkg
+      provider: hydra
+    - path: /storage/scratch1/8/razarcon3/Microscopic-3D-Reconstruction/reconstruction/configs
+      schema: file
+      provider: main
+    - path: ''
+      schema: structured
+      provider: schema
+    output_dir: /storage/scratch1/8/razarcon3/Microscopic-3D-Reconstruction/reconstruction/outputs/main_paper/pinecone_20260513_205949
+    choices:
+      experiment: main_paper
+      gs_3d: default
+      colmap: default
+      masking: default
+      focus_stack: default
+      hydra/env: default
+      hydra/callbacks: null
+      hydra/job_logging: default
+      hydra/hydra_logging: default
+      hydra/hydra_help: default
+      hydra/help: default
+      hydra/sweeper: basic
+      hydra/launcher: basic
+      hydra/output: default
+  verbose: false
diff --git a/outputs/main_paper/pinecone_20260513_205949/.hydra/overrides.yaml b/outputs/main_paper/pinecone_20260513_205949/.hydra/overrides.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..36e9acfa027d42cdd583ddb7bd6ba6b88ca86b1a
--- /dev/null
+++ b/outputs/main_paper/pinecone_20260513_205949/.hydra/overrides.yaml
@@ -0,0 +1,3 @@
+- +experiment=main_paper
+- experiment_name=pinecone_20260513_205949
+- dataset_dir=data/pinecone_20260513_205949
diff --git a/outputs/main_paper/pinecone_20260513_205949/database.db b/outputs/main_paper/pinecone_20260513_205949/database.db
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--- /dev/null
+++ b/outputs/main_paper/pinecone_20260513_205949/database.db
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:8ace9bddd1a3dca691f35f0e44b6266b26915a4858a231d9084804dc08cbfde8
+size 137183232
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+version https://git-lfs.github.com/spec/v1
+oid sha256:5203b3d2ca6b8f2599c88e459af906db156d560ad9c36f70975ff478b6626275
+size 224378
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+version https://git-lfs.github.com/spec/v1
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+version https://git-lfs.github.com/spec/v1
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+version https://git-lfs.github.com/spec/v1
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+version https://git-lfs.github.com/spec/v1
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diff --git a/outputs/main_paper/pinecone_20260513_205949/run_pipeline.log b/outputs/main_paper/pinecone_20260513_205949/run_pipeline.log
new file mode 100644
index 0000000000000000000000000000000000000000..6d5b7a22e4cc7221eb5fe05b9653669fb56d4ef2
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+++ b/outputs/main_paper/pinecone_20260513_205949/run_pipeline.log
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+[2026-05-27 00:00:26,395][httpx][INFO] - HTTP Request: HEAD https://huggingface.co/facebook/sam2.1-hiera-large/resolve/main/sam2.1_hiera_large.pt "HTTP/1.1 302 Found"
+[2026-05-27 00:00:37,132][httpx][INFO] - HTTP Request: HEAD https://huggingface.co/facebook/sam2.1-hiera-large/resolve/main/sam2.1_hiera_large.pt "HTTP/1.1 302 Found"
+[2026-05-27 00:00:38,617][root][INFO] - For numpy array image, we assume (HxWxC) format
+[2026-05-27 00:00:40,167][root][INFO] - Computing image embeddings for the provided image...
+[2026-05-27 00:00:54,349][root][INFO] - Image embeddings computed.
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index 0000000000000000000000000000000000000000..f5a80293086199eaafc48e225055030960a80714
--- /dev/null
+++ b/outputs/main_paper/pinecone_20260513_205949/sparse_model/rigs.txt
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:8472bec629acf5f8204018b1b34b699709d2b4d203898facf500c0edec35ca68
+size 218
diff --git a/outputs/main_paper/pinecone_20260513_205949/sparse_model/sparse_pointcloud.ply b/outputs/main_paper/pinecone_20260513_205949/sparse_model/sparse_pointcloud.ply
new file mode 100644
index 0000000000000000000000000000000000000000..99a3c6c630e47f69a17c2480685258b0f0990d5b
--- /dev/null
+++ b/outputs/main_paper/pinecone_20260513_205949/sparse_model/sparse_pointcloud.ply
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:3d92bc355c86894a2d4794b7b151b4014529a20bfbeb990df83fc9753bf10c3c
+size 469634
diff --git a/outputs/main_paper/red_circuit_20260518_153017/.hydra/config.yaml b/outputs/main_paper/red_circuit_20260518_153017/.hydra/config.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..156716927c194b0511acb4b521c277ea3e2b32d9
--- /dev/null
+++ b/outputs/main_paper/red_circuit_20260518_153017/.hydra/config.yaml
@@ -0,0 +1,235 @@
+focus_stack:
+  dataset_dir: ${dataset_dir}
+  scan_prefix: scan
+  scan_dirs: null
+  output_dir: ${output_dir}
+  experiment_name: ${experiment_name}
+  find_sharpest_image: true
+  sharpness_score: tenengrad
+  sharpness_selection_mode: window
+  sharpness_window_weights: uniform
+  sharpness_gaussian_sigma: null
+  output_paths:
+    output_dir: ${..output_dir}/${..experiment_name}/focus_stack
+    images_subdir: focus_stacked_images
+    masks_subdir: focus_stacked_masks
+    depthmaps_subdir: depthmaps
+    sharpness_scores_subdir: sharpness_scores
+    poses_filename: poses.json
+    intrinsics_filename: intrinsics.json
+  focus_stack_params:
+    focal_stack_size: 7
+    full_resolution_align: true
+    global_align: true
+    align_keep_size: true
+    no_contrast: true
+  low_pass_output: true
+  low_pass_kernel_size: 5
+  hydra:
+    job:
+      chdir: false
+    run:
+      dir: ${output_dir}/${experiment_name}
+    output_subdir: .hydra
+  random_seed: ${random_seed}
+masking:
+  output_dir: ${output_dir}
+  experiment_name: ${experiment_name}
+  random_seed: ${random_seed}
+  input_paths:
+    images_dir: ${...output_dir}/${...experiment_name}/focus_stack/focus_stacked_images
+    valid_regions_dir: ${...output_dir}/${...experiment_name}/focus_stack/focus_stacked_masks
+  output_paths:
+    output_dir: ${..output_dir}/${..experiment_name}/masking
+    masks_subdir: masks
+  bootstrap:
+    bootstrap_stem: scan00
+    focus_mask_border_padding: 8
+    edge_blur_kernel_size: 5
+    canny_threshold1: 25.0
+    canny_threshold2: 150.0
+    point_sampling_scale: 0.9
+    point_prompt_count: 80
+    firstpass_shrink_scale: 0.9
+    points_refine_kernel_size: 9
+    points_refine_dilate_iterations: 1
+  sam2:
+    model_id: facebook/sam2.1-hiera-large
+    device: cuda
+    offload_video_to_cpu: true
+  visualization:
+    overlay_alpha: 0.4
+    overlay_color:
+    - 255
+    - 0
+    - 0
+  hydra:
+    job:
+      chdir: false
+    run:
+      dir: ${output_dir}/${experiment_name}
+    output_subdir: .hydra
+colmap:
+  random_seed: ${random_seed}
+  run:
+    colmap_feat_extract_match: true
+    colmap_reconstruct: true
+  output_dir: ${output_dir}
+  experiment_name: ${experiment_name}
+  feat_extract_match:
+    input_paths:
+      images_dir: ${...output_dir}/${...experiment_name}/focus_stack/focus_stacked_images
+      masks_dir: ${...output_dir}/${...experiment_name}/masking/masks
+    output_paths:
+      output_dir: ${...output_dir}/${...experiment_name}
+      database_filename: database.db
+    extraction:
+      device: cpu
+      camera_model: OPENCV
+      num_threads: 1
+      max_num_features: 8192
+      estimate_affine_shape: true
+    matching:
+      use_gpu: false
+      num_threads: 1
+      guided_matching: true
+  reconstruction:
+    mode: automatic
+    load_prior_poses: true
+    load_prior_intrinsics: true
+    refine_intrinsics: true
+    input_paths:
+      poses_json: ${...output_dir}/${...experiment_name}/poses.json
+      prior_intrinsics_filepath: ${...output_dir}/${...experiment_name}/intrinsics.json
+      images_dir: ${...feat_extract_match.input_paths.images_dir}
+      database_filepath: ${...feat_extract_match.output_paths.output_dir}/${...feat_extract_match.output_paths.database_filename}
+    output_paths:
+      output_dir: ${...output_dir}/${...experiment_name}
+      model_dirname: sparse_model
+    mapping_params:
+      min_focal_length_ratio: 0.1
+      max_focal_length_ratio: 10.0
+      max_extra_param: .inf
+      ba_local_max_num_iterations: 30
+      ba_local_max_refinements: 3
+      ba_global_max_num_iterations: 75
+      ba_use_gpu: true
+      num_threads: 1
+  hydra:
+    job:
+      chdir: false
+    run:
+      dir: ${output_dir}/${experiment_name}
+    output_subdir: .hydra
+gs_3d:
+  random_seed: ${random_seed}
+  strategy:
+    _target_: gsplat.strategy.DefaultStrategy
+    verbose: true
+    prune_opa: 0.1
+    grow_grad2d: 0.0004
+    grow_scale3d: 0.01
+    prune_scale3d: 0.1
+    refine_start_iter: 500
+    refine_stop_iter: 15000
+    reset_every: 3000
+    refine_every: 100
+    absgrad: false
+    revised_opacity: false
+    key_for_gradient: means2d
+  disable_viewer: true
+  ckpt: null
+  compression: null
+  render_traj_path: interp
+  render_traj_trim: 5
+  output_dir: ${output_dir}
+  experiment_name: ${experiment_name}
+  input_paths:
+    model_dir: ${..output_dir}/${..experiment_name}/sparse_model
+    images_dir: ${..output_dir}/${..experiment_name}/masking/masked_images
+    masks_dir: ${..output_dir}/${..experiment_name}/masking/masks
+    valid_region_masks_dir: ${..output_dir}/${..experiment_name}/focus_stack/focus_stacked_masks
+  output_paths:
+    splat_dir: ${..output_dir}/${..experiment_name}/gs_3d
+  data_factor: 1
+  test_every: 8
+  patch_size: null
+  global_scale: 1.0
+  normalize_world_space: true
+  camera_model: pinhole
+  port: 8080
+  batch_size: 1
+  steps_scaler: 1.0
+  max_steps: 30000
+  eval_steps:
+  - 7000
+  - 30000
+  save_steps:
+  - 7000
+  - 30000
+  save_ply: true
+  ply_steps:
+  - 7000
+  - 30000
+  disable_video: true
+  init_type: sfm
+  init_num_pts: 100000
+  init_extent: 3.0
+  sh_degree: 3
+  sh_degree_interval: 1000
+  init_opa: 0.1
+  init_scale: 1.0
+  ssim_lambda: 0.2
+  near_plane: 0.01
+  far_plane: 10000000000.0
+  packed: false
+  sparse_grad: false
+  visible_adam: false
+  antialiased: false
+  random_bkgd: false
+  means_lr: 0.00016
+  scales_lr: 0.005
+  opacities_lr: 0.05
+  quats_lr: 0.001
+  sh0_lr: 0.0025
+  shN_lr: 0.000125
+  opacity_reg: 0.0
+  scale_reg: 0.0
+  pose_opt: false
+  pose_opt_lr: 1.0e-05
+  pose_opt_reg: 1.0e-06
+  pose_noise: 0.0
+  app_opt: false
+  app_embed_dim: 16
+  app_opt_lr: 0.001
+  app_opt_reg: 1.0e-06
+  use_bilateral_grid: false
+  bilateral_grid_shape:
+  - 16
+  - 16
+  - 8
+  depth_loss: false
+  depth_lambda: 0.01
+  bg_alpha_loss: true
+  bg_alpha_lambda: 0.5
+  tb_every: 100
+  tb_save_image: false
+  lpips_net: alex
+  with_ut: false
+  with_eval3d: false
+  use_fused_bilagrid: false
+  hydra:
+    job:
+      chdir: false
+    run:
+      dir: outputs/hydra/${now:%Y-%m-%d_%H-%M-%S}
+    output_subdir: .hydra
+output_dir: outputs/main_paper
+experiment_name: red_circuit_20260518_153017
+random_seed: 0
+dataset_dir: data/red_circuit_20260518_153017
+run:
+  focus_stack: true
+  masking: true
+  colmap: true
+  gs_3d: true
diff --git a/outputs/main_paper/red_circuit_20260518_153017/.hydra/hydra.yaml b/outputs/main_paper/red_circuit_20260518_153017/.hydra/hydra.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..0190a1b120b68fdb911ee963bfdbd6c7effb11c9
--- /dev/null
+++ b/outputs/main_paper/red_circuit_20260518_153017/.hydra/hydra.yaml
@@ -0,0 +1,162 @@
+hydra:
+  run:
+    dir: ${output_dir}/${experiment_name}
+  sweep:
+    dir: multirun/${now:%Y-%m-%d}/${now:%H-%M-%S}
+    subdir: ${hydra.job.num}
+  launcher:
+    _target_: hydra._internal.core_plugins.basic_launcher.BasicLauncher
+  sweeper:
+    _target_: hydra._internal.core_plugins.basic_sweeper.BasicSweeper
+    max_batch_size: null
+    params: null
+  help:
+    app_name: ${hydra.job.name}
+    header: '${hydra.help.app_name} is powered by Hydra.
+
+      '
+    footer: 'Powered by Hydra (https://hydra.cc)
+
+      Use --hydra-help to view Hydra specific help
+
+      '
+    template: '${hydra.help.header}
+
+      == Configuration groups ==
+
+      Compose your configuration from those groups (group=option)
+
+
+      $APP_CONFIG_GROUPS
+
+
+      == Config ==
+
+      Override anything in the config (foo.bar=value)
+
+
+      $CONFIG
+
+
+      ${hydra.help.footer}
+
+      '
+  hydra_help:
+    template: 'Hydra (${hydra.runtime.version})
+
+      See https://hydra.cc for more info.
+
+
+      == Flags ==
+
+      $FLAGS_HELP
+
+
+      == Configuration groups ==
+
+      Compose your configuration from those groups (For example, append hydra/job_logging=disabled
+      to command line)
+
+
+      $HYDRA_CONFIG_GROUPS
+
+
+      Use ''--cfg hydra'' to Show the Hydra config.
+
+      '
+    hydra_help: ???
+  hydra_logging:
+    version: 1
+    formatters:
+      simple:
+        format: '[%(asctime)s][HYDRA] %(message)s'
+    handlers:
+      console:
+        class: logging.StreamHandler
+        formatter: simple
+        stream: ext://sys.stdout
+    root:
+      level: INFO
+      handlers:
+      - console
+    loggers:
+      logging_example:
+        level: DEBUG
+    disable_existing_loggers: false
+  job_logging:
+    version: 1
+    formatters:
+      simple:
+        format: '[%(asctime)s][%(name)s][%(levelname)s] - %(message)s'
+    handlers:
+      console:
+        class: logging.StreamHandler
+        formatter: simple
+        stream: ext://sys.stdout
+      file:
+        class: logging.FileHandler
+        formatter: simple
+        filename: ${hydra.runtime.output_dir}/${hydra.job.name}.log
+    root:
+      level: INFO
+      handlers:
+      - console
+      - file
+    disable_existing_loggers: false
+  env: {}
+  mode: RUN
+  searchpath: []
+  callbacks: {}
+  output_subdir: .hydra
+  overrides:
+    hydra:
+    - hydra.mode=RUN
+    task:
+    - +experiment=main_paper
+    - experiment_name=red_circuit_20260518_153017
+    - dataset_dir=data/red_circuit_20260518_153017
+  job:
+    name: run_pipeline
+    chdir: false
+    override_dirname: +experiment=main_paper,dataset_dir=data/red_circuit_20260518_153017,experiment_name=red_circuit_20260518_153017
+    id: ???
+    num: ???
+    config_name: pipeline
+    env_set: {}
+    env_copy: []
+    config:
+      override_dirname:
+        kv_sep: '='
+        item_sep: ','
+        exclude_keys: []
+  runtime:
+    version: 1.3.2
+    version_base: '1.3'
+    cwd: /storage/scratch1/8/razarcon3/Microscopic-3D-Reconstruction/reconstruction
+    config_sources:
+    - path: hydra.conf
+      schema: pkg
+      provider: hydra
+    - path: /storage/scratch1/8/razarcon3/Microscopic-3D-Reconstruction/reconstruction/configs
+      schema: file
+      provider: main
+    - path: ''
+      schema: structured
+      provider: schema
+    output_dir: /storage/scratch1/8/razarcon3/Microscopic-3D-Reconstruction/reconstruction/outputs/main_paper/red_circuit_20260518_153017
+    choices:
+      experiment: main_paper
+      gs_3d: default
+      colmap: default
+      masking: default
+      focus_stack: default
+      hydra/env: default
+      hydra/callbacks: null
+      hydra/job_logging: default
+      hydra/hydra_logging: default
+      hydra/hydra_help: default
+      hydra/help: default
+      hydra/sweeper: basic
+      hydra/launcher: basic
+      hydra/output: default
+  verbose: false
diff --git a/outputs/main_paper/red_circuit_20260518_153017/.hydra/overrides.yaml b/outputs/main_paper/red_circuit_20260518_153017/.hydra/overrides.yaml
new file mode 100644
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--- /dev/null
+++ b/outputs/main_paper/red_circuit_20260518_153017/.hydra/overrides.yaml
@@ -0,0 +1,3 @@
+- +experiment=main_paper
+- experiment_name=red_circuit_20260518_153017
+- dataset_dir=data/red_circuit_20260518_153017
diff --git a/outputs/main_paper/red_circuit_20260518_153017/database.db b/outputs/main_paper/red_circuit_20260518_153017/database.db
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+++ b/outputs/main_paper/red_circuit_20260518_153017/database.db
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+version https://git-lfs.github.com/spec/v1
+oid sha256:ba236c1f033578d7137d87081c390921db2fcc4514332d4816c3d9eeb94be81b
+size 149757952
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+    ]
+  ],
+  "scan134.png": [
+    [
+      -0.6597217333729926,
+      0.5221557306651183,
+      0.5404818474740019,
+      0.7551534103361971
+    ],
+    [
+      -0.6407849239835502,
+      -0.015093144465457937,
+      -0.7675720670956837,
+      0.0755108892374278
+    ],
+    [
+      -0.39263458292759934,
+      -0.8527165941411722,
+      0.34454679561062374,
+      0.35898205678361994
+    ],
+    [
+      0.0,
+      0.0,
+      0.0,
+      1.0
+    ]
+  ]
+}
\ No newline at end of file
diff --git a/outputs/main_paper/red_circuit_20260518_153017/run_pipeline.log b/outputs/main_paper/red_circuit_20260518_153017/run_pipeline.log
new file mode 100644
index 0000000000000000000000000000000000000000..3c096eae37e3180f9b767246499a4c1f77b1a558
--- /dev/null
+++ b/outputs/main_paper/red_circuit_20260518_153017/run_pipeline.log
@@ -0,0 +1,5 @@
+[2026-05-27 00:37:24,712][httpx][INFO] - HTTP Request: HEAD https://huggingface.co/facebook/sam2.1-hiera-large/resolve/main/sam2.1_hiera_large.pt "HTTP/1.1 302 Found"
+[2026-05-27 00:37:34,453][httpx][INFO] - HTTP Request: HEAD https://huggingface.co/facebook/sam2.1-hiera-large/resolve/main/sam2.1_hiera_large.pt "HTTP/1.1 302 Found"
+[2026-05-27 00:37:35,930][root][INFO] - For numpy array image, we assume (HxWxC) format
+[2026-05-27 00:37:36,031][root][INFO] - Computing image embeddings for the provided image...
+[2026-05-27 00:37:37,862][root][INFO] - Image embeddings computed.
diff --git a/outputs/main_paper/red_circuit_20260518_153017/sparse_model/cameras.bin b/outputs/main_paper/red_circuit_20260518_153017/sparse_model/cameras.bin
new file mode 100644
index 0000000000000000000000000000000000000000..aa8ab6adc13eaf0011a028154d069e76cd9b79b4
--- /dev/null
+++ b/outputs/main_paper/red_circuit_20260518_153017/sparse_model/cameras.bin
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:278bf872d55cd7569e814dffe3fae14a7acbfd090473f9a67a6172dcaa098f22
+size 96
diff --git a/outputs/main_paper/red_circuit_20260518_153017/sparse_model/cameras.txt b/outputs/main_paper/red_circuit_20260518_153017/sparse_model/cameras.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cb95b2d3e971a1a748d25925b5bbc8eb90e3bca1
--- /dev/null
+++ b/outputs/main_paper/red_circuit_20260518_153017/sparse_model/cameras.txt
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:9c2fe12c4307ffae59564e1519ae16e6609fbcbb5d775f2b525d3339571671ee
+size 299
diff --git a/outputs/main_paper/red_circuit_20260518_153017/sparse_model/frames.bin b/outputs/main_paper/red_circuit_20260518_153017/sparse_model/frames.bin
new file mode 100644
index 0000000000000000000000000000000000000000..caef91f1f8489bf9ff5a7a11a6e133bde2a3c907
--- /dev/null
+++ b/outputs/main_paper/red_circuit_20260518_153017/sparse_model/frames.bin
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:d4c81552f9ea35beaeb089891f154ee6e446e31170b5e8ab05ddf460aa6a73f6
+size 8660
diff --git a/outputs/main_paper/red_circuit_20260518_153017/sparse_model/frames.txt b/outputs/main_paper/red_circuit_20260518_153017/sparse_model/frames.txt
new file mode 100644
index 0000000000000000000000000000000000000000..494683495c6a81b7c76a531d21a5bc1e5f626425
--- /dev/null
+++ b/outputs/main_paper/red_circuit_20260518_153017/sparse_model/frames.txt
@@ -0,0 +1,3 @@
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+size 16552
diff --git a/outputs/main_paper/red_circuit_20260518_153017/sparse_model/images.bin b/outputs/main_paper/red_circuit_20260518_153017/sparse_model/images.bin
new file mode 100644
index 0000000000000000000000000000000000000000..e8d314630676789f6175c2bd1fd8721eb244f74c
--- /dev/null
+++ b/outputs/main_paper/red_circuit_20260518_153017/sparse_model/images.bin
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:c57e80b3e3e35cd90340bbfbc550d8a616a55cccbc0ddfb348d4f33de8397990
+size 20045081
diff --git a/outputs/main_paper/red_circuit_20260518_153017/sparse_model/images.txt b/outputs/main_paper/red_circuit_20260518_153017/sparse_model/images.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a5a49d0566cbfec6b9feedd0039000f3b4f3097c
--- /dev/null
+++ b/outputs/main_paper/red_circuit_20260518_153017/sparse_model/images.txt
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:659dcda677c2c184fdbc4aa1467fa98bb25d7dc3b1335ff7a6d79145c4a656e7
+size 33546355
diff --git a/outputs/main_paper/red_circuit_20260518_153017/sparse_model/points3D.bin b/outputs/main_paper/red_circuit_20260518_153017/sparse_model/points3D.bin
new file mode 100644
index 0000000000000000000000000000000000000000..9259f860397dcc63edfd1751427237796c0217a8
--- /dev/null
+++ b/outputs/main_paper/red_circuit_20260518_153017/sparse_model/points3D.bin
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:4ba0179025c7756ff050db2fa78068365df9badaf76a02d7b5de77c0cb68d2b6
+size 3420213
diff --git a/outputs/main_paper/red_circuit_20260518_153017/sparse_model/points3D.txt b/outputs/main_paper/red_circuit_20260518_153017/sparse_model/points3D.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c633871261da61f5f86a4c4047c9296aa22481f5
--- /dev/null
+++ b/outputs/main_paper/red_circuit_20260518_153017/sparse_model/points3D.txt
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:c99f84b11da5f1f0ce4daac220e8dbcbc82daafc4901d0c777c8c2a1299e2031
+size 4454154
diff --git a/outputs/main_paper/red_circuit_20260518_153017/sparse_model/rigs.bin b/outputs/main_paper/red_circuit_20260518_153017/sparse_model/rigs.bin
new file mode 100644
index 0000000000000000000000000000000000000000..1f7b8c4eb6144d4a8702e6db6c0ab22f478e591b
--- /dev/null
+++ b/outputs/main_paper/red_circuit_20260518_153017/sparse_model/rigs.bin
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
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+size 24
diff --git a/outputs/main_paper/red_circuit_20260518_153017/sparse_model/rigs.txt b/outputs/main_paper/red_circuit_20260518_153017/sparse_model/rigs.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f5a80293086199eaafc48e225055030960a80714
--- /dev/null
+++ b/outputs/main_paper/red_circuit_20260518_153017/sparse_model/rigs.txt
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
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+size 218
diff --git a/outputs/main_paper/red_circuit_20260518_153017/sparse_model/sparse_pointcloud.ply b/outputs/main_paper/red_circuit_20260518_153017/sparse_model/sparse_pointcloud.ply
new file mode 100644
index 0000000000000000000000000000000000000000..98930b825ab794075589de2e6ac42512ba376005
--- /dev/null
+++ b/outputs/main_paper/red_circuit_20260518_153017/sparse_model/sparse_pointcloud.ply
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:0d16b07a8fbd1c31da7f896922dd73a13a06e7311b768d29697d072bb3e47fb6
+size 413804
diff --git a/outputs/main_paper/rock_20260519_210035/.hydra/config.yaml b/outputs/main_paper/rock_20260519_210035/.hydra/config.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..4a5071f71a2b839fb0a6f2120f5aa0055fbba281
--- /dev/null
+++ b/outputs/main_paper/rock_20260519_210035/.hydra/config.yaml
@@ -0,0 +1,235 @@
+focus_stack:
+  dataset_dir: ${dataset_dir}
+  scan_prefix: scan
+  scan_dirs: null
+  output_dir: ${output_dir}
+  experiment_name: ${experiment_name}
+  find_sharpest_image: true
+  sharpness_score: tenengrad
+  sharpness_selection_mode: window
+  sharpness_window_weights: uniform
+  sharpness_gaussian_sigma: null
+  output_paths:
+    output_dir: ${..output_dir}/${..experiment_name}/focus_stack
+    images_subdir: focus_stacked_images
+    masks_subdir: focus_stacked_masks
+    depthmaps_subdir: depthmaps
+    sharpness_scores_subdir: sharpness_scores
+    poses_filename: poses.json
+    intrinsics_filename: intrinsics.json
+  focus_stack_params:
+    focal_stack_size: 7
+    full_resolution_align: true
+    global_align: true
+    align_keep_size: true
+    no_contrast: true
+  low_pass_output: true
+  low_pass_kernel_size: 5
+  hydra:
+    job:
+      chdir: false
+    run:
+      dir: ${output_dir}/${experiment_name}
+    output_subdir: .hydra
+  random_seed: ${random_seed}
+masking:
+  output_dir: ${output_dir}
+  experiment_name: ${experiment_name}
+  random_seed: ${random_seed}
+  input_paths:
+    images_dir: ${...output_dir}/${...experiment_name}/focus_stack/focus_stacked_images
+    valid_regions_dir: ${...output_dir}/${...experiment_name}/focus_stack/focus_stacked_masks
+  output_paths:
+    output_dir: ${..output_dir}/${..experiment_name}/masking
+    masks_subdir: masks
+  bootstrap:
+    bootstrap_stem: scan00
+    focus_mask_border_padding: 8
+    edge_blur_kernel_size: 5
+    canny_threshold1: 25.0
+    canny_threshold2: 150.0
+    point_sampling_scale: 0.9
+    point_prompt_count: 80
+    firstpass_shrink_scale: 0.9
+    points_refine_kernel_size: 9
+    points_refine_dilate_iterations: 1
+  sam2:
+    model_id: facebook/sam2.1-hiera-large
+    device: cuda
+    offload_video_to_cpu: true
+  visualization:
+    overlay_alpha: 0.4
+    overlay_color:
+    - 255
+    - 0
+    - 0
+  hydra:
+    job:
+      chdir: false
+    run:
+      dir: ${output_dir}/${experiment_name}
+    output_subdir: .hydra
+colmap:
+  random_seed: ${random_seed}
+  run:
+    colmap_feat_extract_match: true
+    colmap_reconstruct: true
+  output_dir: ${output_dir}
+  experiment_name: ${experiment_name}
+  feat_extract_match:
+    input_paths:
+      images_dir: ${...output_dir}/${...experiment_name}/focus_stack/focus_stacked_images
+      masks_dir: ${...output_dir}/${...experiment_name}/masking/masks
+    output_paths:
+      output_dir: ${...output_dir}/${...experiment_name}
+      database_filename: database.db
+    extraction:
+      device: cpu
+      camera_model: OPENCV
+      num_threads: 1
+      max_num_features: 8192
+      estimate_affine_shape: true
+    matching:
+      use_gpu: false
+      num_threads: 1
+      guided_matching: true
+  reconstruction:
+    mode: automatic
+    load_prior_poses: true
+    load_prior_intrinsics: true
+    refine_intrinsics: true
+    input_paths:
+      poses_json: ${...output_dir}/${...experiment_name}/poses.json
+      prior_intrinsics_filepath: ${...output_dir}/${...experiment_name}/intrinsics.json
+      images_dir: ${...feat_extract_match.input_paths.images_dir}
+      database_filepath: ${...feat_extract_match.output_paths.output_dir}/${...feat_extract_match.output_paths.database_filename}
+    output_paths:
+      output_dir: ${...output_dir}/${...experiment_name}
+      model_dirname: sparse_model
+    mapping_params:
+      min_focal_length_ratio: 0.1
+      max_focal_length_ratio: 10.0
+      max_extra_param: .inf
+      ba_local_max_num_iterations: 30
+      ba_local_max_refinements: 3
+      ba_global_max_num_iterations: 75
+      ba_use_gpu: true
+      num_threads: 1
+  hydra:
+    job:
+      chdir: false
+    run:
+      dir: ${output_dir}/${experiment_name}
+    output_subdir: .hydra
+gs_3d:
+  random_seed: ${random_seed}
+  strategy:
+    _target_: gsplat.strategy.DefaultStrategy
+    verbose: true
+    prune_opa: 0.1
+    grow_grad2d: 0.0004
+    grow_scale3d: 0.01
+    prune_scale3d: 0.1
+    refine_start_iter: 500
+    refine_stop_iter: 15000
+    reset_every: 3000
+    refine_every: 100
+    absgrad: false
+    revised_opacity: false
+    key_for_gradient: means2d
+  disable_viewer: true
+  ckpt: null
+  compression: null
+  render_traj_path: interp
+  render_traj_trim: 5
+  output_dir: ${output_dir}
+  experiment_name: ${experiment_name}
+  input_paths:
+    model_dir: ${..output_dir}/${..experiment_name}/sparse_model
+    images_dir: ${..output_dir}/${..experiment_name}/masking/masked_images
+    masks_dir: ${..output_dir}/${..experiment_name}/masking/masks
+    valid_region_masks_dir: ${..output_dir}/${..experiment_name}/focus_stack/focus_stacked_masks
+  output_paths:
+    splat_dir: ${..output_dir}/${..experiment_name}/gs_3d
+  data_factor: 1
+  test_every: 8
+  patch_size: null
+  global_scale: 1.0
+  normalize_world_space: true
+  camera_model: pinhole
+  port: 8080
+  batch_size: 1
+  steps_scaler: 1.0
+  max_steps: 30000
+  eval_steps:
+  - 7000
+  - 30000
+  save_steps:
+  - 7000
+  - 30000
+  save_ply: true
+  ply_steps:
+  - 7000
+  - 30000
+  disable_video: true
+  init_type: sfm
+  init_num_pts: 100000
+  init_extent: 3.0
+  sh_degree: 3
+  sh_degree_interval: 1000
+  init_opa: 0.1
+  init_scale: 1.0
+  ssim_lambda: 0.2
+  near_plane: 0.01
+  far_plane: 10000000000.0
+  packed: false
+  sparse_grad: false
+  visible_adam: false
+  antialiased: false
+  random_bkgd: false
+  means_lr: 0.00016
+  scales_lr: 0.005
+  opacities_lr: 0.05
+  quats_lr: 0.001
+  sh0_lr: 0.0025
+  shN_lr: 0.000125
+  opacity_reg: 0.0
+  scale_reg: 0.0
+  pose_opt: false
+  pose_opt_lr: 1.0e-05
+  pose_opt_reg: 1.0e-06
+  pose_noise: 0.0
+  app_opt: false
+  app_embed_dim: 16
+  app_opt_lr: 0.001
+  app_opt_reg: 1.0e-06
+  use_bilateral_grid: false
+  bilateral_grid_shape:
+  - 16
+  - 16
+  - 8
+  depth_loss: false
+  depth_lambda: 0.01
+  bg_alpha_loss: true
+  bg_alpha_lambda: 0.5
+  tb_every: 100
+  tb_save_image: false
+  lpips_net: alex
+  with_ut: false
+  with_eval3d: false
+  use_fused_bilagrid: false
+  hydra:
+    job:
+      chdir: false
+    run:
+      dir: outputs/hydra/${now:%Y-%m-%d_%H-%M-%S}
+    output_subdir: .hydra
+output_dir: outputs/main_paper
+experiment_name: rock_20260519_210035
+random_seed: 0
+dataset_dir: data/rock_20260519_210035
+run:
+  focus_stack: true
+  masking: true
+  colmap: true
+  gs_3d: true
diff --git a/outputs/main_paper/rock_20260519_210035/.hydra/hydra.yaml b/outputs/main_paper/rock_20260519_210035/.hydra/hydra.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..e9f5d51b35b7465e33c63e4d571e88fca85c0918
--- /dev/null
+++ b/outputs/main_paper/rock_20260519_210035/.hydra/hydra.yaml
@@ -0,0 +1,162 @@
+hydra:
+  run:
+    dir: ${output_dir}/${experiment_name}
+  sweep:
+    dir: multirun/${now:%Y-%m-%d}/${now:%H-%M-%S}
+    subdir: ${hydra.job.num}
+  launcher:
+    _target_: hydra._internal.core_plugins.basic_launcher.BasicLauncher
+  sweeper:
+    _target_: hydra._internal.core_plugins.basic_sweeper.BasicSweeper
+    max_batch_size: null
+    params: null
+  help:
+    app_name: ${hydra.job.name}
+    header: '${hydra.help.app_name} is powered by Hydra.
+
+      '
+    footer: 'Powered by Hydra (https://hydra.cc)
+
+      Use --hydra-help to view Hydra specific help
+
+      '
+    template: '${hydra.help.header}
+
+      == Configuration groups ==
+
+      Compose your configuration from those groups (group=option)
+
+
+      $APP_CONFIG_GROUPS
+
+
+      == Config ==
+
+      Override anything in the config (foo.bar=value)
+
+
+      $CONFIG
+
+
+      ${hydra.help.footer}
+
+      '
+  hydra_help:
+    template: 'Hydra (${hydra.runtime.version})
+
+      See https://hydra.cc for more info.
+
+
+      == Flags ==
+
+      $FLAGS_HELP
+
+
+      == Configuration groups ==
+
+      Compose your configuration from those groups (For example, append hydra/job_logging=disabled
+      to command line)
+
+
+      $HYDRA_CONFIG_GROUPS
+
+
+      Use ''--cfg hydra'' to Show the Hydra config.
+
+      '
+    hydra_help: ???
+  hydra_logging:
+    version: 1
+    formatters:
+      simple:
+        format: '[%(asctime)s][HYDRA] %(message)s'
+    handlers:
+      console:
+        class: logging.StreamHandler
+        formatter: simple
+        stream: ext://sys.stdout
+    root:
+      level: INFO
+      handlers:
+      - console
+    loggers:
+      logging_example:
+        level: DEBUG
+    disable_existing_loggers: false
+  job_logging:
+    version: 1
+    formatters:
+      simple:
+        format: '[%(asctime)s][%(name)s][%(levelname)s] - %(message)s'
+    handlers:
+      console:
+        class: logging.StreamHandler
+        formatter: simple
+        stream: ext://sys.stdout
+      file:
+        class: logging.FileHandler
+        formatter: simple
+        filename: ${hydra.runtime.output_dir}/${hydra.job.name}.log
+    root:
+      level: INFO
+      handlers:
+      - console
+      - file
+    disable_existing_loggers: false
+  env: {}
+  mode: RUN
+  searchpath: []
+  callbacks: {}
+  output_subdir: .hydra
+  overrides:
+    hydra:
+    - hydra.mode=RUN
+    task:
+    - +experiment=main_paper
+    - experiment_name=rock_20260519_210035
+    - dataset_dir=data/rock_20260519_210035
+  job:
+    name: run_pipeline
+    chdir: false
+    override_dirname: +experiment=main_paper,dataset_dir=data/rock_20260519_210035,experiment_name=rock_20260519_210035
+    id: ???
+    num: ???
+    config_name: pipeline
+    env_set: {}
+    env_copy: []
+    config:
+      override_dirname:
+        kv_sep: '='
+        item_sep: ','
+        exclude_keys: []
+  runtime:
+    version: 1.3.2
+    version_base: '1.3'
+    cwd: /storage/scratch1/8/razarcon3/Microscopic-3D-Reconstruction/reconstruction
+    config_sources:
+    - path: hydra.conf
+      schema: pkg
+      provider: hydra
+    - path: /storage/scratch1/8/razarcon3/Microscopic-3D-Reconstruction/reconstruction/configs
+      schema: file
+      provider: main
+    - path: ''
+      schema: structured
+      provider: schema
+    output_dir: /storage/scratch1/8/razarcon3/Microscopic-3D-Reconstruction/reconstruction/outputs/main_paper/rock_20260519_210035
+    choices:
+      experiment: main_paper
+      gs_3d: default
+      colmap: default
+      masking: default
+      focus_stack: default
+      hydra/env: default
+      hydra/callbacks: null
+      hydra/job_logging: default
+      hydra/hydra_logging: default
+      hydra/hydra_help: default
+      hydra/help: default
+      hydra/sweeper: basic
+      hydra/launcher: basic
+      hydra/output: default
+  verbose: false
diff --git a/outputs/main_paper/rock_20260519_210035/.hydra/overrides.yaml b/outputs/main_paper/rock_20260519_210035/.hydra/overrides.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..f5bc641f15605b24258c9526ec3b10669e266f06
--- /dev/null
+++ b/outputs/main_paper/rock_20260519_210035/.hydra/overrides.yaml
@@ -0,0 +1,3 @@
+- +experiment=main_paper
+- experiment_name=rock_20260519_210035
+- dataset_dir=data/rock_20260519_210035
diff --git a/outputs/main_paper/rock_20260519_210035/database.db b/outputs/main_paper/rock_20260519_210035/database.db
new file mode 100644
index 0000000000000000000000000000000000000000..3d145c15e81b138579ebdb5ad6a747da08b0728d
--- /dev/null
+++ b/outputs/main_paper/rock_20260519_210035/database.db
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:3cf1f2824dfab409e94e9e2a9e6888d68fab2eac9d9b0afdb7927ac85dd79bea
+size 146014208
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+}
\ No newline at end of file
diff --git a/outputs/main_paper/rock_20260519_210035/run_pipeline.log b/outputs/main_paper/rock_20260519_210035/run_pipeline.log
new file mode 100644
index 0000000000000000000000000000000000000000..fe293eca58b3491b5590c93ba2817bf0b849f608
--- /dev/null
+++ b/outputs/main_paper/rock_20260519_210035/run_pipeline.log
@@ -0,0 +1,5 @@
+[2026-05-27 00:58:37,103][httpx][INFO] - HTTP Request: HEAD https://huggingface.co/facebook/sam2.1-hiera-large/resolve/main/sam2.1_hiera_large.pt "HTTP/1.1 302 Found"
+[2026-05-27 00:59:01,377][httpx][INFO] - HTTP Request: HEAD https://huggingface.co/facebook/sam2.1-hiera-large/resolve/main/sam2.1_hiera_large.pt "HTTP/1.1 302 Found"
+[2026-05-27 00:59:02,854][root][INFO] - For numpy array image, we assume (HxWxC) format
+[2026-05-27 00:59:05,177][root][INFO] - Computing image embeddings for the provided image...
+[2026-05-27 00:59:51,081][root][INFO] - Image embeddings computed.
diff --git a/outputs/main_paper/rock_20260519_210035/sparse_model/cameras.bin b/outputs/main_paper/rock_20260519_210035/sparse_model/cameras.bin
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@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
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diff --git a/outputs/main_paper/rock_20260519_210035/sparse_model/sparse_pointcloud.ply b/outputs/main_paper/rock_20260519_210035/sparse_model/sparse_pointcloud.ply
new file mode 100644
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diff --git a/outputs/main_paper/seashell_20260513_223020/.hydra/config.yaml b/outputs/main_paper/seashell_20260513_223020/.hydra/config.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..36b9a9ac3c1127f4f082063e4a134d2c20275803
--- /dev/null
+++ b/outputs/main_paper/seashell_20260513_223020/.hydra/config.yaml
@@ -0,0 +1,235 @@
+focus_stack:
+  dataset_dir: ${dataset_dir}
+  scan_prefix: scan
+  scan_dirs: null
+  output_dir: ${output_dir}
+  experiment_name: ${experiment_name}
+  find_sharpest_image: true
+  sharpness_score: tenengrad
+  sharpness_selection_mode: window
+  sharpness_window_weights: uniform
+  sharpness_gaussian_sigma: null
+  output_paths:
+    output_dir: ${..output_dir}/${..experiment_name}/focus_stack
+    images_subdir: focus_stacked_images
+    masks_subdir: focus_stacked_masks
+    depthmaps_subdir: depthmaps
+    sharpness_scores_subdir: sharpness_scores
+    poses_filename: poses.json
+    intrinsics_filename: intrinsics.json
+  focus_stack_params:
+    focal_stack_size: 7
+    full_resolution_align: true
+    global_align: true
+    align_keep_size: true
+    no_contrast: true
+  low_pass_output: true
+  low_pass_kernel_size: 5
+  hydra:
+    job:
+      chdir: false
+    run:
+      dir: ${output_dir}/${experiment_name}
+    output_subdir: .hydra
+  random_seed: ${random_seed}
+masking:
+  output_dir: ${output_dir}
+  experiment_name: ${experiment_name}
+  random_seed: ${random_seed}
+  input_paths:
+    images_dir: ${...output_dir}/${...experiment_name}/focus_stack/focus_stacked_images
+    valid_regions_dir: ${...output_dir}/${...experiment_name}/focus_stack/focus_stacked_masks
+  output_paths:
+    output_dir: ${..output_dir}/${..experiment_name}/masking
+    masks_subdir: masks
+  bootstrap:
+    bootstrap_stem: scan00
+    focus_mask_border_padding: 8
+    edge_blur_kernel_size: 5
+    canny_threshold1: 25.0
+    canny_threshold2: 150.0
+    point_sampling_scale: 0.9
+    point_prompt_count: 80
+    firstpass_shrink_scale: 0.9
+    points_refine_kernel_size: 9
+    points_refine_dilate_iterations: 1
+  sam2:
+    model_id: facebook/sam2.1-hiera-large
+    device: cuda
+    offload_video_to_cpu: true
+  visualization:
+    overlay_alpha: 0.4
+    overlay_color:
+    - 255
+    - 0
+    - 0
+  hydra:
+    job:
+      chdir: false
+    run:
+      dir: ${output_dir}/${experiment_name}
+    output_subdir: .hydra
+colmap:
+  random_seed: ${random_seed}
+  run:
+    colmap_feat_extract_match: true
+    colmap_reconstruct: true
+  output_dir: ${output_dir}
+  experiment_name: ${experiment_name}
+  feat_extract_match:
+    input_paths:
+      images_dir: ${...output_dir}/${...experiment_name}/focus_stack/focus_stacked_images
+      masks_dir: ${...output_dir}/${...experiment_name}/masking/masks
+    output_paths:
+      output_dir: ${...output_dir}/${...experiment_name}
+      database_filename: database.db
+    extraction:
+      device: cpu
+      camera_model: OPENCV
+      num_threads: 1
+      max_num_features: 8192
+      estimate_affine_shape: true
+    matching:
+      use_gpu: false
+      num_threads: 1
+      guided_matching: true
+  reconstruction:
+    mode: automatic
+    load_prior_poses: true
+    load_prior_intrinsics: true
+    refine_intrinsics: true
+    input_paths:
+      poses_json: ${...output_dir}/${...experiment_name}/poses.json
+      prior_intrinsics_filepath: ${...output_dir}/${...experiment_name}/intrinsics.json
+      images_dir: ${...feat_extract_match.input_paths.images_dir}
+      database_filepath: ${...feat_extract_match.output_paths.output_dir}/${...feat_extract_match.output_paths.database_filename}
+    output_paths:
+      output_dir: ${...output_dir}/${...experiment_name}
+      model_dirname: sparse_model
+    mapping_params:
+      min_focal_length_ratio: 0.1
+      max_focal_length_ratio: 10.0
+      max_extra_param: .inf
+      ba_local_max_num_iterations: 30
+      ba_local_max_refinements: 3
+      ba_global_max_num_iterations: 75
+      ba_use_gpu: true
+      num_threads: 1
+  hydra:
+    job:
+      chdir: false
+    run:
+      dir: ${output_dir}/${experiment_name}
+    output_subdir: .hydra
+gs_3d:
+  random_seed: ${random_seed}
+  strategy:
+    _target_: gsplat.strategy.DefaultStrategy
+    verbose: true
+    prune_opa: 0.1
+    grow_grad2d: 0.0004
+    grow_scale3d: 0.01
+    prune_scale3d: 0.1
+    refine_start_iter: 500
+    refine_stop_iter: 15000
+    reset_every: 3000
+    refine_every: 100
+    absgrad: false
+    revised_opacity: false
+    key_for_gradient: means2d
+  disable_viewer: true
+  ckpt: null
+  compression: null
+  render_traj_path: interp
+  render_traj_trim: 5
+  output_dir: ${output_dir}
+  experiment_name: ${experiment_name}
+  input_paths:
+    model_dir: ${..output_dir}/${..experiment_name}/sparse_model
+    images_dir: ${..output_dir}/${..experiment_name}/masking/masked_images
+    masks_dir: ${..output_dir}/${..experiment_name}/masking/masks
+    valid_region_masks_dir: ${..output_dir}/${..experiment_name}/focus_stack/focus_stacked_masks
+  output_paths:
+    splat_dir: ${..output_dir}/${..experiment_name}/gs_3d
+  data_factor: 1
+  test_every: 8
+  patch_size: null
+  global_scale: 1.0
+  normalize_world_space: true
+  camera_model: pinhole
+  port: 8080
+  batch_size: 1
+  steps_scaler: 1.0
+  max_steps: 30000
+  eval_steps:
+  - 7000
+  - 30000
+  save_steps:
+  - 7000
+  - 30000
+  save_ply: true
+  ply_steps:
+  - 7000
+  - 30000
+  disable_video: true
+  init_type: sfm
+  init_num_pts: 100000
+  init_extent: 3.0
+  sh_degree: 3
+  sh_degree_interval: 1000
+  init_opa: 0.1
+  init_scale: 1.0
+  ssim_lambda: 0.2
+  near_plane: 0.01
+  far_plane: 10000000000.0
+  packed: false
+  sparse_grad: false
+  visible_adam: false
+  antialiased: false
+  random_bkgd: false
+  means_lr: 0.00016
+  scales_lr: 0.005
+  opacities_lr: 0.05
+  quats_lr: 0.001
+  sh0_lr: 0.0025
+  shN_lr: 0.000125
+  opacity_reg: 0.0
+  scale_reg: 0.0
+  pose_opt: false
+  pose_opt_lr: 1.0e-05
+  pose_opt_reg: 1.0e-06
+  pose_noise: 0.0
+  app_opt: false
+  app_embed_dim: 16
+  app_opt_lr: 0.001
+  app_opt_reg: 1.0e-06
+  use_bilateral_grid: false
+  bilateral_grid_shape:
+  - 16
+  - 16
+  - 8
+  depth_loss: false
+  depth_lambda: 0.01
+  bg_alpha_loss: true
+  bg_alpha_lambda: 0.5
+  tb_every: 100
+  tb_save_image: false
+  lpips_net: alex
+  with_ut: false
+  with_eval3d: false
+  use_fused_bilagrid: false
+  hydra:
+    job:
+      chdir: false
+    run:
+      dir: outputs/hydra/${now:%Y-%m-%d_%H-%M-%S}
+    output_subdir: .hydra
+output_dir: outputs/main_paper
+experiment_name: seashell_20260513_223020
+random_seed: 0
+dataset_dir: data/seashell_20260513_223020
+run:
+  focus_stack: true
+  masking: true
+  colmap: true
+  gs_3d: true
diff --git a/outputs/main_paper/seashell_20260513_223020/.hydra/hydra.yaml b/outputs/main_paper/seashell_20260513_223020/.hydra/hydra.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..879bf5f4eaa219f02d9be60bc34c7ec1bda02cd1
--- /dev/null
+++ b/outputs/main_paper/seashell_20260513_223020/.hydra/hydra.yaml
@@ -0,0 +1,162 @@
+hydra:
+  run:
+    dir: ${output_dir}/${experiment_name}
+  sweep:
+    dir: multirun/${now:%Y-%m-%d}/${now:%H-%M-%S}
+    subdir: ${hydra.job.num}
+  launcher:
+    _target_: hydra._internal.core_plugins.basic_launcher.BasicLauncher
+  sweeper:
+    _target_: hydra._internal.core_plugins.basic_sweeper.BasicSweeper
+    max_batch_size: null
+    params: null
+  help:
+    app_name: ${hydra.job.name}
+    header: '${hydra.help.app_name} is powered by Hydra.
+
+      '
+    footer: 'Powered by Hydra (https://hydra.cc)
+
+      Use --hydra-help to view Hydra specific help
+
+      '
+    template: '${hydra.help.header}
+
+      == Configuration groups ==
+
+      Compose your configuration from those groups (group=option)
+
+
+      $APP_CONFIG_GROUPS
+
+
+      == Config ==
+
+      Override anything in the config (foo.bar=value)
+
+
+      $CONFIG
+
+
+      ${hydra.help.footer}
+
+      '
+  hydra_help:
+    template: 'Hydra (${hydra.runtime.version})
+
+      See https://hydra.cc for more info.
+
+
+      == Flags ==
+
+      $FLAGS_HELP
+
+
+      == Configuration groups ==
+
+      Compose your configuration from those groups (For example, append hydra/job_logging=disabled
+      to command line)
+
+
+      $HYDRA_CONFIG_GROUPS
+
+
+      Use ''--cfg hydra'' to Show the Hydra config.
+
+      '
+    hydra_help: ???
+  hydra_logging:
+    version: 1
+    formatters:
+      simple:
+        format: '[%(asctime)s][HYDRA] %(message)s'
+    handlers:
+      console:
+        class: logging.StreamHandler
+        formatter: simple
+        stream: ext://sys.stdout
+    root:
+      level: INFO
+      handlers:
+      - console
+    loggers:
+      logging_example:
+        level: DEBUG
+    disable_existing_loggers: false
+  job_logging:
+    version: 1
+    formatters:
+      simple:
+        format: '[%(asctime)s][%(name)s][%(levelname)s] - %(message)s'
+    handlers:
+      console:
+        class: logging.StreamHandler
+        formatter: simple
+        stream: ext://sys.stdout
+      file:
+        class: logging.FileHandler
+        formatter: simple
+        filename: ${hydra.runtime.output_dir}/${hydra.job.name}.log
+    root:
+      level: INFO
+      handlers:
+      - console
+      - file
+    disable_existing_loggers: false
+  env: {}
+  mode: RUN
+  searchpath: []
+  callbacks: {}
+  output_subdir: .hydra
+  overrides:
+    hydra:
+    - hydra.mode=RUN
+    task:
+    - +experiment=main_paper
+    - experiment_name=seashell_20260513_223020
+    - dataset_dir=data/seashell_20260513_223020
+  job:
+    name: run_pipeline
+    chdir: false
+    override_dirname: +experiment=main_paper,dataset_dir=data/seashell_20260513_223020,experiment_name=seashell_20260513_223020
+    id: ???
+    num: ???
+    config_name: pipeline
+    env_set: {}
+    env_copy: []
+    config:
+      override_dirname:
+        kv_sep: '='
+        item_sep: ','
+        exclude_keys: []
+  runtime:
+    version: 1.3.2
+    version_base: '1.3'
+    cwd: /storage/scratch1/8/razarcon3/Microscopic-3D-Reconstruction/reconstruction
+    config_sources:
+    - path: hydra.conf
+      schema: pkg
+      provider: hydra
+    - path: /storage/scratch1/8/razarcon3/Microscopic-3D-Reconstruction/reconstruction/configs
+      schema: file
+      provider: main
+    - path: ''
+      schema: structured
+      provider: schema
+    output_dir: /storage/scratch1/8/razarcon3/Microscopic-3D-Reconstruction/reconstruction/outputs/main_paper/seashell_20260513_223020
+    choices:
+      experiment: main_paper
+      gs_3d: default
+      colmap: default
+      masking: default
+      focus_stack: default
+      hydra/env: default
+      hydra/callbacks: null
+      hydra/job_logging: default
+      hydra/hydra_logging: default
+      hydra/hydra_help: default
+      hydra/help: default
+      hydra/sweeper: basic
+      hydra/launcher: basic
+      hydra/output: default
+  verbose: false
diff --git a/outputs/main_paper/seashell_20260513_223020/.hydra/overrides.yaml b/outputs/main_paper/seashell_20260513_223020/.hydra/overrides.yaml
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--- /dev/null
+++ b/outputs/main_paper/seashell_20260513_223020/.hydra/overrides.yaml
@@ -0,0 +1,3 @@
+- +experiment=main_paper
+- experiment_name=seashell_20260513_223020
+- dataset_dir=data/seashell_20260513_223020
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diff --git a/outputs/main_paper/seashell_20260513_223020/run_pipeline.log b/outputs/main_paper/seashell_20260513_223020/run_pipeline.log
new file mode 100644
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+[2026-05-27 00:59:33,553][httpx][INFO] - HTTP Request: HEAD https://huggingface.co/facebook/sam2.1-hiera-large/resolve/main/sam2.1_hiera_large.pt "HTTP/1.1 302 Found"
+[2026-05-27 00:59:35,717][httpx][INFO] - HTTP Request: HEAD https://huggingface.co/facebook/sam2.1-hiera-large/resolve/main/sam2.1_hiera_large.pt "HTTP/1.1 302 Found"
+[2026-05-27 00:59:37,168][root][INFO] - For numpy array image, we assume (HxWxC) format
+[2026-05-27 00:59:37,232][root][INFO] - Computing image embeddings for the provided image...
+[2026-05-27 00:59:51,081][root][INFO] - Image embeddings computed.
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