diff --git a/outputs/main_paper/blueberry_20260526_160106/.hydra/config.yaml b/outputs/main_paper/blueberry_20260526_160106/.hydra/config.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..919d75ee1e3c42a9f3ce4c8b62ee8a2ce6f51baf
--- /dev/null
+++ b/outputs/main_paper/blueberry_20260526_160106/.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: blueberry_20260526_160106
+random_seed: 0
+dataset_dir: data/blueberry_20260526_160106
+run:
+  focus_stack: true
+  masking: true
+  colmap: true
+  gs_3d: true
diff --git a/outputs/main_paper/blueberry_20260526_160106/.hydra/hydra.yaml b/outputs/main_paper/blueberry_20260526_160106/.hydra/hydra.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..939e1e5cb4d314f92dae8932e5934300b5d61dba
--- /dev/null
+++ b/outputs/main_paper/blueberry_20260526_160106/.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=blueberry_20260526_160106
+    - dataset_dir=data/blueberry_20260526_160106
+  job:
+    name: run_pipeline
+    chdir: false
+    override_dirname: +experiment=main_paper,dataset_dir=data/blueberry_20260526_160106,experiment_name=blueberry_20260526_160106
+    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/blueberry_20260526_160106
+    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/blueberry_20260526_160106/.hydra/overrides.yaml b/outputs/main_paper/blueberry_20260526_160106/.hydra/overrides.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..6647fb3455b717c6ae34dd4022f0139d7b08cd64
--- /dev/null
+++ b/outputs/main_paper/blueberry_20260526_160106/.hydra/overrides.yaml
@@ -0,0 +1,3 @@
+- +experiment=main_paper
+- experiment_name=blueberry_20260526_160106
+- dataset_dir=data/blueberry_20260526_160106
diff --git a/outputs/main_paper/blueberry_20260526_160106/database.db b/outputs/main_paper/blueberry_20260526_160106/database.db
new file mode 100644
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--- /dev/null
+++ b/outputs/main_paper/blueberry_20260526_160106/database.db
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:445ead555738a7a83cd2aaa7b59ad5819438cecb91ac6e449ea384d14ebce286
+size 128966656
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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/blueberry_20260526_160106/run_pipeline.log b/outputs/main_paper/blueberry_20260526_160106/run_pipeline.log
new file mode 100644
index 0000000000000000000000000000000000000000..2a73b7fb3fe52646aa9b6001c4e5353303de3e23
--- /dev/null
+++ b/outputs/main_paper/blueberry_20260526_160106/run_pipeline.log
@@ -0,0 +1,6 @@
+[2026-05-26 22:27:47,840][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 22:27:47,906][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 22:28:36,221][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 22:28:37,766][root][INFO] - For numpy array image, we assume (HxWxC) format
+[2026-05-26 22:28:41,131][root][INFO] - Computing image embeddings for the provided image...
+[2026-05-26 22:29:32,234][root][INFO] - Image embeddings computed.
diff --git a/outputs/main_paper/blueberry_20260526_160106/sparse_model/cameras.bin b/outputs/main_paper/blueberry_20260526_160106/sparse_model/cameras.bin
new file mode 100644
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+++ b/outputs/main_paper/blueberry_20260526_160106/sparse_model/cameras.bin
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@@ -0,0 +1,3 @@
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new file mode 100644
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diff --git a/outputs/main_paper/blueberry_20260526_160106/sparse_model/sparse_pointcloud.ply b/outputs/main_paper/blueberry_20260526_160106/sparse_model/sparse_pointcloud.ply
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@@ -0,0 +1,3 @@
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diff --git a/outputs/main_paper/bolt_20260525_172139/.hydra/config.yaml b/outputs/main_paper/bolt_20260525_172139/.hydra/config.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..cb5dec7cfad80c499549b01033fb5fb650243f62
--- /dev/null
+++ b/outputs/main_paper/bolt_20260525_172139/.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: bolt_20260525_172139
+random_seed: 0
+dataset_dir: data/bolt_20260525_172139
+run:
+  focus_stack: true
+  masking: true
+  colmap: true
+  gs_3d: true
diff --git a/outputs/main_paper/bolt_20260525_172139/.hydra/hydra.yaml b/outputs/main_paper/bolt_20260525_172139/.hydra/hydra.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..cc374643747ad25270d83267943ff938eb79bfb7
--- /dev/null
+++ b/outputs/main_paper/bolt_20260525_172139/.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=bolt_20260525_172139
+    - dataset_dir=data/bolt_20260525_172139
+  job:
+    name: run_pipeline
+    chdir: false
+    override_dirname: +experiment=main_paper,dataset_dir=data/bolt_20260525_172139,experiment_name=bolt_20260525_172139
+    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/bolt_20260525_172139
+    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/bolt_20260525_172139/.hydra/overrides.yaml b/outputs/main_paper/bolt_20260525_172139/.hydra/overrides.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..cf2104215921e007b9061cc3a2a5870306d0affc
--- /dev/null
+++ b/outputs/main_paper/bolt_20260525_172139/.hydra/overrides.yaml
@@ -0,0 +1,3 @@
+- +experiment=main_paper
+- experiment_name=bolt_20260525_172139
+- dataset_dir=data/bolt_20260525_172139
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+size 162660352
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diff --git a/outputs/main_paper/bolt_20260525_172139/run_pipeline.log b/outputs/main_paper/bolt_20260525_172139/run_pipeline.log
new file mode 100644
index 0000000000000000000000000000000000000000..05d22d9e48e6896dd30dd6cfa2367f0cb07c74ea
--- /dev/null
+++ b/outputs/main_paper/bolt_20260525_172139/run_pipeline.log
@@ -0,0 +1,6 @@
+[2026-05-26 23:39:00,315][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 23:39:00,316][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 23:39:02,454][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 23:39:03,902][root][INFO] - For numpy array image, we assume (HxWxC) format
+[2026-05-26 23:39:03,967][root][INFO] - Computing image embeddings for the provided image...
+[2026-05-26 23:39:04,147][root][INFO] - Image embeddings computed.
diff --git a/outputs/main_paper/bolt_20260525_172139/sparse_model/cameras.bin b/outputs/main_paper/bolt_20260525_172139/sparse_model/cameras.bin
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new file mode 100644
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diff --git a/outputs/main_paper/bolt_20260525_172139/sparse_model/sparse_pointcloud.ply b/outputs/main_paper/bolt_20260525_172139/sparse_model/sparse_pointcloud.ply
new file mode 100644
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diff --git a/outputs/main_paper/cheburashka_20260524_202944/.hydra/config.yaml b/outputs/main_paper/cheburashka_20260524_202944/.hydra/config.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..63aa4d6a84caca1b1980626ff8b781e239e10516
--- /dev/null
+++ b/outputs/main_paper/cheburashka_20260524_202944/.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: cheburashka_20260524_202944
+random_seed: 0
+dataset_dir: data/cheburashka_20260524_202944
+run:
+  focus_stack: true
+  masking: true
+  colmap: true
+  gs_3d: true
diff --git a/outputs/main_paper/cheburashka_20260524_202944/.hydra/hydra.yaml b/outputs/main_paper/cheburashka_20260524_202944/.hydra/hydra.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..e8aecd0228a57b4f86e41166732330c75dabf0f5
--- /dev/null
+++ b/outputs/main_paper/cheburashka_20260524_202944/.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=cheburashka_20260524_202944
+    - dataset_dir=data/cheburashka_20260524_202944
+  job:
+    name: run_pipeline
+    chdir: false
+    override_dirname: +experiment=main_paper,dataset_dir=data/cheburashka_20260524_202944,experiment_name=cheburashka_20260524_202944
+    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/cheburashka_20260524_202944
+    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/cheburashka_20260524_202944/.hydra/overrides.yaml b/outputs/main_paper/cheburashka_20260524_202944/.hydra/overrides.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..c13842a3186df7d5e7efa1cbd574345a8158da6b
--- /dev/null
+++ b/outputs/main_paper/cheburashka_20260524_202944/.hydra/overrides.yaml
@@ -0,0 +1,3 @@
+- +experiment=main_paper
+- experiment_name=cheburashka_20260524_202944
+- dataset_dir=data/cheburashka_20260524_202944
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--- /dev/null
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@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:bd3a4a113a78fc28884888570325c204cf76559a5f0e66e83c5e8931306199a5
+size 44154880
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diff --git a/outputs/main_paper/cheburashka_20260524_202944/run_pipeline.log b/outputs/main_paper/cheburashka_20260524_202944/run_pipeline.log
new file mode 100644
index 0000000000000000000000000000000000000000..ebb37ca7629b3cda83e3fa8b0b759e6257dc1d53
--- /dev/null
+++ b/outputs/main_paper/cheburashka_20260524_202944/run_pipeline.log
@@ -0,0 +1,6 @@
+[2026-05-26 23:38:13,450][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 23:38:15,595][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 23:38:15,595][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 23:38:17,052][root][INFO] - For numpy array image, we assume (HxWxC) format
+[2026-05-26 23:38:17,116][root][INFO] - Computing image embeddings for the provided image...
+[2026-05-26 23:38:17,294][root][INFO] - Image embeddings computed.
diff --git a/outputs/main_paper/cheburashka_20260524_202944/sparse_model/cameras.bin b/outputs/main_paper/cheburashka_20260524_202944/sparse_model/cameras.bin
new file mode 100644
index 0000000000000000000000000000000000000000..4db096dcb05e62b1b8be4de68f263aa613ad4c57
--- /dev/null
+++ b/outputs/main_paper/cheburashka_20260524_202944/sparse_model/cameras.bin
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:ef1577d9a07514dc25a36ce51cc1ec10c215d3062637c38ae12037c1a831c165
+size 96
diff --git a/outputs/main_paper/cheburashka_20260524_202944/sparse_model/cameras.txt b/outputs/main_paper/cheburashka_20260524_202944/sparse_model/cameras.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e970f4dbce32cd06b1fb37bceaa6b7e8a5a876bf
--- /dev/null
+++ b/outputs/main_paper/cheburashka_20260524_202944/sparse_model/cameras.txt
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:512695de60c1961d5808f964452612096d4541e07b69daa3eb9dc810efb466c6
+size 297
diff --git a/outputs/main_paper/cheburashka_20260524_202944/sparse_model/frames.bin b/outputs/main_paper/cheburashka_20260524_202944/sparse_model/frames.bin
new file mode 100644
index 0000000000000000000000000000000000000000..e15d58b9abe5b2112f7acc41f131430fa3c35b96
--- /dev/null
+++ b/outputs/main_paper/cheburashka_20260524_202944/sparse_model/frames.bin
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:ba4b9a1384336db62a6dc6bacdc66e017c6af07a9c056cf3bef79dd1368a6251
+size 8828
diff --git a/outputs/main_paper/cheburashka_20260524_202944/sparse_model/frames.txt b/outputs/main_paper/cheburashka_20260524_202944/sparse_model/frames.txt
new file mode 100644
index 0000000000000000000000000000000000000000..923fee2e858003e0a6b18bbc6cb33a835e267cfa
--- /dev/null
+++ b/outputs/main_paper/cheburashka_20260524_202944/sparse_model/frames.txt
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
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+size 16874
diff --git a/outputs/main_paper/cheburashka_20260524_202944/sparse_model/images.bin b/outputs/main_paper/cheburashka_20260524_202944/sparse_model/images.bin
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--- /dev/null
+++ b/outputs/main_paper/cheburashka_20260524_202944/sparse_model/images.bin
@@ -0,0 +1,3 @@
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+size 6362392
diff --git a/outputs/main_paper/cheburashka_20260524_202944/sparse_model/images.txt b/outputs/main_paper/cheburashka_20260524_202944/sparse_model/images.txt
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--- /dev/null
+++ b/outputs/main_paper/cheburashka_20260524_202944/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/cheburashka_20260524_202944/sparse_model/points3D.bin b/outputs/main_paper/cheburashka_20260524_202944/sparse_model/points3D.bin
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--- /dev/null
+++ b/outputs/main_paper/cheburashka_20260524_202944/sparse_model/points3D.bin
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
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+size 447526
diff --git a/outputs/main_paper/cheburashka_20260524_202944/sparse_model/points3D.txt b/outputs/main_paper/cheburashka_20260524_202944/sparse_model/points3D.txt
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index 0000000000000000000000000000000000000000..de705bb7376f35bf6f439077629da2d646bdec09
--- /dev/null
+++ b/outputs/main_paper/cheburashka_20260524_202944/sparse_model/points3D.txt
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
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+size 591085
diff --git a/outputs/main_paper/cheburashka_20260524_202944/sparse_model/rigs.bin b/outputs/main_paper/cheburashka_20260524_202944/sparse_model/rigs.bin
new file mode 100644
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--- /dev/null
+++ b/outputs/main_paper/cheburashka_20260524_202944/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/cheburashka_20260524_202944/sparse_model/rigs.txt b/outputs/main_paper/cheburashka_20260524_202944/sparse_model/rigs.txt
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--- /dev/null
+++ b/outputs/main_paper/cheburashka_20260524_202944/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/cheburashka_20260524_202944/sparse_model/sparse_pointcloud.ply b/outputs/main_paper/cheburashka_20260524_202944/sparse_model/sparse_pointcloud.ply
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--- /dev/null
+++ b/outputs/main_paper/cheburashka_20260524_202944/sparse_model/sparse_pointcloud.ply
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
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+size 62608
diff --git a/outputs/main_paper/hydrangea_20260513_214340/.hydra/config.yaml b/outputs/main_paper/hydrangea_20260513_214340/.hydra/config.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..eaaba25971c88b68b1daf016df2c0dca8e132167
--- /dev/null
+++ b/outputs/main_paper/hydrangea_20260513_214340/.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: hydrangea_20260513_214340
+random_seed: 0
+dataset_dir: data/hydrangea_20260513_214340
+run:
+  focus_stack: true
+  masking: true
+  colmap: true
+  gs_3d: true
diff --git a/outputs/main_paper/hydrangea_20260513_214340/.hydra/hydra.yaml b/outputs/main_paper/hydrangea_20260513_214340/.hydra/hydra.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..f9e0c8129fa14470d164492cbf903cde52e00f4f
--- /dev/null
+++ b/outputs/main_paper/hydrangea_20260513_214340/.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=hydrangea_20260513_214340
+    - dataset_dir=data/hydrangea_20260513_214340
+  job:
+    name: run_pipeline
+    chdir: false
+    override_dirname: +experiment=main_paper,dataset_dir=data/hydrangea_20260513_214340,experiment_name=hydrangea_20260513_214340
+    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/hydrangea_20260513_214340
+    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/hydrangea_20260513_214340/.hydra/overrides.yaml b/outputs/main_paper/hydrangea_20260513_214340/.hydra/overrides.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..483b3f70e42a14790fbcad3136fb3d58d152a556
--- /dev/null
+++ b/outputs/main_paper/hydrangea_20260513_214340/.hydra/overrides.yaml
@@ -0,0 +1,3 @@
+- +experiment=main_paper
+- experiment_name=hydrangea_20260513_214340
+- dataset_dir=data/hydrangea_20260513_214340
diff --git a/outputs/main_paper/hydrangea_20260513_214340/database.db b/outputs/main_paper/hydrangea_20260513_214340/database.db
new file mode 100644
index 0000000000000000000000000000000000000000..627058e0ca2498cea381dc12567b4bc54409737c
--- /dev/null
+++ b/outputs/main_paper/hydrangea_20260513_214340/database.db
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:c46d7b2a8f2be26f0342a18e9576a09aa51f3b23db7cd3baee8cccb3eae8f96c
+size 16388096
diff --git a/outputs/main_paper/hydrangea_20260513_214340/focus_stack/depthmaps/scan00.png b/outputs/main_paper/hydrangea_20260513_214340/focus_stack/depthmaps/scan00.png
new file mode 100644
index 0000000000000000000000000000000000000000..a1ace96f180df148eeb261faa850630c91d400e9
--- /dev/null
+++ b/outputs/main_paper/hydrangea_20260513_214340/focus_stack/depthmaps/scan00.png
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:90a5a4240d00b38e45fbb491fa1faba416d61d0c919242307e654e1fc066aa6c
+size 182352
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+    ]
+  ],
+  "scan131.png": [
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+      -0.5499171494246394,
+      -0.12276844556716136,
+      0.8261471040569599,
+      0.7340575190302022
+    ],
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+      -0.010854466050940804,
+      -0.555193408801366,
+      0.04182511752393247
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+      0.07712761748174649,
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+      0.413051115527257
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+      0.0,
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+      1.0
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+  "scan132.png": [
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+      -0.35681624905642995,
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+      0.9228261518159412,
+      0.7239203679447774
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+      -0.9323064514555122,
+      -0.007104751082101116,
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+      0.022404606521625185
+    ],
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+      0.05904951298470172,
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+      -0.1328069668281342,
+      0.41689792872985626
+    ],
+    [
+      0.0,
+      0.0,
+      0.0,
+      1.0
+    ]
+  ],
+  "scan133.png": [
+    [
+      -0.3459860789900377,
+      -0.34627044906585447,
+      0.872003675020255,
+      0.7297163928919802
+    ],
+    [
+      -0.9285055638265366,
+      -0.007164370481195684,
+      -0.3712493632839974,
+      0.023416809613186783
+    ],
+    [
+      0.13480004112857158,
+      -0.9381073754636724,
+      -0.3190352660951385,
+      0.4360734976782963
+    ],
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+      0.0,
+      0.0,
+      0.0,
+      1.0
+    ]
+  ],
+  "scan134.png": [
+    [
+      -0.6597730348885728,
+      0.5220480324523238,
+      0.5405232596721252,
+      0.7622683981223474
+    ],
+    [
+      -0.6408338202540733,
+      -0.015204681401651775,
+      -0.7675290434127199,
+      0.06213114243614375
+    ],
+    [
+      -0.3924685430101276,
+      -0.8527805517694053,
+      0.34457767378542664,
+      0.3669438599147881
+    ],
+    [
+      0.0,
+      0.0,
+      0.0,
+      1.0
+    ]
+  ]
+}
\ No newline at end of file
diff --git a/outputs/main_paper/hydrangea_20260513_214340/run_pipeline.log b/outputs/main_paper/hydrangea_20260513_214340/run_pipeline.log
new file mode 100644
index 0000000000000000000000000000000000000000..ea8bc7692ad5d9aa6698f68a339bdf4418e85e93
--- /dev/null
+++ b/outputs/main_paper/hydrangea_20260513_214340/run_pipeline.log
@@ -0,0 +1,6 @@
+[2026-05-26 23:37:41,909][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 23:37:41,911][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 23:37:51,605][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 23:37:53,121][root][INFO] - For numpy array image, we assume (HxWxC) format
+[2026-05-26 23:37:53,475][root][INFO] - Computing image embeddings for the provided image...
+[2026-05-26 23:38:09,436][root][INFO] - Image embeddings computed.
diff --git a/outputs/main_paper/hydrangea_20260513_214340/sparse_model/cameras.bin b/outputs/main_paper/hydrangea_20260513_214340/sparse_model/cameras.bin
new file mode 100644
index 0000000000000000000000000000000000000000..29bb7e523a99bed7b837203bbb8189574204940d
--- /dev/null
+++ b/outputs/main_paper/hydrangea_20260513_214340/sparse_model/cameras.bin
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:9ee35e481b9fb4cf12d6e8f14cca051a5df224885f6a63030fd99c02746f45c1
+size 96
diff --git a/outputs/main_paper/hydrangea_20260513_214340/sparse_model/cameras.txt b/outputs/main_paper/hydrangea_20260513_214340/sparse_model/cameras.txt
new file mode 100644
index 0000000000000000000000000000000000000000..26b41c1f83a2c834c3d42f2df3a9f183c7533dfb
--- /dev/null
+++ b/outputs/main_paper/hydrangea_20260513_214340/sparse_model/cameras.txt
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:5b495cf85cbb46c8060f711d91457a94beee4f18e57ed5f8e9ecb4f0515bf167
+size 294
diff --git a/outputs/main_paper/hydrangea_20260513_214340/sparse_model/frames.bin b/outputs/main_paper/hydrangea_20260513_214340/sparse_model/frames.bin
new file mode 100644
index 0000000000000000000000000000000000000000..89c7f05f98969b06ca684cacd7d2d35be224d076
--- /dev/null
+++ b/outputs/main_paper/hydrangea_20260513_214340/sparse_model/frames.bin
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:8ece651d116c38e0fe5d4b70be9f77daff7e9fb3cc6906d2caa3f49001a89065
+size 512
diff --git a/outputs/main_paper/hydrangea_20260513_214340/sparse_model/frames.txt b/outputs/main_paper/hydrangea_20260513_214340/sparse_model/frames.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eab38be53c537c5cfaecec6f233d717ab8596699
--- /dev/null
+++ b/outputs/main_paper/hydrangea_20260513_214340/sparse_model/frames.txt
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:e612b3c74b5ac228dd5dc91a8c11ba4acf463ad405bea5c735fbbabd89213901
+size 1152
diff --git a/outputs/main_paper/hydrangea_20260513_214340/sparse_model/images.bin b/outputs/main_paper/hydrangea_20260513_214340/sparse_model/images.bin
new file mode 100644
index 0000000000000000000000000000000000000000..6189356ae9ca4f2178b4fe38c70b88e1dc0df261
--- /dev/null
+++ b/outputs/main_paper/hydrangea_20260513_214340/sparse_model/images.bin
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:69955c1c1b220db7019fb196dc673708b0a3b47277bc3e01380b8000443570e5
+size 187802
diff --git a/outputs/main_paper/hydrangea_20260513_214340/sparse_model/images.txt b/outputs/main_paper/hydrangea_20260513_214340/sparse_model/images.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0be9200b0e4e04fe6b0825abe0b957883789ed6f
--- /dev/null
+++ b/outputs/main_paper/hydrangea_20260513_214340/sparse_model/images.txt
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:41c0920ed44251141d9128283e409cfb644296184073cde48cd94ec2a9d058b3
+size 310235
diff --git a/outputs/main_paper/hydrangea_20260513_214340/sparse_model/points3D.bin b/outputs/main_paper/hydrangea_20260513_214340/sparse_model/points3D.bin
new file mode 100644
index 0000000000000000000000000000000000000000..1e7c32e78caf371995084262794cbc3a461d9bba
--- /dev/null
+++ b/outputs/main_paper/hydrangea_20260513_214340/sparse_model/points3D.bin
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:8227138abfa58ae30fb6d813c933002912f44373dccbdfa287ab09cd158854e6
+size 63714
diff --git a/outputs/main_paper/hydrangea_20260513_214340/sparse_model/points3D.txt b/outputs/main_paper/hydrangea_20260513_214340/sparse_model/points3D.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7d1dfcebca06759c9771d33b75e1278638890303
--- /dev/null
+++ b/outputs/main_paper/hydrangea_20260513_214340/sparse_model/points3D.txt
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:2ad9d533da45f6fc025f4c9f088fdb337e6e142c5417f73e9b2fc55c4f3e384c
+size 95446
diff --git a/outputs/main_paper/hydrangea_20260513_214340/sparse_model/rigs.bin b/outputs/main_paper/hydrangea_20260513_214340/sparse_model/rigs.bin
new file mode 100644
index 0000000000000000000000000000000000000000..1f7b8c4eb6144d4a8702e6db6c0ab22f478e591b
--- /dev/null
+++ b/outputs/main_paper/hydrangea_20260513_214340/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/hydrangea_20260513_214340/sparse_model/rigs.txt b/outputs/main_paper/hydrangea_20260513_214340/sparse_model/rigs.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f5a80293086199eaafc48e225055030960a80714
--- /dev/null
+++ b/outputs/main_paper/hydrangea_20260513_214340/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/hydrangea_20260513_214340/sparse_model/sparse_pointcloud.ply b/outputs/main_paper/hydrangea_20260513_214340/sparse_model/sparse_pointcloud.ply
new file mode 100644
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--- /dev/null
+++ b/outputs/main_paper/hydrangea_20260513_214340/sparse_model/sparse_pointcloud.ply
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
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+size 12867
diff --git a/outputs/main_paper/leaf_20260518_171207/.hydra/config.yaml b/outputs/main_paper/leaf_20260518_171207/.hydra/config.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..1d4710166b42f737e8c00e9428a53e785fd434aa
--- /dev/null
+++ b/outputs/main_paper/leaf_20260518_171207/.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: leaf_20260518_171207
+random_seed: 0
+dataset_dir: data/leaf_20260518_171207
+run:
+  focus_stack: true
+  masking: true
+  colmap: true
+  gs_3d: true
diff --git a/outputs/main_paper/leaf_20260518_171207/.hydra/hydra.yaml b/outputs/main_paper/leaf_20260518_171207/.hydra/hydra.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..abb4d6e4a38bb97c769d1e116a08b5121f9ff8d7
--- /dev/null
+++ b/outputs/main_paper/leaf_20260518_171207/.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=leaf_20260518_171207
+    - dataset_dir=data/leaf_20260518_171207
+  job:
+    name: run_pipeline
+    chdir: false
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+      schema: file
+      provider: main
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+      schema: structured
+      provider: schema
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+    choices:
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+      gs_3d: default
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diff --git a/outputs/main_paper/leaf_20260518_171207/run_pipeline.log b/outputs/main_paper/leaf_20260518_171207/run_pipeline.log
new file mode 100644
index 0000000000000000000000000000000000000000..dea256c0e0a6c2512cfbeb6d55cc1066fad780ae
--- /dev/null
+++ b/outputs/main_paper/leaf_20260518_171207/run_pipeline.log
@@ -0,0 +1,5 @@
+[2026-05-26 23:39:08,954][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 23:39:11,219][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 23:39:12,752][root][INFO] - For numpy array image, we assume (HxWxC) format
+[2026-05-26 23:39:12,818][root][INFO] - Computing image embeddings for the provided image...
+[2026-05-26 23:39:13,009][root][INFO] - Image embeddings computed.
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diff --git a/outputs/main_paper/purple_hydrangea_20260518_144141/.hydra/config.yaml b/outputs/main_paper/purple_hydrangea_20260518_144141/.hydra/config.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..6028b186bf1db78e3ced1002c3b79a60a4a49eee
--- /dev/null
+++ b/outputs/main_paper/purple_hydrangea_20260518_144141/.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: purple_hydrangea_20260518_144141
+random_seed: 0
+dataset_dir: data/purple_hydrangea_20260518_144141
+run:
+  focus_stack: true
+  masking: true
+  colmap: true
+  gs_3d: true
diff --git a/outputs/main_paper/purple_hydrangea_20260518_144141/.hydra/hydra.yaml b/outputs/main_paper/purple_hydrangea_20260518_144141/.hydra/hydra.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..40309e70fbc5ec7bdaaec8d00cb6985de9a56088
--- /dev/null
+++ b/outputs/main_paper/purple_hydrangea_20260518_144141/.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=purple_hydrangea_20260518_144141
+    - dataset_dir=data/purple_hydrangea_20260518_144141
+  job:
+    name: run_pipeline
+    chdir: false
+    override_dirname: +experiment=main_paper,dataset_dir=data/purple_hydrangea_20260518_144141,experiment_name=purple_hydrangea_20260518_144141
+    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/purple_hydrangea_20260518_144141
+    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/purple_hydrangea_20260518_144141/.hydra/overrides.yaml b/outputs/main_paper/purple_hydrangea_20260518_144141/.hydra/overrides.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..1053b2939f148ac327d9c0ec5736480132f3b96e
--- /dev/null
+++ b/outputs/main_paper/purple_hydrangea_20260518_144141/.hydra/overrides.yaml
@@ -0,0 +1,3 @@
+- +experiment=main_paper
+- experiment_name=purple_hydrangea_20260518_144141
+- dataset_dir=data/purple_hydrangea_20260518_144141
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--- /dev/null
+++ b/outputs/main_paper/purple_hydrangea_20260518_144141/database.db
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:1028233428c73dd74c1221eb27efcbaf1d801b727fedba144be5a68cafa27e71
+size 20602880
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diff --git a/outputs/main_paper/purple_hydrangea_20260518_144141/run_pipeline.log b/outputs/main_paper/purple_hydrangea_20260518_144141/run_pipeline.log
new file mode 100644
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+[2026-05-27 00:09:08,140][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 00:09:08,141][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.
+[2026-05-27 00:09:20,159][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 00:09:21,823][root][INFO] - For numpy array image, we assume (HxWxC) format
+[2026-05-27 00:09:22,568][root][INFO] - Computing image embeddings for the provided image...
+[2026-05-27 00:09:50,520][root][INFO] - Image embeddings computed.
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