new data w background

.gitattributes

@@ -61,3 +61,4 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 # 3D files and database
 *.db filter=lfs diff=lfs merge=lfs -text
 *.ply filter=lfs diff=lfs merge=lfs -text
+*.vis filter=lfs diff=lfs merge=lfs -text

scans/03_08_2026/colmap/database.db

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+version https://git-lfs.github.com/spec/v1
+oid sha256:72432343fd6204221d5e3b6aef363878ebad63a248c49287f0ae306c20fab41d
+size 53743616

scans/03_08_2026/colmap/project.ini

@@ -0,0 +1,209 @@
+log_to_stderr=true
+random_seed=0
+log_level=0
+database_path=/home/codaero/Projects/Microscopic-3D-Reconstruction/microscope-data/scans/03_08_2026/colmap/database.db
+image_path=/home/codaero/Projects/Microscopic-3D-Reconstruction/microscope-data/scans/03_08_2026/focus_stacked
+[ImageReader]
+single_camera=false
+single_camera_per_folder=false
+single_camera_per_image=false
+existing_camera_id=-1
+default_focal_length_factor=1.2
+mask_path=
+camera_model=SIMPLE_RADIAL
+camera_params=
+camera_mask_path=
+[SiftExtraction]
+use_gpu=true
+estimate_affine_shape=false
+upright=false
+domain_size_pooling=false
+num_threads=-1
+max_image_size=3200
+max_num_features=8192
+first_octave=-1
+num_octaves=4
+octave_resolution=3
+max_num_orientations=2
+dsp_num_scales=10
+peak_threshold=0.0066666666666666671
+edge_threshold=10
+dsp_min_scale=0.16666666666666666
+dsp_max_scale=3
+gpu_index=-1
+[SiftMatching]
+use_gpu=true
+cross_check=true
+guided_matching=false
+num_threads=-1
+max_num_matches=32768
+max_ratio=0.80000000000000004
+max_distance=0.69999999999999996
+gpu_index=-1
+[TwoViewGeometry]
+multiple_models=false
+compute_relative_pose=false
+min_num_inliers=15
+max_num_trials=10000
+max_error=4
+confidence=0.999
+min_inlier_ratio=0.25
+[SequentialMatching]
+quadratic_overlap=true
+loop_detection=false
+overlap=10
+loop_detection_period=10
+loop_detection_num_images=50
+loop_detection_num_nearest_neighbors=1
+loop_detection_num_checks=256
+loop_detection_num_images_after_verification=0
+loop_detection_max_num_features=-1
+vocab_tree_path=
+[SpatialMatching]
+is_gps=true
+ignore_z=true
+max_num_neighbors=50
+max_distance=100
+[BundleAdjustment]
+refine_focal_length=true
+refine_principal_point=false
+refine_extra_params=true
+refine_extrinsics=true
+max_num_iterations=100
+max_linear_solver_iterations=200
+function_tolerance=0
+gradient_tolerance=0
+parameter_tolerance=0
+[Mapper]
+ignore_watermarks=false
+multiple_models=true
+extract_colors=true
+ba_refine_focal_length=true
+ba_refine_principal_point=false
+ba_refine_extra_params=true
+fix_existing_images=false
+tri_ignore_two_view_tracks=true
+min_num_matches=15
+max_num_models=50
+max_model_overlap=20
+min_model_size=10
+init_image_id1=-1
+init_image_id2=-1
+init_num_trials=200
+num_threads=-1
+ba_min_num_residuals_for_multi_threading=50000
+ba_local_num_images=6
+ba_local_max_num_iterations=25
+ba_global_images_freq=500
+ba_global_points_freq=250000
+ba_global_max_num_iterations=50
+ba_global_max_refinements=5
+ba_local_max_refinements=2
+snapshot_images_freq=0
+init_min_num_inliers=100
+init_max_reg_trials=2
+abs_pose_min_num_inliers=30
+max_reg_trials=3
+tri_max_transitivity=1
+tri_complete_max_transitivity=5
+tri_re_max_trials=1
+min_focal_length_ratio=0.10000000000000001
+max_focal_length_ratio=10
+max_extra_param=1
+ba_local_function_tolerance=0
+ba_global_images_ratio=1.1000000000000001
+ba_global_points_ratio=1.1000000000000001
+ba_global_function_tolerance=0
+ba_global_max_refinement_change=0.00050000000000000001
+ba_local_max_refinement_change=0.001
+init_max_error=4
+init_max_forward_motion=0.94999999999999996
+init_min_tri_angle=16
+abs_pose_max_error=12
+abs_pose_min_inlier_ratio=0.25
+filter_max_reproj_error=4
+filter_min_tri_angle=1.5
+local_ba_min_tri_angle=6
+tri_create_max_angle_error=2
+tri_continue_max_angle_error=2
+tri_merge_max_reproj_error=4
+tri_complete_max_reproj_error=4
+tri_re_max_angle_error=5
+tri_re_min_ratio=0.20000000000000001
+tri_min_angle=1.5
+snapshot_path=
+[PatchMatchStereo]
+geom_consistency=true
+filter=true
+allow_missing_files=false
+write_consistency_graph=false
+max_image_size=2000
+window_radius=5
+window_step=1
+num_samples=15
+num_iterations=5
+filter_min_num_consistent=2
+depth_min=-1
+depth_max=-1
+sigma_spatial=-1
+sigma_color=0.20000000298023224
+ncc_sigma=0.60000002384185791
+min_triangulation_angle=1
+incident_angle_sigma=0.89999997615814209
+geom_consistency_regularizer=0.30000001192092896
+geom_consistency_max_cost=3
+filter_min_ncc=0.10000000149011612
+filter_min_triangulation_angle=3
+filter_geom_consistency_max_cost=1
+cache_size=32
+gpu_index=-1
+[StereoFusion]
+use_cache=false
+num_threads=-1
+max_image_size=-1
+min_num_pixels=5
+max_num_pixels=10000
+max_traversal_depth=100
+check_num_images=50
+max_reproj_error=2
+max_depth_error=0.0099999997764825821
+max_normal_error=10
+cache_size=32
+mask_path=
+[Render]
+adapt_refresh_rate=true
+image_connections=false
+min_track_len=3
+refresh_rate=1
+projection_type=0
+max_error=2
+[ExhaustiveMatching]
+block_size=50
+[VocabTreeMatching]
+num_images=100
+num_nearest_neighbors=5
+num_checks=256
+num_images_after_verification=0
+max_num_features=-1
+vocab_tree_path=
+match_list_path=
+[TransitiveMatching]
+batch_size=1000
+num_iterations=3
+[ImagePairsMatching]
+block_size=1225
+[PoissonMeshing]
+depth=13
+num_threads=-1
+point_weight=1
+color=32
+trim=10
+[DelaunayMeshing]
+num_threads=-1
+max_proj_dist=20
+max_depth_dist=0.050000000000000003
+visibility_sigma=3
+distance_sigma_factor=1
+quality_regularization=1
+max_side_length_factor=25
+max_side_length_percentile=95

scans/03_08_2026/colmap/sparse/0/cameras.bin

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+version https://git-lfs.github.com/spec/v1
+oid sha256:fa5898b8e1f7de29dbb270401f2c92bd246ef70149a6ec6089dc0c14a2d8c0d9
+size 1912

scans/03_08_2026/colmap/sparse/0/images.bin

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+version https://git-lfs.github.com/spec/v1
+oid sha256:58a6126c70374a19ed1ef73e34c9a97ab86bd91946fb53392b51d95e2cbd1806
+size 8198230

scans/03_08_2026/colmap/sparse/0/points3D.bin

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:cfe84b4e9b45154a2e92b5b3bddf500cc9cfa5dc3fbd69e38ca16792cd30a46d
+size 1281328

scans/03_08_2026/colmap/sparse/project.ini

@@ -0,0 +1,209 @@
+log_to_stderr=true
+random_seed=0
+log_level=0
+database_path=/home/codaero/Projects/Microscopic-3D-Reconstruction/microscope-data/scans/03_08_2026/colmap/database.db
+image_path=/home/codaero/Projects/Microscopic-3D-Reconstruction/microscope-data/scans/03_08_2026/focus_stacked
+[ImageReader]
+single_camera=false
+single_camera_per_folder=false
+single_camera_per_image=false
+existing_camera_id=-1
+default_focal_length_factor=1.2
+mask_path=
+camera_model=SIMPLE_RADIAL
+camera_params=
+camera_mask_path=
+[SiftExtraction]
+use_gpu=true
+estimate_affine_shape=true
+upright=false
+domain_size_pooling=false
+num_threads=-1
+max_image_size=2400
+max_num_features=8192
+first_octave=-1
+num_octaves=4
+octave_resolution=3
+max_num_orientations=2
+dsp_num_scales=10
+peak_threshold=0.0066666666666666671
+edge_threshold=10
+dsp_min_scale=0.16666666666666666
+dsp_max_scale=3
+gpu_index=-1
+[SiftMatching]
+use_gpu=true
+cross_check=true
+guided_matching=true
+num_threads=-1
+max_num_matches=32768
+max_ratio=0.80000000000000004
+max_distance=0.69999999999999996
+gpu_index=-1
+[TwoViewGeometry]
+multiple_models=false
+compute_relative_pose=false
+min_num_inliers=15
+max_num_trials=10000
+max_error=4
+confidence=0.999
+min_inlier_ratio=0.25
+[SequentialMatching]
+quadratic_overlap=true
+loop_detection=false
+overlap=10
+loop_detection_period=10
+loop_detection_num_images=50
+loop_detection_num_nearest_neighbors=1
+loop_detection_num_checks=256
+loop_detection_num_images_after_verification=0
+loop_detection_max_num_features=-1
+vocab_tree_path=
+[SpatialMatching]
+is_gps=true
+ignore_z=true
+max_num_neighbors=50
+max_distance=100
+[BundleAdjustment]
+refine_focal_length=true
+refine_principal_point=false
+refine_extra_params=true
+refine_extrinsics=true
+max_num_iterations=100
+max_linear_solver_iterations=200
+function_tolerance=0
+gradient_tolerance=0
+parameter_tolerance=0
+[Mapper]
+ignore_watermarks=false
+multiple_models=true
+extract_colors=true
+ba_refine_focal_length=true
+ba_refine_principal_point=false
+ba_refine_extra_params=true
+fix_existing_images=false
+tri_ignore_two_view_tracks=true
+min_num_matches=15
+max_num_models=50
+max_model_overlap=20
+min_model_size=10
+init_image_id1=-1
+init_image_id2=-1
+init_num_trials=200
+num_threads=-1
+ba_min_num_residuals_for_multi_threading=50000
+ba_local_num_images=6
+ba_local_max_num_iterations=30
+ba_global_images_freq=500
+ba_global_points_freq=250000
+ba_global_max_num_iterations=75
+ba_global_max_refinements=5
+ba_local_max_refinements=3
+snapshot_images_freq=0
+init_min_num_inliers=100
+init_max_reg_trials=2
+abs_pose_min_num_inliers=30
+max_reg_trials=3
+tri_max_transitivity=1
+tri_complete_max_transitivity=5
+tri_re_max_trials=1
+min_focal_length_ratio=0.10000000000000001
+max_focal_length_ratio=10
+max_extra_param=1.7976931348623157e+308
+ba_local_function_tolerance=0
+ba_global_images_ratio=1.1000000000000001
+ba_global_points_ratio=1.1000000000000001
+ba_global_function_tolerance=0
+ba_global_max_refinement_change=0.00050000000000000001
+ba_local_max_refinement_change=0.001
+init_max_error=4
+init_max_forward_motion=0.94999999999999996
+init_min_tri_angle=16
+abs_pose_max_error=12
+abs_pose_min_inlier_ratio=0.25
+filter_max_reproj_error=4
+filter_min_tri_angle=1.5
+local_ba_min_tri_angle=6
+tri_create_max_angle_error=2
+tri_continue_max_angle_error=2
+tri_merge_max_reproj_error=4
+tri_complete_max_reproj_error=4
+tri_re_max_angle_error=5
+tri_re_min_ratio=0.20000000000000001
+tri_min_angle=1.5
+snapshot_path=
+[PatchMatchStereo]
+geom_consistency=true
+filter=true
+allow_missing_files=false
+write_consistency_graph=false
+max_image_size=2400
+window_radius=5
+window_step=1
+num_samples=15
+num_iterations=5
+filter_min_num_consistent=2
+depth_min=-1
+depth_max=-1
+sigma_spatial=-1
+sigma_color=0.20000000298023224
+ncc_sigma=0.60000002384185791
+min_triangulation_angle=1
+incident_angle_sigma=0.89999997615814209
+geom_consistency_regularizer=0.30000001192092896
+geom_consistency_max_cost=3
+filter_min_ncc=0.10000000149011612
+filter_min_triangulation_angle=3
+filter_geom_consistency_max_cost=1
+cache_size=32
+gpu_index=-1
+[StereoFusion]
+use_cache=false
+num_threads=-1
+max_image_size=2400
+min_num_pixels=5
+max_num_pixels=10000
+max_traversal_depth=100
+check_num_images=50
+max_reproj_error=2
+max_depth_error=0.0099999997764825821
+max_normal_error=10
+cache_size=32
+mask_path=
+[Render]
+adapt_refresh_rate=true
+image_connections=false
+min_track_len=3
+refresh_rate=1
+projection_type=0
+max_error=2
+[ExhaustiveMatching]
+block_size=50
+[VocabTreeMatching]
+num_images=100
+num_nearest_neighbors=5
+num_checks=256
+num_images_after_verification=0
+max_num_features=-1
+vocab_tree_path=
+match_list_path=
+[TransitiveMatching]
+batch_size=1000
+num_iterations=3
+[ImagePairsMatching]
+block_size=1225
+[PoissonMeshing]
+depth=13
+num_threads=-1
+point_weight=1
+color=32
+trim=10
+[DelaunayMeshing]
+num_threads=-1
+max_proj_dist=20
+max_depth_dist=0.050000000000000003
+visibility_sigma=3
+distance_sigma_factor=1
+quality_regularization=1
+max_side_length_factor=25
+max_side_length_percentile=95

scans/03_08_2026_cleaned/colmap/database.db

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+version https://git-lfs.github.com/spec/v1
+oid sha256:bdb82c07f51c598cace2d0ae860e09d437ffaf8aca7cc08195dc7285a1684d6f
+size 41865216

scans/03_08_2026_cleaned/colmap/dense/0/fused.ply

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+version https://git-lfs.github.com/spec/v1
+oid sha256:493c34dc44df4a88c8f6e3f5bdb4512b2da20deb890ea9b6d2dcafe9eedfc57b
+size 5530590

scans/03_08_2026_cleaned/colmap/dense/0/fused.ply.vis

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+version https://git-lfs.github.com/spec/v1
+oid sha256:5c19b31904f62db02733e1d375e3483e6b41f45485330703739a2c852e036e42
+size 5623440