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+++ b/scans/20260401_205638/colmap/dense/0/images/scan40.jpg
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:b68705b55130e531ab5960d72a1da49c04736591eb1cd4417f0bd86670a97878
+size 981815
diff --git a/scans/20260401_205638/colmap/dense/0/images/scan42.jpg b/scans/20260401_205638/colmap/dense/0/images/scan42.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..81289f339735cc932c663523c76eae5d02e74865
--- /dev/null
+++ b/scans/20260401_205638/colmap/dense/0/images/scan42.jpg
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:261932592111ff860b46921fa6557fde82c45c489f3dbaf73013ddd5771f85b7
+size 1613060
diff --git a/scans/20260401_205638/colmap/dense/0/run-colmap-geometric.sh b/scans/20260401_205638/colmap/dense/0/run-colmap-geometric.sh
new file mode 100644
index 0000000000000000000000000000000000000000..3a6cb07e671c196ac0178ec73d612c27ee8cb3ca
--- /dev/null
+++ b/scans/20260401_205638/colmap/dense/0/run-colmap-geometric.sh
@@ -0,0 +1,19 @@
+# You must set $COLMAP_EXE_PATH to 
+# the directory containing the COLMAP executables.
+$COLMAP_EXE_PATH/colmap patch_match_stereo \
+  --workspace_path . \
+  --workspace_format COLMAP \
+  --PatchMatchStereo.max_image_size 2000 \
+  --PatchMatchStereo.geom_consistency true
+$COLMAP_EXE_PATH/colmap stereo_fusion \
+  --workspace_path . \
+  --workspace_format COLMAP \
+  --input_type geometric \
+  --output_path ./fused.ply
+$COLMAP_EXE_PATH/colmap poisson_mesher \
+  --input_path ./fused.ply \
+  --output_path ./meshed-poisson.ply
+$COLMAP_EXE_PATH/colmap delaunay_mesher \
+  --input_path . \
+  --input_type dense \
+  --output_path ./meshed-delaunay.ply
diff --git a/scans/20260401_205638/colmap/dense/0/run-colmap-photometric.sh b/scans/20260401_205638/colmap/dense/0/run-colmap-photometric.sh
new file mode 100644
index 0000000000000000000000000000000000000000..86e8aa28cc5c8dd4a45dc0a6cd6b1174d076e4a8
--- /dev/null
+++ b/scans/20260401_205638/colmap/dense/0/run-colmap-photometric.sh
@@ -0,0 +1,19 @@
+# You must set $COLMAP_EXE_PATH to 
+# the directory containing the COLMAP executables.
+$COLMAP_EXE_PATH/colmap patch_match_stereo \
+  --workspace_path . \
+  --workspace_format COLMAP \
+  --PatchMatchStereo.max_image_size 2000 \
+  --PatchMatchStereo.geom_consistency false
+$COLMAP_EXE_PATH/colmap stereo_fusion \
+  --workspace_path . \
+  --workspace_format COLMAP \
+  --input_type photometric \
+  --output_path ./fused.ply
+$COLMAP_EXE_PATH/colmap poisson_mesher \
+  --input_path ./fused.ply \
+  --output_path ./meshed-poisson.ply
+$COLMAP_EXE_PATH/colmap delaunay_mesher \
+  --input_path . \
+  --input_type dense \
+  --output_path ./meshed-delaunay.ply
diff --git a/scans/20260401_205638/colmap/dense/0/sparse/cameras.bin b/scans/20260401_205638/colmap/dense/0/sparse/cameras.bin
new file mode 100644
index 0000000000000000000000000000000000000000..db33e63c137c2ae2ddf680f53ab4cedd58bbe637
--- /dev/null
+++ b/scans/20260401_205638/colmap/dense/0/sparse/cameras.bin
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:8fe6ad2f0c5e5c0c0e7e6ddbd0bc6f581f6d0315749c00eb8266fc89eae3474c
+size 2192
diff --git a/scans/20260401_205638/colmap/dense/0/sparse/images.bin b/scans/20260401_205638/colmap/dense/0/sparse/images.bin
new file mode 100644
index 0000000000000000000000000000000000000000..2c775a17aed615ce07f0a1af8789f9df22dd03ea
--- /dev/null
+++ b/scans/20260401_205638/colmap/dense/0/sparse/images.bin
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:62c248ba9e2aa6379aa061ee8b80dae0bc54acb9b0193225f08a376c0c252615
+size 6916181
diff --git a/scans/20260401_205638/colmap/dense/0/sparse/points3D.bin b/scans/20260401_205638/colmap/dense/0/sparse/points3D.bin
new file mode 100644
index 0000000000000000000000000000000000000000..eaa8afd964e6324b30b0a46c628cc2b26bf2d8d0
--- /dev/null
+++ b/scans/20260401_205638/colmap/dense/0/sparse/points3D.bin
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:b88b89fac91b8b2e08cc900d5c21b097639a433432579c4312c4275033d2a380
+size 458079
diff --git a/scans/20260401_205638/colmap/dense/0/stereo/fusion.cfg b/scans/20260401_205638/colmap/dense/0/stereo/fusion.cfg
new file mode 100644
index 0000000000000000000000000000000000000000..bf94a885609e0246f5e19f918e7cdcafbdd76c19
--- /dev/null
+++ b/scans/20260401_205638/colmap/dense/0/stereo/fusion.cfg
@@ -0,0 +1,39 @@
+scan39.jpg
+scan21.jpg
+scan13.jpg
+scan34.jpg
+scan18.jpg
+scan31.jpg
+scan26.jpg
+scan10.jpg
+scan05.jpg
+scan08.jpg
+scan23.jpg
+scan29.jpg
+scan16.jpg
+scan03.jpg
+scan02.jpg
+scan01.jpg
+scan37.jpg
+scan07.jpg
+scan28.jpg
+scan20.jpg
+scan33.jpg
+scan36.jpg
+scan12.jpg
+scan25.jpg
+scan42.jpg
+scan15.jpg
+scan17.jpg
+scan04.jpg
+scan09.jpg
+scan30.jpg
+scan06.jpg
+scan14.jpg
+scan22.jpg
+scan35.jpg
+scan19.jpg
+scan32.jpg
+scan27.jpg
+scan40.jpg
+scan11.jpg
diff --git a/scans/20260401_205638/colmap/dense/0/stereo/patch-match.cfg b/scans/20260401_205638/colmap/dense/0/stereo/patch-match.cfg
new file mode 100644
index 0000000000000000000000000000000000000000..aebb48200ec611540f4184f12a68bf04673add1c
--- /dev/null
+++ b/scans/20260401_205638/colmap/dense/0/stereo/patch-match.cfg
@@ -0,0 +1,78 @@
+scan39.jpg
+__auto__, 20
+scan21.jpg
+__auto__, 20
+scan13.jpg
+__auto__, 20
+scan34.jpg
+__auto__, 20
+scan18.jpg
+__auto__, 20
+scan31.jpg
+__auto__, 20
+scan26.jpg
+__auto__, 20
+scan10.jpg
+__auto__, 20
+scan05.jpg
+__auto__, 20
+scan08.jpg
+__auto__, 20
+scan23.jpg
+__auto__, 20
+scan29.jpg
+__auto__, 20
+scan16.jpg
+__auto__, 20
+scan03.jpg
+__auto__, 20
+scan02.jpg
+__auto__, 20
+scan01.jpg
+__auto__, 20
+scan37.jpg
+__auto__, 20
+scan07.jpg
+__auto__, 20
+scan28.jpg
+__auto__, 20
+scan20.jpg
+__auto__, 20
+scan33.jpg
+__auto__, 20
+scan36.jpg
+__auto__, 20
+scan12.jpg
+__auto__, 20
+scan25.jpg
+__auto__, 20
+scan42.jpg
+__auto__, 20
+scan15.jpg
+__auto__, 20
+scan17.jpg
+__auto__, 20
+scan04.jpg
+__auto__, 20
+scan09.jpg
+__auto__, 20
+scan30.jpg
+__auto__, 20
+scan06.jpg
+__auto__, 20
+scan14.jpg
+__auto__, 20
+scan22.jpg
+__auto__, 20
+scan35.jpg
+__auto__, 20
+scan19.jpg
+__auto__, 20
+scan32.jpg
+__auto__, 20
+scan27.jpg
+__auto__, 20
+scan40.jpg
+__auto__, 20
+scan11.jpg
+__auto__, 20
diff --git a/scans/20260401_205638/colmap/project.ini b/scans/20260401_205638/colmap/project.ini
new file mode 100644
index 0000000000000000000000000000000000000000..886fb54a936235e45d0921b5bb7cdfac85643d2a
--- /dev/null
+++ b/scans/20260401_205638/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/20260401_205638/colmap/database.db
+image_path=/home/codaero/Projects/Microscopic-3D-Reconstruction/microscope-data/scans/20260401_205638/images
+[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
diff --git a/scans/20260401_205638/colmap/sparse/0/cameras.bin b/scans/20260401_205638/colmap/sparse/0/cameras.bin
new file mode 100644
index 0000000000000000000000000000000000000000..d8f2427f5276956a28550135b17f3ca68ac184df
--- /dev/null
+++ b/scans/20260401_205638/colmap/sparse/0/cameras.bin
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:72984d5fab7fe8cadc3d13c4ca1b23190fadd01b46c3b44c20eb4deab56c4e30
+size 2192
diff --git a/scans/20260401_205638/colmap/sparse/0/images.bin b/scans/20260401_205638/colmap/sparse/0/images.bin
new file mode 100644
index 0000000000000000000000000000000000000000..fd22f27e9386441230f7e813c681e3868801aea5
--- /dev/null
+++ b/scans/20260401_205638/colmap/sparse/0/images.bin
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:ff10dc58b973de2578039c10806b5b8ec4cc4e152d60ddddd76b7d9676c54d21
+size 6916181
diff --git a/scans/20260401_205638/colmap/sparse/0/points3D.bin b/scans/20260401_205638/colmap/sparse/0/points3D.bin
new file mode 100644
index 0000000000000000000000000000000000000000..eaa8afd964e6324b30b0a46c628cc2b26bf2d8d0
--- /dev/null
+++ b/scans/20260401_205638/colmap/sparse/0/points3D.bin
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:b88b89fac91b8b2e08cc900d5c21b097639a433432579c4312c4275033d2a380
+size 458079
diff --git a/scans/20260401_205638/colmap/sparse/project.ini b/scans/20260401_205638/colmap/sparse/project.ini
new file mode 100644
index 0000000000000000000000000000000000000000..95ae0017e18e971c895ade28b1d2dd3688f5c6a2
--- /dev/null
+++ b/scans/20260401_205638/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/20260401_205638/colmap/database.db
+image_path=/home/codaero/Projects/Microscopic-3D-Reconstruction/microscope-data/scans/20260401_205638/images
+[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
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+[BundleAdjustment]
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+[Mapper]
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+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
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+tri_complete_max_transitivity=5
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+ba_local_max_refinement_change=0.001
+init_max_error=4
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+init_min_tri_angle=16
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+tri_re_max_angle_error=5
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+[PatchMatchStereo]
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+incident_angle_sigma=0.89999997615814209
+geom_consistency_regularizer=0.30000001192092896
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+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