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[Auto-generated] Submodule Updates 30403845845 #92

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2 changes: 1 addition & 1 deletion repos/ac_reconstruction_analysis
Open in desktop
Submodule ac_reconstruction_analysis updated 66 files
+3 −7 .github/workflows/pixi.yml
+0 −0 .github/workflows/submodule-update.yml
+0 −0 .gitignore
+20 −0 Dockerfile
+0 −0 MANIFEST.in
+45 −1 README.md
+0 −0 acanalysis/__init__.py
+0 −0 acanalysis/acalignment/__init__.py
+0 −0 acanalysis/acalignment/examples/2_example_generate_keypoints.ipynb
+0 −0 acanalysis/acalignment/examples/3_example_match_keypoints.ipynb
+0 −0 acanalysis/acalignment/examples/align_S32_S33_roi1_mip0.json
+74 −20 acanalysis/acalignment/generate_keypoints.py
+0 −0 acanalysis/acalignment/keypoints.py
+0 −0 acanalysis/acalignment/match_keypoints.py
+0 −0 acanalysis/acalignment/transforms.py
+0 −0 acanalysis/acalignment/utils/__init__.py
+557 −0 acanalysis/acalignment/utils/h5_utils.py
+160 −2 acanalysis/acalignment/utils/kevin_utils.py
+0 −0 acanalysis/acalignment/utils/olga_utils.py
+1 −1 acanalysis/acalignment/utils/swc_utils.py
+0 −0 acanalysis/odf/__init__.py
+38 −0 acanalysis/odf/plotting.py
+35 −0 acanalysis/odf/utils.py
+0 −0 acanalysis/save_cutout_for_segmentation.py
+0 −0 acanalysis/skeleton_reconstruction/__init__.py
+0 −0 acanalysis/skeleton_reconstruction/catmaid.py
+71 −0 acanalysis/skeleton_reconstruction/generate_precomputed_skels.py
+0 −212 acanalysis/skeleton_reconstruction/interstrip_reconnect.py
+1 −1 acanalysis/skeleton_reconstruction/neuroglancer.py
+0 −239 acanalysis/skeleton_reconstruction/notebooks/Interstrip_Connect.ipynb
+0 −121 acanalysis/skeleton_reconstruction/notebooks/Reconnect_Skeletons.ipynb
+0 −117 acanalysis/skeleton_reconstruction/notebooks/S32_file_trans.json
+0 −374 acanalysis/skeleton_reconstruction/notebooks/Stitch_Skeletons.ipynb
+0 −0 acanalysis/skeleton_reconstruction/reconnection/__init__.py
+190 −0 acanalysis/skeleton_reconstruction/reconnection/create_components.py
+169 −0 acanalysis/skeleton_reconstruction/reconnection/find_pairs.py
+773 −0 acanalysis/skeleton_reconstruction/reconnection/h5_reconnect.py
+581 −0 acanalysis/skeleton_reconstruction/reconnection/h5_skeletons.py
+165 −0 acanalysis/skeleton_reconstruction/reconnection/merge_overlap.py
+151 −0 acanalysis/skeleton_reconstruction/reconnection/merge_pairs.py
+6 −6 acanalysis/skeleton_reconstruction/reconnection/reconnect_navis.py
+42 −2 acanalysis/skeleton_reconstruction/reconnection/utils.py
+0 −0 acanalysis/splitup_swc.py
+0 −0 acanalysis/utils.py
+0 −0 acanalysis/write_swc_state.py
+0 −0 demos/CATMAID_Functions.ipynb
+0 −0 demos/Neuroglancer_Functions.ipynb
+0 −0 demos/alignment/1_example_surface_detection.ipynb
+0 −0 demos/alignment/2_example_generate_keypoints.ipynb
+0 −0 demos/alignment/3_example_match_keypoints_new.ipynb
+0 −0 demos/alignment/4_example_skeleton_warp_updated.ipynb
+0 −0 demos/alignment/6_example_materialize_to_tiff.ipynb
+0 −0 demos/alignment/align_S32_S33_roi4_mip1_240408.json
+3 −0 entrypoint.sh
+ − examples/analysis/data/box_000.pkl
+ − examples/analysis/data/box_pos_5x10.pkl
+ − examples/analysis/data/mean_vectors_5x10.pkl
+ − examples/analysis/figures/skels_ori.pdf
+489 −0 examples/analysis/odf_analysis.ipynb
+12 −11 pyproject.toml
+5 −1 requirements.txt
+0 −0 test/__init__.py
+ − test/model/LR_1.joblib
+ − test/model/scaler.joblib
+0 −0 test/test_import.py
+0 −11 test/test_reconnect.py
2 changes: 1 addition & 1 deletion repos/ac_segmentation
Open in desktop
Submodule ac_segmentation updated 191 files
2 changes: 1 addition & 1 deletion repos/axonal_connectomics
Open in desktop
Submodule axonal_connectomics updated 14 files
+4 −4 .github/workflows/ci.yml
+23 −0 .github/workflows/pixi.yml
+8 −4 README.md
+0 −0 acpreprocessing/stitching_modules/acstitch/__init__.py
+132 −0 acpreprocessing/stitching_modules/acstitch/extract_points.py
+59 −79 acpreprocessing/stitching_modules/acstitch/stitch.py
+32 −3 acpreprocessing/stitching_modules/acstitch/zarrutils.py
+3 −3 acpreprocessing/stitching_modules/convert_to_n5/acquisition_dir_to_ngff.py
+5 −5 acpreprocessing/stitching_modules/convert_to_n5/psdeskew.py
+133 −189 acpreprocessing/stitching_modules/convert_to_n5/tiff_to_ngff.py
+0 −181 acpreprocessing/stitching_modules/convert_to_n5/tiff_to_visor.py
+247 −0 acpreprocessing/stitching_modules/convert_to_n5/ts_utils.py
+564 −0 acpreprocessing/stitching_modules/convert_to_n5/zarrv3_to_ngff.py
+6 −9 pyproject.toml