.gitignore
.gitlab-ci.yml
.gitreview
.readthedocs.yml
AUTHORS.txt
CONTRIBUTING.md
Dockerfile
LICENSE.txt
bbp_atlas_cli.py
cellCompVolume_payload.py
config.yaml
convert_singularity_image.sh
create_BMO_MR.py
forge-config.json
forge-config.yml
keycloak_config.yml
nexus_ids.json
pyproject.toml
readme.md
requirements.txt
requirements_doc.txt
setup.py
snakeMake.sbatch
snakefile
synch_nexus.py
.github/workflows/on_tag.yml
all_rules_legacy/snakefile_legacy
all_rules_legacy/rules_config_dir_templates/push_dataset_config_template_legacy.yaml
bba_pipeline.egg-info/PKG-INFO
bba_pipeline.egg-info/SOURCES.txt
bba_pipeline.egg-info/dependency_links.txt
bba_pipeline.egg-info/entry_points.txt
bba_pipeline.egg-info/requires.txt
bba_pipeline.egg-info/top_level.txt
customize_pipeline/available_vars.yaml
customize_pipeline/custom_snakefile
customize_pipeline/customize_pipeline.py
customize_pipeline/user_config.json
doc/Dockerfile
doc/Makefile
doc/make.bat
doc/nginx.conf
doc/release_notes.md
doc/upload.sh
doc/source/conf.py
doc/source/doc
doc/source/index.md
doc/source/index_doc.md
doc/source/figures/README_annotation_pipeline_DAG.png
doc/source/figures/README_annotation_pipeline_DAG.svg
doc/source/figures/dag_cellcomp.gv
doc/source/figures/dag_cellcomp.svg
doc/source/figures/dag_push_atlas.gv
doc/source/figures/dag_push_atlas.svg
doc/source/figures/dag_push_atlas_fg.gv
doc/source/figures/dag_push_atlas_fg.svg
doc/source/figures/dag_pushvol.gv
doc/source/figures/dag_pushvol.svg
doc/source/figures/old_README_annotation_pipeline_DAG.png
metadata/PH_layers_regions_map.json
metadata/file_nexus_map.json
metadata/isocortex_metadata.json
metadata/measurements.csv
metadata/probability_map_L1.csv
metadata/probability_map_L23.csv
metadata/probability_map_L4.csv
metadata/probability_map_L5.csv
metadata/probability_map_L6.csv
metadata/probability_map_TH_INH.csv
metadata/regions_layers_map.json
metadata/docs/probability_map_L1.txt
metadata/docs/probability_map_L23.txt
metadata/docs/probability_map_L4.txt
metadata/docs/probability_map_L5.txt
metadata/docs/probability_map_L6.txt
metadata/docs/probability_map_TH_INH.txt
notebooks/CellComposition.ipynb
notebooks/Download_Atlas.ipynb
notebooks/Extract_property_from_graph.ipynb
notebooks/Query_Atlas.ipynb
notebooks/Release_Cell_Composition_Volume.ipynb
notebooks/copy-token.png
notebooks/login-ui.png
notebooks/register_resource_givenID.ipynb
notebooks/update-dkeller-density-data.ipynb
rules_config_dir_templates/cell_positions_ccfv2_config_template.yaml
rules_config_dir_templates/cell_positions_ccfv2_correctednissl_config_template.yaml
rules_config_dir_templates/cell_positions_ccfv2_l23split_correctednissl_config_template.yaml
rules_config_dir_templates/cell_positions_correctednissl_config_template.yaml
rules_config_dir_templates/cell_positions_hybrid_config_template.yaml
rules_config_dir_templates/cell_positions_hybrid_l23split_correctednissl_config_template.yaml
rules_config_dir_templates/cell_positions_realigned_config_template.yaml
rules_config_dir_templates/combine_markers_ccfv2_config_template.yaml
rules_config_dir_templates/combine_markers_ccfv2_l23split_config_template.yaml
rules_config_dir_templates/combine_markers_config_template.yaml
rules_config_dir_templates/combine_markers_hybrid_config_template.yaml
rules_config_dir_templates/combine_markers_hybrid_l23split_config_template.yaml
rules_config_dir_templates/combine_markers_realigned_config_template.yaml
rules_config_dir_templates/fit_average_densities_config_template.yaml
rules_config_dir_templates/fit_average_densities_correctednissl_config_template.yaml
rules_config_dir_templates/mtypes_probability_map_config_template.yaml
rules_config_dir_templates/mtypes_probability_map_correctednissl_linprog_ccfv2_config_template.yaml
rules_config_dir_templates/mtypes_probability_map_correctednissl_linprog_ccfv2_l23split_config_template.yaml
rules_config_dir_templates/mtypes_probability_map_correctednissl_linprog_config_template.yaml
rules_config_dir_templates/mtypes_profile_ccfv2_config_template.yaml
rules_config_dir_templates/mtypes_profile_ccfv2_correctednissl_config_template.yaml
rules_config_dir_templates/provenance_metadata_template.json
rules_config_dir_templates/push_dataset_config_template.yaml
rules_config_dir_templates/push_dataset_config_template_old.yaml
scripts/cellCompositionSummary_payload.py
scripts/cellCompositionVolume_payload.py
scripts/compute_lamp5.py
scripts/create_hemispheres.py
scripts/export_brain_regions_meshes.py
scripts/leaves_only.py
scripts/merge_rule.py
scripts/placement_hints.py
shell-rules/annotation_generate_all.sh
shell-rules/config.sh
shell-rules/environment.yml
shell-rules/forge-config.yml
shell-rules/push_atlasrelease.py
shell-rules/push_non_mask_volumes.py
shell-rules/push_region_masks.py
shell-rules/push_region_meshes.py
shell-rules/push_region_summaries.py
shell-rules/readme.md
tests/__init__.py
tests/test_cellCompVolume_payload.py
tests/test_cli.py
tests/test_customize_pipeline.py
tests/test_metadata.py
tests/validate_atlas_release.py
tests/data/annotation_leaves_only.nrrd
tests/data/hierarchy_leaves_only.json
tests/data/output.nrrd
tests/data/output_expected.nrrd
tests/data/output_315/output.nrrd
tests/data/output_549/output.nrrd
utils/fix_brain_regions.py