CHANGELOG.md
CITATION.cff
CONTRIBUTING.md
LICENSE
LOGO_REQUIRED_BEFORE_RELEASE.md
MANIFEST.in
NOTICE.md
README.md
SECURITY.md
pyproject.toml
.github/pull_request_template.md
.github/ISSUE_TEMPLATE/bug_report.yml
.github/ISSUE_TEMPLATE/feature_request.yml
.github/workflows/publish.yml
.github/workflows/tests.yml
assets/allen_mask.csv
docs/atlas_csv.md
docs/batch_workflows.md
docs/custom_import.md
docs/custom_mask.md
docs/development.md
docs/ibl.md
docs/releasing.md
examples/batch_workflow.cortyxabatch
examples/make_synthetic_stack.py
examples/plugin_example.py
src/cortyxa/__init__.py
src/cortyxa/__main__.py
src/cortyxa/app.py
src/cortyxa/atlas.py
src/cortyxa/export.py
src/cortyxa/importing.py
src/cortyxa/masking.py
src/cortyxa/models.py
src/cortyxa/plugins.py
src/cortyxa/processing.py
src/cortyxa/resources.py
src/cortyxa/session.py
src/cortyxa/stack.py
src/cortyxa/visualization.py
src/cortyxa.egg-info/PKG-INFO
src/cortyxa.egg-info/SOURCES.txt
src/cortyxa.egg-info/dependency_links.txt
src/cortyxa.egg-info/entry_points.txt
src/cortyxa.egg-info/requires.txt
src/cortyxa.egg-info/top_level.txt
src/cortyxa/analysis/__init__.py
src/cortyxa/analysis/events.py
src/cortyxa/analysis/ibl.py
src/cortyxa/analysis/pca.py
src/cortyxa/analysis/seed.py
src/cortyxa/batch/__init__.py
src/cortyxa/batch/discovery.py
src/cortyxa/batch/engine.py
src/cortyxa/batch/models.py
src/cortyxa/batch/operations.py
src/cortyxa/batch/persistence.py
src/cortyxa/data/__init__.py
src/cortyxa/data/allen_dorsal_schematic.csv
src/cortyxa/data/cortyxa_logo.png
src/cortyxa/gui/__init__.py
src/cortyxa/gui/batch_window.py
src/cortyxa/gui/canvas.py
src/cortyxa/gui/custom_import.py
src/cortyxa/gui/dialogs.py
src/cortyxa/gui/main_window.py
src/cortyxa/gui/mask_editor.py
src/cortyxa/gui/results.py
src/cortyxa/gui/workers.py
tests/conftest.py
tests/test_analysis.py
tests/test_atlas.py
tests/test_batch.py
tests/test_custom_import.py
tests/test_export.py
tests/test_gui_smoke.py
tests/test_ibl.py
tests/test_masking.py
tests/test_processing.py
tests/test_resources.py
tests/test_session.py
tests/test_stack.py
tests/test_visualization.py