.gitignore

**/.DS_Store
docs/notebooks/pipelines/demo*
**-checkpoint.ipynb

# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]

# C extensions
*.so

# Distribution / packaging
.Python
env/
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
*.egg-info/
.installed.cfg
*.egg

# PyInstaller
#  Usually these files are written by a python script from a template
#  before PyInstaller builds the exe, so as to inject date/other infos into it.
*.manifest
*.spec

# Installer logs
pip-log.txt
pip-delete-this-directory.txt

# Unit test / coverage reports
htmlcov/
.tox/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
*,cover
.vscode/

# Translations
*.mo
*.pot

# Django stuff:
*.log

# Sphinx documentation
docs/_build/

# Pytest data
data/test_napari_plugin
data/test_upload
data/test_upload_segments

# Documentation notebook data
docs/notebooks/utils/data
docs/notebooks/pipelines/BrainLine/validation-data/soma/
docs/notebooks/pipelines/BrainLine/validation-data/axon/250_237_1800.pickle
docs/notebooks/pipelines/BrainLine/validation-data/axon/braintest/val/2054_1951_1825.h5
docs/notebooks/pipelines/BrainLine/validation-data/axon/braintest/val/2054_1951_1825_Probabilities.h5
docs/notebooks/pipelines/BrainLine/validation-data/axon/wholebrain_test.pkl

# PyBuilder
target/

# experiments/axon_geometry
experiments/axon_geometry/.ipynb_checkpoints/
experiments/axon_geometry/figures/
experiments/axon_geometry/data/
**.ipynb_checkpoints/

# experiments/soma_detection
experiments/soma_detection/.ipynb_checkpoints/
experiments/soma_detection/figures/
experiments/soma_detection/data/
experiments/soma_detection/secrets/
**.ipynb_checkpoints/

# experiments/sriram
experiments/sriram/.ipynb_checkpoints/
experiments/sriram/sample/
# experiments/register_axons
experiments/map_neurons/.ipynb_checkpoints/
experiments/map_neurons/data/mapping-files/

experiments/BrainLine/data/models/