WORK IN PROGRESS
A utility for automatically detecting synapses, compatible with CATMAID and synapsesuggestor.
N.B. conda must be version <= 4.3 to work with pyenv
- Use
condato installilastik, and thenpipto install the requirements in./requirements/. cp /usr/lib/x86_64-linux-gnu/libstdc++.so.6 $CONDA_PREFIX/lib/- Use
pip install -r requirements/prod.txtfor production installations, add-r requirements/test.txtto run unit tests, and add-r requirements/travis.txtfor continuous integration and coverage with travis and coveralls.
usage: skeleton_synapses [-h] [-o OUTPUT_DIR] [-r ROI_RADIUS_PX] [-f FORCE]
credentials-path stack-id input-file-dir skeleton-ids
[skeleton-ids ...]
positional arguments:
credentials-path Path to a JSON file containing CATMAID credentials
(see credentials/example.json)
stack-id ID or name of image stack in CATMAID
input-file-dir A directory containing project files.
skeleton-ids Skeleton IDs in CATMAID
optional arguments:
-h, --help show this help message and exit
-o OUTPUT_DIR, --output-dir OUTPUT_DIR
A directory containing output files
-r ROI_RADIUS_PX, --roi-radius-px ROI_RADIUS_PX
The radius (in pixels) around each skeleton node to
search for synapses
-f FORCE, --force FORCE
Whether to delete all prior results for a given
skeleton: pass 1 for true or 0bash bin/skeleton_synapses \
credentials/my_creds.json \
1 \
~/my_project_files/ \
123456 \
654321 \
789012 \
-o ~/my_output_dir/ \
-r 150 \
-f 0pytestA running CATMAID instance is not required; nor is a functioning installation of ilastik. Tests only cover the python code surrounding those two interfaces.
pytest tests/integration_tests --input_dir path/to/input/ --credentials_path path/to/credentials.jsonThis requires ilastik, valid project files, and a running instance of CATMAID.
See ./credentials/example.json for the credentials file required by skeleton_synapses.
Environment variables control skeleton_synapses' utilisation of compute resources.
Store different environment variable configurations in ./env_vars/ (see example).
Source these environment variables with ./bin/set_env_vars <file_name>