README.md

Circuit Map

Circuit Map is a Django application which can act as a drop-in extension for CATMAID.

Circuit Map provides tooling to integrate remote skeletons derived from automated segmentations and automatically generated synaptic link data into CATMAID circuit mapping workflows.

An example use of the tool is based on automatically generated synaptic link data by Buhmann et al. 2019 for the FAFB dataset. Synaptic link data can be added to manually reconstructed skeletons or automatically generated skeletons derived from a whole brain segmentation. Up- and downstream skeleton partners derived from this synaptic link data can be imported automatically into the current CATMAID project.

Integration into CATMAID

1. Install the dependencies with pip install -r requirements.txt.

2. Install circuitmap in whichever python environment is running CATMAID with pip install -e .

3. Run python manage.py migrate (in the CATMAID folder) to create the circuitmap models.

4. Run python manage.py collectstatic -l (in the CATMAID folder) to pick up circuitmap's static files.

5. The synaptic link data needs to be ingested into the generated Postgres table circuitmap_synlinks from the SQL database dump.

6. A few additional settings have to be configured to interoperate with segmentation data and CATMAID import procedure (see circuitmap/control/settings.py.example).