mdseg

Requirements

Install MDSeg & additional packages

pip install -U git+https://github.com/htem/segway.utils#egg=segway.utils git+https://github.com/htem/segway.mdseg#egg=segway.mdseg
pip install jsmin requests

Download the database

We need to download a copy of the exported proofread neuron database.

• See https://github.com/htem/cb2_project_analysis/tree/main/database for up-to-date instructions. Below is a snippet for convenience:

# assuming the current directory is `cb2_project_analysis/mdseg/`
cd ../database/data
wget https://github.com/htem/cb2_project_analysis_files/releases/download/230414/neurons_grc_mf_pc_230414.db.tar.gz
tar xf neurons_grc_mf_pc_230414.db.tar.gz

Neuron viewer

You can use make_static_view.py to view proofread neurons.

The below assumes the current directory is cb2_project_analysis/mdseg/

• Example Granule cells:
  • python make_static_view.py grc_253,grc_270,grc_276,grc_292,grc_304,grc_310,grc_312
• Example Purkinje cell:
  • python make_static_view.py pc_1

Tips

• We can tune viewing position:
  • python make_static_view.py grc_253,grc_270,grc_276,grc_292,grc_304,grc_310,grc_312 --crossSectionScale 10 --projectionScale 60000 --position 95689,103170,164
• These config files have neuron_ids of proofread neurons:
  • https://github.com/htem/cb2_project_analysis/tree/main/graphs/configs
• If there's an error with outdated GitHub token, try to make a new one by visiting https://github.com/settings/tokens/new. You would need a GitHub account and remember to select gist in the permissions.
  • Then run the command with --token YOUR_TOKEN appended
  • To see existing tokens, visit https://github.com/settings/tokens