Fitting Splines to Axonal Arbors Quantifies Relationship between Branch Order and Geometry¶

Publication¶

Athey, T. L., Teneggi, J., Vogelstein, J. T., Tward, D. J., Mueller, U., & Miller, M. I. (2021). Fitting splines to axonal arbors quantifies relationship between branch order and geometry. Frontiers in Neuroinformatics, 38.

DOI: https://doi.org/10.3389/fninf.2021.704627

Relevant directory¶

brainlit/experiemnts/axon_geometry

How to reproduce this experiment¶

Before reproducing this experiment, make sure that:

You have installed the brainlit package [Documentation]. Currently, you need to install the package from source to execute these codes.
You have installed PyTorch [Documentation].

This experiment does not require a GPU (CUDA is not needed for PyTorch).

N.B. if you are using conda, make sure that both brainlit and PyTorch are installed within the same environment.

Now, follow these steps to reproduce the results of the experiment:

Download segments, which are stored in the publicly available S3 bucket open-neurodata

python scripts/download_segments.py

This script will prepare the experiment folder scaffolding

axon_geometry
├── data
│   ├── brain1
│   │   ├── segments_swc
│   │   └── trace_data
│   └── brain2
│       ├── segments_swc
│       └── trace_data
├── figures
│
... etc.

and download data from S3 (no credentials are required).

Compute and save trace analysis data

python scripts/generate_trace_data.py

Run any of the notebooks in the notebooks folder, which will save the results in the figures folder