README.md

---
license: mit
tags:
- connectomics
- simulation-based-inference
- neuroscience
- computational-biology
pretty_name: SBI for Connectomics - Data and Results
---

# Dataset Card: SBI for Connectomics — Data and Results

This dataset contains the binary data, inference results, and figures accompanying the paper
[Simulation-based inference for efficient identification of generative models in connectomics](https://www.biorxiv.org/content/10.1101/2023.01.31.526269v1).

It is the companion data repository for the code at
[github.com/mackelab/sbi-for-connectomics](https://github.com/mackelab/sbi-for-connectomics), which uses
[simulation-based inference (SBI)](http://simulation-based-inference.org) to infer parameters of computational
wiring-rule models of the rat barrel cortex used in connectomics research.

These files were previously distributed via `git-lfs` in the code repository and have been moved here to keep the
git repository lightweight.

## Dataset structure

~3.0 GB across 219 binary files, organized into three top-level folders that mirror the paths expected by the
code and notebooks in the companion repository:

```
data/
├── structural_model/       # masks and feature tables for the structural (barrel cortex) model
├── subcellular_features/   # masks and feature tables for the subcellular model
├── cube_model/             # masks, feature tables, and depth-profile data for the cube model
└── presimulated_dso_*.p    # presimulated prior/posterior samples for various wiring-rule parameterizations

figures/
├── fig2_structural_model.pdf
├── fig3/                   # main-text figure 3 (SBI results) source data/renders
├── fig4-5/                  # main-text figures 4-5 (distance-rule results)
└── supplementary_figures/   # supplementary figure renders

results/
├── amortized_posterior_*.p          # amortized NPE posteriors
├── npe_*.p                          # NPE posteriors trained on various wiring-rule datasets
├── prior_predictive_*.p / posterior_predictive_*.p
├── sbc_results_*.p                  # simulation-based calibration results
├── cross_validation_results_*.p
└── tutorial_posterior_*.p           # posteriors used in the tutorial notebooks
```

File formats:
- `.p` — Python pickle files (mostly `torch`/`sbi` posterior objects and sample arrays; see the companion
  repository's `consbi` package and notebooks for how they're loaded)
- `.txt` / `.tsv` — mask and feature tables for the structural/subcellular/cube models
- `.pdf` / `.png` / `.eps` — rendered paper figures

Code, notebooks, and small config/log files (plotting scripts, `.ipynb` notebooks, `.hydra` run configs, etc.)
are **not** included here — those remain version-controlled in the
[GitHub repository](https://github.com/mackelab/sbi-for-connectomics).

## How to use

Download directly into a local clone of the [companion repository](https://github.com/mackelab/sbi-for-connectomics)
so the folder layout matches what the code expects:

```shell
pip install -U huggingface_hub
hf download mackelab/sbi-for-connectomics-data --repo-type dataset --local-dir .
```

This populates `data/`, `figures/`, and `results/` in the current directory.

## Citation

If you use this data, please cite the associated paper:

> Simulation-based inference for efficient identification of generative models in connectomics.
> https://www.biorxiv.org/content/10.1101/2023.01.31.526269v1

## License

MIT License, matching the [companion code repository](https://github.com/mackelab/sbi-for-connectomics/blob/main/LICENSE.md).