https://github.com/int-brain-lab/paper-ephys-atlas

Code related to the electrophysiology atlas paper
https://github.com/int-brain-lab/paper-ephys-atlas

Last synced: 9 days ago
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Code related to the electrophysiology atlas paper

• Host: GitHub
• URL: https://github.com/int-brain-lab/paper-ephys-atlas
• Owner: int-brain-lab
• License: mit
• Created: 2021-12-09T14:06:40.000Z (about 3 years ago)
• Default Branch: main
• Last Pushed: 2024-12-06T15:16:57.000Z (about 1 month ago)
• Last Synced: 2024-12-06T16:28:00.621Z (about 1 month ago)
• Language: Python
• Size: 415 KB
• Stars: 1
• Watchers: 28
• Forks: 0
• Open Issues: 6
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# paper-ephys-atlas

Code related to the electrophysiology atlas paper

## Getting started

To get the features dataframe needed to train models, see [the loading example](sources/examples/00_load_clusters_tables.py)

To get a naive example of decoding model out of ephys features, see [a raw ephys decoder](sources/decoding/raw_ephys_decodes_regions.py)

## Configuration instructions

The configuration file is located in `config-ephys-atlas.yaml`.

It contains local data storage paths and some parameters for the analysis. To avoid committing changes to this file, it is ignored by git. To make changes to the configuration, copy the template file and edit the copy:

```bash

cp config-ephys-atlas.template.yaml config-ephys-atlas.yaml

```

## Install instructions

Clone the repository

```bash

git clone https://github.com/int-brain-lab/paper-ephys-atlas.git

```

Activate your environment of choice (usually a conda `iblenv` as described here: https://github.com/int-brain-lab/iblenv).

```bash

conda activate iblenv

```

Cd into the repository and install in-place

```bash

cd paper-ephys-atlas

pip install -e .

```

## Download the features table

The features table is stored with our aggregates dataset as part of IBL data. To download it, run the following commands in Python:

```python

from pathlib import Path

from one.api import ONE

import ephys_atlas.data

LOCAL_DATA_PATH = Path.home().joinpath("Downloads")

LABEL = "2023_W41"  # or put "latest"

one = ONE(base_url="https://alyx.internationalbrainlab.org", mode='local')

df_raw_features, df_clusters, df_channels, df_probes = ephys_atlas.data.download_tables(label=LABEL, local_path=LOCAL_DATA_PATH, one=one)

```