# Squirrel data sharing format

## Overview

The squirrel data sharing format is designed to allow easy sharing of neuroimaging data. All research imaging data can be categorized into one of 10 object types. Squirrel organizes these objects into a heirarchy, allowing sharing of complex datasets that span raw data (and experiments used to collect it) to analyzed data (and the methods used to analyze), and everything in between.

<div align="center"><figure><img src="https://3554845051-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FL3u9jHWiUxpaiEOdRc0w%2Fuploads%2FUacpOAECY8moCLJwmNrP%2Fsquirrel.png?alt=media&#x26;token=1cda7eb5-0031-4997-818b-d9990c460a4f" alt=""><figcaption><p>Cute and corny, but an accurate description of the squirrel format</p></figcaption></figure></div>

## Get squirrel

Squirrel utilities are available from our github repository: <https://github.com/gbook/squirrel/releases>

<p align="center"><a href="https://github.com/gbook/squirrel/releases" class="button primary">Download squirrel utilities</a></p>

Package installers are available for

* RHEL 8 and compatible
* RHEL 9 and compatible
* RHEL 10 and compatible
* debian 12
* Ubuntu 24

Source code is avilable to build squirrel utilities or library.

### Squirrel object types

All neuroimaging data can be categorized into one of these 10 object types

| Object              | Description                                                                                                | Example                                             |
| ------------------- | ---------------------------------------------------------------------------------------------------------- | --------------------------------------------------- |
| **analysis**        | Analysis results                                                                                           | freesurfer analysis results                         |
| **data-dictionary** | Data dictionary with key-value pairs to describe variables                                                 | Female=1, Male=2...                                 |
| **experiment**      | An experiment used to collect raw data. Can include task instructions, or behavioral data analysis scripts | A go-no-go task; with ePrime  files                 |
| **group-analysis**  | Contains all data related to a group analysis                                                              |                                                     |
| **intervention**    | Data about something administered to the subject                                                           | Drug dosing information                             |
| **observation**     | Data about something observed from the subject                                                             | PANS, SCID, etc                                     |
| **pipeline**        | Analysis pipeline script; with extra script or other files necessary to perform the analysis.              | A script to run an FSL analysis                     |
| **series**          | Unique imaging series. A study can have more than one imaging series.                                      | T1w from an MRI                                     |
| **study**           | Unique imaging session. A subject can have more than one study                                             | A set of MRI images collected during a scan session |
| **subject**         | Unique subject                                                                                             | A human, monkey, bacteria, etc                      |

## Contribute

Squirrel format is open-source and we are always looking for contributions.

## Publications

* Book GA, Calhoun VD, Stevens MC, Pearlson GD. *Sharing Neuroimaging Data with Squirrel - A Relational Data Format to Store Raw to Analyzed Data and Everything in Between.* Neuroinformatics. 2025 Jul 3;23(3):37. doi: 10.1007/s12021-025-09732-7. PMID: 40610663.