siibra

Open software toolkit for exploring brain atlases and integrating parcellations, reference spaces, and anatomically anchored data into neuroscience workflows

Neuroscience-Specific Analysis Tools Intermediate Atlas Software Toolkit Explore Provisional Teaching
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Our View

Explore Provisional Teaching

siibra provides structured programmatic access to integrated brain atlases, including the Allen Mouse Common Coordinate Framework used in atlas-registration workflows. It is worth exploring when analyses need reproducible region assignment or access to anatomically anchored data.

Provisional positions are editorial proposals awaiting group review.

Teaching — Recorded in a scheduled calcium-imaging offering; consult the dated event link for availability.

1 topics with recorded teaching · 0 past offerings · 1 upcoming offerings

Related themes: Neural Data Analysis

Related topics: Calcium Imaging Analysis

Common use cases

  • Access brain atlases, reference spaces, and parcellations
  • Assign spatial locations and image signals to brain regions
  • Retrieve multimodal data associated with anatomical regions
  • Build reproducible atlas-based analysis workflows

Getting started

siibra (software interfaces for interacting with brain atlases) is an open toolkit for working with integrated brain atlases. Its Python client connects reference spaces and parcellations across spatial scales with multimodal data features, while siibra-explorer provides an interactive browser-based atlas viewer.

Why siibra?

  • Structured atlas access: Work with atlases, reference spaces, parcellations, maps, and regions through a consistent interface
  • Reproducible workflows: Query atlas resources programmatically with siibra-python
  • Spatial assignment: Associate coordinates and image signals with anatomical regions
  • Multiple interfaces: Explore resources interactively in siibra-explorer or integrate them into Python analyses
  • EBRAINS integration: Access atlas content and services from the EBRAINS ecosystem

Installation

pixi add siibra
# or
pip install siibra

Getting Started

import siibra

mouse_atlas = siibra.atlases.get("allen mouse")
print(mouse_atlas)

Use the documented examples to select atlas versions, reference spaces, and parcellations explicitly. Record those choices together with registration parameters so that anatomical assignments remain reproducible.