This release is a pre-release and may not be stable for production use.
siibra - Software interface for interacting with brain atlases
Copyright 2018-2025, Forschungszentrum Jülich GmbH
Authors: Big Data Analytics Group, Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
siibra-python is a Python client to a brain atlas framework that integrates brain parcellations and reference spaces at different spatial scales, and connects them with a broad range of multimodal regional data features. It aims to facilitate programmatic and reproducible incorporation of brain parcellations and brain region features from different sources into neuroscience workflows.
siibra provides structured access to parcellation schemes in different brain reference spaces, including volumetric reference templates at macroscopic and microscopic resolutions as well as surface representations. It supports both discretely labelled and statistical (probabilistic) parcellation maps, which can be used to assign brain regions to spatial locations and image signals, to retrieve region-specific neuroscience datasets from multiple online repositories, and to sample information from high-resolution image data. The datasets anchored to brain regions address features of molecular, cellular and architecture as well as connectivity, and are complemented with live queries to external repositories as well as dynamic extraction from “big” image volumes such as the 20 micrometer BigBrain model.
siibra hides much of the complexity that would be required to collect and interact with the individual parcellations, templates and data repositories. By encapsulating many aspects of interacting with different maps and reference templates spaces, it also minimizes common errors like misinterpretation of coordinates from different reference spaces, confusing label indices of brain regions, or using inconsistent versions of parcellation maps. It aims to provide a safe way of using maps defined across multiple spatial scales for reproducible analysis.
siibra was developed in the frame of the Human Brain Project for accessing the EBRAINS human brain atlas. It stores most of its contents as sustainable and open datasets in the EBRAINS Knowledge Graph, and is designed to support the OpenMINDS metadata standards. Its functionalities include common actions known from the interactive viewer siibra-explorer hosted at EBRAINS. In fact, the viewer is a good resource for exploring siibra’s core functionalities interactively: Selecting different parcellations, browsing and searching brain region hierarchies, downloading maps, identifying brain regions, and accessing multimodal features and connectivity information associated with brain regions. Feature queries in siibra are parameterized by data modality and anatomical location, while the latter could be a brain region, brain parcellation, or location in reference space. Beyond the explorative focus of siibra-explorer, the Python library supports a range of data analysis functions suitable for typical neuroscience workflows.
Installation
siibra is available on pypi. To install the latest released version, simply run pip install siibra. The installation typically takes about 2 minutes on a standard computer where Python is already installed. In order to work with the latest version from github, use pip install git+https://github.com/FZJ-INM1-BDA/siibra-python.git@main.
siibra-python should be installable on recent versions of Windows, Linux and Mac OS in a recent Python 3 environment. We run continuous integration tests for versions 3.7 - 3.12 on recent Ubuntu images.
The library requires a couple of open source packages, namely: ` anytree >= 2.12.1 nibabel >= 5.3.2 appdirs >= 1.4.4 scikit-image >= 0.25.0 requests >= 2.32.3 neuroglancer-scripts >= 1.2.0 nilearn >= 0.11.0 filelock >= 3.16.1 ebrains-drive >= 0.6.0 `
You can also install a docker image with all dependencies included: .. code-block:: sh
- docker run -dit
-p 10000:8888 –rm –name siibra docker-registry.ebrains.eu/siibra/siibra-python:latest
Documentation & Help
siibra-python’s documentation is hosted on https://siibra-python.readthedocs.io. The documentation includes a catalogue of documented code examples that walk you through the different concepts and functionalities. These examples use real data and include both the code and the produced expected outputs. They can be accessed at https://siibra-python.readthedocs.io/en/latest/examples.html, and are automatically tested and updated whenever a new version of siibra-python is published. As a new user, it is recommended to go through these examples - they are easy and will quickly provide you with the right code snippets that get you started. The documentation on readthedocs further includes introductory explanations and an API reference.
If you run into issues, please open a ticket on EBRAINS support or file bugs and feature requests on github.
How to contribute
If you want to contribute to siibra, feel free to fork it and open a pull request with your changes. You are also welcome to contribute to discussions in the issue tracker and of course to report issues you are facing. If you find the software useful, please reference this repository URL in publications and derived work. You can also star the project to show us that you are using it.
Acknowledgements
This software code is funded from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Specific Grant Agreement No. 945539 (Human Brain Project SGA3).
How to cite
Please cite the version used according to the citation file or all versions by Timo Dickscheid, Xiayun Gui, Ahmet Nihat Simsek, Vadim Marcenko, Louisa Köhnen, Sebastian Bludau, & Katrin Amunts. (2023). siibra-python - Software interface for interacting with brain atlases. Zenodo. https://doi.org/10.5281/zenodo.7885728.
Versioning
- Given a version number MAJOR.MINOR.PATCH, increments imply:
MAJOR: incompatible API changes
MINOR: a functionality in a backward compatible manner is added
PATCH: backward compatible bug fixes and new configuration added such as new maps or features
Pre-release
For x.y.z, a full release, - x.y.z-alpha.t is the development prerelease. By changing t, different siibra-configurations are targeted.
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