Package: siibra-cli
siibra - Software interface for interacting with brain atlasesCopyright 2020-2022, Forschungszentrum Jülich GmbHAuthors: Big Data Analytics Group, Institute of Neuroscience and
Medicine (INM-1), Forschungszentrum Jülich GmbHsiibrais a Python client for working with brain atlas frameworks
that integrate multiple brain parcellations and reference spaces across
different spatial scales, and connect them with a multimodal regional
data features. It aims to facilitate the programmatic and reproducible
incorporation of brain region features from different sources into
reproducible neuroscience workflows.This repository implements a basic commandline interface (CLI) for siibra.Note:``siibra-cli`` is still in development. While care is taken that it works reliably, its API is not yet stable and you may still encounter bugs when using it.siibraprovides structured acccess to parcellation schemes in
different brain reference spaces, including volumetric reference
templates at both macroscopic and microscopic resolutions as well as
surface representations. It supports both discretely labelled and
continuous (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. Among the
datasets anchored to brain regions are many different modalities from
in-vivo and post mortem studies, including regional information about
cell and transmitter receptor densties, structural and functional
connectivity, gene expressions, and more.siibrais mainly developed by theHuman Brain
Projectfor accessing theEBRAINS
human brain atlas. It
stores much of its contents in theEBRAINS Knowledge
Graph, and is designed to support theOpenMINDS metadata
standards. Its
functionalities include common actions known from the interactive viewersiibra explorerhosted on
EBRAINS. In fact, the viewer is a
good resource for exploringsiibra’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 insiibraare
parameterized by data modality and anatomical location, while the latter
could be a brain region, brain parcellation, or location in reference
space. Beyond the functionality ofsiibra-explorer, the Python
library also supports a range of data analysis features suitable for
typical neuroscience workflows.siibrahides much of the complexity that would be required to
collect and interact with the individual paracellations,templates andd
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, mixing up label indices of brain regions, or utilisation of
inconsistent versions of parcellation maps. It aims to provide a safe
way of using maps defined across multiple spatial scales for
reproducible analysis.Installationsiibra-cliis available on pypi. To install the latest released version,
simply runpip installsiibra-cli. In order to work with the latest
version from github, usepip installgit+https://github.com/FZJ-INM1-BDA/siibra-cli.git@main.Access to EBRAINSsiibraretrieves much of its data from theEBRAINS Knowledge
Graph, which requires authentication.
Therefore you have to provide an EBRAINS authentication token for using
all features provided bysiibra. Please make sure that you have a
valid EBRAINS user account byregistering to
EBRAINS.HelpIf you run into issues, please open a ticket onEBRAINS
supportor directly file bugs and
feature requests ongithub.AcknowledgementsThis 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).