API Documentation

The class and package diagrams can be found at the developer documentation.

Siibra

Main Packages and Modules

siibra.commons

Constants, functions, and classes used commonly across siibra.

siibra.configuration

Handles reconfiguration management and building instances

siibra.core

Main siibra concepts

siibra.exceptions

Siibra specific exceptions

siibra.experimental

siibra.explorer

Interface to create links to siibra-explorer

siibra.features

Multimodal data features types and query mechanisms.

siibra.livequeries

Feature queries requiring live query or on-the-fly calculations.

siibra.locations

Handles spatial concepts and spatial operation like warping between spaces.

siibra.retrieval

File digestion and caching.

siibra.vocabularies

Abbreviations and aliases.

siibra.volumes

Package handling variety of volumes and volume operations

Core Concepts

siibra.core.assignment

Qualification between two BrainStructures

siibra.core.atlas

Provides reference systems for brains.

siibra.core.concept

Parent class to siibra main concepts.

siibra.core.parcellation

Hierarchal brain regions and metadata.

siibra.core.region

Representation of a brain region.

siibra.core.space

A particular brain reference space.

siibra.core.structure

Abstract base class for any kind of brain structure.

Volumes

siibra.volumes.parcellationmap

Provides spatial representations for parcellations and regions.

siibra.volumes.providers

Subpackage handling the digestion of different volume and mesh types

siibra.volumes.sparsemap

Represents lists of probabilistic brain region maps.

siibra.volumes.volume

A specific mesh or 3D array.

Locations

siibra.locations.boundingbox

A box defined by two farthest corner coordinates on a specific space.

siibra.locations.location

Concepts that have primarily spatial meaning.

siibra.locations.point

Singular coordinate defined on a space, possibly with an uncertainty.

siibra.locations.pointset

A set of coordinates on a reference space.

Features

siibra.features.anchor

Handles the relation between study targets and BrainStructures.

siibra.features.connectivity

Multimodal data features concerning connectivity data.

siibra.features.dataset

Non-preconfigured data features published as datasets.

siibra.features.feature

Handles multimodal data features and related queries.

siibra.features.image

Multimodal data features in volume or image formats.

siibra.features.tabular

Multimodal data features in tabular formats.

Live queries

siibra.livequeries.allen

Query Allen Human Brain Atlas microarray data in specified volume.

siibra.livequeries.bigbrain

Matches BigBrain intesity profiles extracted by Wagstyl et al. to volumes.

siibra.livequeries.ebrains

Query data features published as Ebrains datasets with AtlasConcepts

siibra.livequeries.query

Handles feature queries that rely on live or on-the-fly calculations.

Retrieval

siibra.retrieval.cache

Maintaining and handling caching files on disk.

siibra.retrieval.datasets

Metadata connection to EBRAINS datasets.

siibra.retrieval.exceptions

Exceptions concerning file retrieval processes.

siibra.retrieval.repositories

Connect to repositories to browse and pull files within.

siibra.retrieval.requests

Request files with decoders, lazy loading, and caching.