CLABTOOLKIT: An Open-Source Toolkit for Routine Processing, Manipulation, and Visualization of Neuroimaging Data

Yasser Alemán-Gómez, Nino Hervé, Patric Hagmann

Neuroimaging research requires manipulating heterogeneous data structures, including raw MRI volumes, volumetric parcellations, cortical surface meshes, tractograms, and connectivity matrices, across tools with incompatible interfaces and file formats, forcing researchers to repeatedly re-implement routine but technically demanding operations. We present CLABTOOLKIT, an open-source Python package that consolidates these operations into a single, coherent framework by representing volumetric, surface, and streamline data as interoperable Python objects. Five core data structures (Parcellation, Surface, AnnotParcellation, Tractogram, and Connectome) encapsulate common neuroanatomical entities and provide consistent methods for loading, processing, and exporting data across standard neuroimaging formats (e.g., NIfTI, GIFTI, FreeSurfer annotations, TCK/TRK), including connectome generation from a parcellation and scalar-map projection onto tractogram streamlines. Complementary modules support BIDS dataset management, FreeSurfer integration, diffusion MRI processing, morphometric analysis, graph-theoretical network analysis, and GPU-accelerated multi-panel visualization via PyVista. The toolkit comprises 19 modules organised into six layers, exposing 13 object-oriented classes with 234 methods and 207 standalone functions, and a JSON-based configuration system enables workflow customization without code changes. Unlike existing neuroimaging libraries, which typically address these tasks separately, CLABTOOLKIT combines color and lookup-table management, parcellation manipulation, multi-surface visualization, and tractography utilities within a single framework. CLABTOOLKIT is compatible with Python 3.9-3.12 and released under the Apache 2.0 license. Source code, documentation, and example workflows are available at https://github.com/connectomicslab/clabtoolkit.