Beyond Tool Development: Building the Nipoppy Pipeline Store, Ecosystem and Community
Year: 2026
Type: conference-paper
Abstract: Neuroimaging research relies on increasingly complex computational workflows and large-scale datasets. The Brain Imaging Data Structure (BIDS)1 has successfully standardized data organization, while Boutiques2—a descriptive command-line framework—has facilitated the reproducible execution of processing pipelines. However, standardizing the entire flow of multi-site data processings and tracking the status of individual distributed datasets for collaborative projects remain significant challenges. Moreover, software availability alone does not guarantee accessibility; researchers frequently struggle with complex installations, container management, and intricate system configurations. These challenges hinder reproducibility, impede the adoption of FAIR Dugré et al., OHBM 2026 1 principles3, and complicate the harmonization required for advanced applications such as federated learning. To address these hurdles, Nipoppy4 provides a lightweight, standardized framework for the curation, processing, and tracking of clinical-neuroimaging data, from raw clinical and imaging inputs to extracted imaging derived phenotypes (IDPs). Crucially, to mitigate deployment barriers, we introduce the Nipoppy Pipeline Store—a registry of ready-to-use, containerized pipelines actively developed by the community.
Source: HAL
Authors: Dugré, Mathieu, Wang, Michelle, Bhagwat, Nikhil, Pfarr, Julia-Katharina, Macdonald, Austin, d'Angremont, Emile, Dai, Alyssa, Danyluik, Matthew, Gau, Remi, Ismaili, Adam, Jahanpour, Arman, Jahanshad, Neda, Joubert, Alice, Joulot, Matthieu, Laansma, Max, A., Mansour, Salim, Mcpherson, Brent, Mohammadalinejad, Ghazaleh, Prasad, Shweta, Roper, David, Sanz-Robinson, Jacob, Scarsbrook, Joshua, Stewart, Ashley, Tan, Thomas, Torabi, Mohammad, Tu, Jiaxin, Cindy, Urchs, Sebastian, G. W., van Heese, Eva, M., Waller, Lea, Devenyi, Gabriel, A., Chakravarty, M. Mallar, Bollmann, Steffen, M. Thompson, Paul, van der Werf, Ysbrand, D., Dickie, Erin, Burgos, Ninon, Halchenko, Yaroslav, O., Poline, Jean-Baptiste
Institutions: Montreal Neurological Institute and Hospital, Dartmouth College, Amsterdam University Medical Centers, Douglas Mental Health University Institute, MIND: modèles et inférence pour les données de Neuroimagerie, Institut des Sciences Moléculaires, Pitié-Salpêtrière Hospital, Institut du Cerveau, ARAMIS: Algorithmes, modèles et méthodes pour les images et les signaux du cerveau humain sain et pathologique, University of Southern California, University of California, Los Angeles, Vrije Universiteit Amsterdam, Centre for Addiction and Mental Health, Campbell Family Mental Health Research Institute, The University of Queensland, Charité – Universitätsmedizin Berlin, McGill University, University of Toronto
Language: English
Subfield: Information Systems and Management
Field: Decision Sciences
Domain: Social Sciences
Open Access status: green
OpenAlex ID: W7171603461