FlywheelTools: Data Curation and Manipulation on the Flywheel Platform

Tapera, Tinashe M.; Cieslak, Matthew; Bertolero, Max; Adebimpe, Azeez; Aguirre, Geoffrey K.; Butler, Ellyn R.; Cook, Philip A.; Davila, Diego; Elliott, Mark A.; Linguiti, Sophia; Murtha, Kristin; Tackett, William; Detre, John A.; Satterthwaite, Theodore D.

doi:10.3389/fninf.2021.678403

Cited by 13 publications

(7 citation statements)

References 14 publications

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“…In addition, several commercial platforms are available for neuroimaging data management and analytics [e.g., Flywheel (Tapera et al, 2021 ), QMENTA, Nordic Tools, Ceretype], especially for clinical applications. While these platforms offer a wide range of neuroinformatics functionalities, they are difficult to evaluate due to their high cost of services and proprietary content.…”

Section: Discussionmentioning

confidence: 99%

QuNex—An integrative platform for reproducible neuroimaging analytics

Demšar

Fonteneau

et al. 2023

Front. Neuroinform.

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IntroductionNeuroimaging technology has experienced explosive growth and transformed the study of neural mechanisms across health and disease. However, given the diversity of sophisticated tools for handling neuroimaging data, the field faces challenges in method integration, particularly across multiple modalities and species. Specifically, researchers often have to rely on siloed approaches which limit reproducibility, with idiosyncratic data organization and limited software interoperability.MethodsTo address these challenges, we have developed Quantitative Neuroimaging Environment & Toolbox (QuNex), a platform for consistent end-to-end processing and analytics. QuNex provides several novel functionalities for neuroimaging analyses, including a “turnkey” command for the reproducible deployment of custom workflows, from onboarding raw data to generating analytic features.ResultsThe platform enables interoperable integration of multi-modal, community-developed neuroimaging software through an extension framework with a software development kit (SDK) for seamless integration of community tools. Critically, it supports high-throughput, parallel processing in high-performance compute environments, either locally or in the cloud. Notably, QuNex has successfully processed over 10,000 scans across neuroimaging consortia, including multiple clinical datasets. Moreover, QuNex enables integration of human and non-human workflows via a cohesive translational platform.DiscussionCollectively, this effort stands to significantly impact neuroimaging method integration across acquisition approaches, pipelines, datasets, computational environments, and species. Building on this platform will enable more rapid, scalable, and reproducible impact of neuroimaging technology across health and disease.

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Section: Discussionmentioning

confidence: 99%

QuNex—An integrative platform for reproducible neuroimaging analytics

Demšar

Fonteneau

et al. 2023

Front. Neuroinform.

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“…The fact that this application is not freely available provides added issues, as it is not yet very popular, especially within the preclinical imaging facilities. Other recently developed commercial systems based on common preclinical workflow and that can also support multimodality data storage and management are SABER [19] and Flywheel [44]. By contrast, we are developing a new data management system specifically designed to directly support preclinical imaging workflow for all modalities and experimental setups.…”

Section: Discussionmentioning

confidence: 99%

Web-Based Application for Biomedical Image Registry, Analysis, and Translation (BiRAT)

et al. 2022

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Imaging has become an invaluable tool in preclinical research for its capability to non-invasively detect and monitor disease and assess treatment response. With the increased use of preclinical imaging, large volumes of image data are being generated requiring critical data management tools. Due to proprietary issues and continuous technology development, preclinical images, unlike DICOM-based images, are often stored in an unstructured data file in company-specific proprietary formats. This limits the available DICOM-based image management database to be effectively used for preclinical applications. A centralized image registry and management tool is essential for advances in preclinical imaging research. Specifically, such tools may have a high impact in generating large image datasets for the evolving artificial intelligence applications and performing retrospective analyses of previously acquired images. In this study, a web-based server application is developed to address some of these issues. The application is designed to reflect the actual experimentation workflow maintaining detailed records of both individual images and experimental data relevant to specific studies and/or projects. The application also includes a web-based 3D/4D image viewer to easily and quickly view and evaluate images. This paper briefly describes the initial implementation of the web-based application.

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“…Unfortunately, many existing solutions lack the required flexibility for research applications of neuroimaging data analysis 26 . For example, single-install pre-programmed analysis pipelines are a popular solution amongst clinicians, but researchers typically custom-tailor analysis pipelines toward specific research questions [27][28][29] . The issues of inaccessibility in neuroimaging software have been recognized by the NeuroDebian 2 and NeuroFedora 30 projects, which provide a wide range of neuroimaging tools packaged for Linux operating systems.…”

Section: Introductionmentioning

confidence: 99%

Neurodesk: an accessible, flexible and portable data analysis environment for reproducible neuroimaging

Renton,

Dao,

Johnstone

et al. 2024

Nat Methods

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Neuroimaging data analysis often requires purpose-built software, which can be challenging to install and may produce different results across computing environments. Beyond being a roadblock to neuroscientists, these issues of accessibility and portability can hamper the reproducibility of neuroimaging data analysis pipelines. Here, we introduce the Neurodesk platform, which harnesses software containers to support a comprehensive and growing suite of neuroimaging software (https://www.neurodesk.org/). Neurodesk includes a browseraccessible virtual desktop environment and a command line interface, mediating access to containerized neuroimaging software libraries on various computing platforms, including personal and high-performance computers, cloud computing and Jupyter Notebooks. This community-oriented, open-source platform enables a paradigm shift for neuroimaging data analysis, allowing for accessible, flexible, fully reproducible, and portable data analysis pipelines.

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FlywheelTools: Data Curation and Manipulation on the Flywheel Platform

Cited by 13 publications

References 14 publications

QuNex—An integrative platform for reproducible neuroimaging analytics

QuNex—An integrative platform for reproducible neuroimaging analytics

Web-Based Application for Biomedical Image Registry, Analysis, and Translation (BiRAT)

Neurodesk: an accessible, flexible and portable data analysis environment for reproducible neuroimaging

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