The field of neuroscience and the BRAIN Initiative in particular are amassing a wealth of informatics resources for managing, analyzing, and sharing data. Yet every lab must solve similar sets of problems to integrate these tools into the particular workflows of their experiments: data entry, acquisition, processing, analysis, and visualization. We created DataJoint: an open-source general framework for experiment data pipelines and collaborative automated workflows . Either independently or with support from our company, dozens of research groups have adopted DataJoint for diverse data modalities such as multielectrode electrophysiology, calcium imaging, light and electron microscopy, behavior tracking, sensory stimulation, transcriptomics, and optogenetics. In these complex data ecosystems, DataJoint enables groups of scientists to collaborate with clear work flows while sharing data continuously and conserving data integrity. To disseminate and integrate shared data pipelines into neuroscience practice, we propose to compile and disseminate a library of DataJoint Pipelines for Neurophysiology. We will extract essential motifs from DataJoint based open projects and organize them by data modality into a collection of curated, mutually-compatible modules stringing together data collection and computation. Documented and ready for de novo deployment, the modules will feature ancillary tools for data entry (electronic lab books), interactive graphical user inter faces adapted from existing projects (e.g. customizable data processing steps integrating popular algorithms for image segmentation and spike sorting), and integration of existing brain atlases, coordinate frameworks, ontologies for cell classification , and nomenclatures for viruses and transgenic lines. To foster uniform ontologies, we will harmonize these pipelines with emerging neurodata standards. The results of this work will be administered as an online resource showcasing the pipelines along with sample data, executable demos, and guidelines for deployment. Visitors will be able to customize, extend, and combine the modules into complete pipelines suitable for their particular experiments and learn the techniques for building new solutions. The modules will support diverse computing architectures, including specialized hardware and cloud services. We will also conduct web-based trainings and in-person hackathons to help accelerate the adoption of these tools in working neuroscience labs. Vathes LLC is uniquely positioned to perform this work as we co-develop data pipelines for collaborative projects such as IARPA's MICrONS, International Brain Lab, and BRAIN Initiative Ul9 pro jects. The output of this project will enable many new research groups to adopt DataJoint and to effectively integrate informatics tools into neuroscience practice.

Public Health Relevance

The project will systematize and disseminate data pipeline designs from leading neuroscience projects implemented in the open-source DataJoint framework. The designs string together steps for data collection and analysis and integrate diverse informatics tools for neurophysiology experiments. This work will further disseminate the use of DataJoint in neuroscience, streamline integration of new analysis methods and informatics tools, and provide starting points for new projects.

National Institute of Health (NIH)
National Institute of Neurological Disorders and Stroke (NINDS)
Resource-Related Research Projects--Cooperative Agreements (U24)
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Special Emphasis Panel (ZNS1)
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Caporello, Emily Laura
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Vathes LLC
United States
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