Journal: PLOS Biology

Article Title: A guide to the BRAIN Initiative Cell Census Network data ecosystem

doi: 10.1371/journal.pbio.3002133

Figure Lengend Snippet: Primary techniques (right annotation) used in profiling cell types by BICCN investigators (top) are colored by major modality (left) and primary species . Investigator awards are ordered by techniques common to laboratories. BRAIN Initiative data archives store primary data shown by modality; NeMO, Neuroscience Multi-Omic Archive; BIL, Brain Imaging Library; DANDI, Distributed Archives for Neurophysiology Data Integration; BossDB, Brain Observatory Storage Service and Database (see Data archives for the BICCN); The NIH UM1, cooperative agreements involving large-scale research activities; U19, multidisciplinary with specific major objective; U01, discrete, specified, circumscribed project; RF1, discrete, specific project by named investigator ( NIH Grants ).

Article Snippet: DANDI works with BICCN and other BRAIN Initiative groups to curate data using community data standards such as Neurodata without Borders (NWB; [ ]) and Brain Imaging Data Structure (BIDS; [ ]) and to make data and software for cellular neurophysiology FAIR.

Techniques: Imaging

Journal: PLOS Biology

Article Title: A guide to the BRAIN Initiative Cell Census Network data ecosystem

doi: 10.1371/journal.pbio.3002133

Figure Lengend Snippet: ( A) Multimodal cell type data generation by UM1/U01/19, RF1 centers produce high-resolution Level 1 multimodal data. (B) Data are submitted to one of 4 BRAIN archives depending on data type(s): Neuroscience Multi-Omic Data Archive (NeMO), Brain Imaging Library (BIL), Distributed Archives for Neurophysiology Data Integration (DANDI) for neurophysiology data, and Brain Observatory Storage Service and Database (BossDB) for electron microscopy ultrastructural datasets. Datasets are indexed and referenced (C) by the Brain Cell Data Center (BCDC; biccn.org ), which provides a portal for accessing the consortium’s data, tools, and knowledge. (D) Laboratories engage in collaborative cross-modality interpretation of data and results. (E) Terra cloud-based platform for standardized omics processing accessible through BCDC. (F) An infrastructure working group oversees architectural development and workflow management.

Article Snippet: DANDI works with BICCN and other BRAIN Initiative groups to curate data using community data standards such as Neurodata without Borders (NWB; [ ]) and Brain Imaging Data Structure (BIDS; [ ]) and to make data and software for cellular neurophysiology FAIR.

Techniques: Imaging, Electron Microscopy

Journal: Human Brain Mapping

Article Title: Comparative validation of automated presurgical tractography based on constrained spherical deconvolution and diffusion tensor imaging with direct electrical stimulation

doi: 10.1002/hbm.26662

Figure Lengend Snippet: Summarized demographics, pathological type, distribution, and volumes.

Article Snippet: All acquired images were converted to the brain imaging data structure (BIDS) (Gorgolewski et al., ) format using the KU Leuven Neuroimaging suite (KUL_NIS) ( KULeuven Neuro Imaging Suite (KUL_NIS) , 2018/ ) ( https://github.com/treanus/KUL_NIS ) and dcm2bids (Bedetti et al., ).

Techniques:

Journal: Human Brain Mapping

Article Title: Comparative validation of automated presurgical tractography based on constrained spherical deconvolution and diffusion tensor imaging with direct electrical stimulation

doi: 10.1002/hbm.26662

Figure Lengend Snippet: Schematic representation of the data preprocessing and analysis workflow used to compare different tractography results to intraoperative mapping outcome. BIDS, brain imaging data structure; DSC, dice similarity coefficient; DTI, diffusion tensor imaging; FACT, fiber assignment by continuous tracking; JI, Jaccard index; KUL_FWT, KU Leuven fun with tracts; KUL_NIS, KU Leuven neuroimaging suite; KUL_VBG, KU Leuven virtual brain grafting; MRI, magnetic resonance imaging.

Article Snippet: All acquired images were converted to the brain imaging data structure (BIDS) (Gorgolewski et al., ) format using the KU Leuven Neuroimaging suite (KUL_NIS) ( KULeuven Neuro Imaging Suite (KUL_NIS) , 2018/ ) ( https://github.com/treanus/KUL_NIS ) and dcm2bids (Bedetti et al., ).

Techniques: Imaging, Diffusion-based Assay, Magnetic Resonance Imaging