Journal: eLife

Article Title: The Neurodata Without Borders ecosystem for neurophysiological data science

doi: 10.7554/eLife.78362

Figure Lengend Snippet: ( a ) Diversity of experimental systems: species and tasks: (i) mice performing a visual discrimination task; (ii) rats performing a memory-guided navigation task; (iii) humans speaking consonant-vowel syllables; (iv) biophysically detailed simulations of mouse hippocampus during memory formation. The corresponding acquisition modalities and signals are shown in the corresponding columns in figure ( b and c ). ( b ) Diversity of data modalities and acquisition devices: (i) optophysiological Ca 2+ imaging with two-photon microscope; (ii) intra-cortical extracellular electrophysiological recordings with polytrodes in multiple brain areas (indicated by color, see c.ii); (iii) cortical surface electrophysiology recordings with electrocorticography grids; (iv) high-performance computing systems for large-scale, biophysically detailed simulations of large neural networks. ( c ) Diversity of signals and areas: (i) Ca 2+ signals as a function of time from visually identified individual neurons in primary visual cortex (V1) ; (ii) spike-raster (each tick demarcates the time of an action potential) from simultaneously recorded putative single-units after spike-sorting of extracellular signals from medial prefrontal cortex (mPFC; blue), ventral striatum (v. Striatum, red), and orbital frontal cortex (OFC, green) (color corresponds to b.ii ) ; (iii) high-gamma band activity from electrodes over the speech sensorimotor cortex (SMC), with dorsal-ventral distance from Sylvian fissure color coded red-to-black (color corresponds to b.iii) ; (iv) simulated intracellular membrane potentials from different cell-types from large-scale biophysical simulation of the hippocampus (BC, Basket Cell); HC, Hilar Interneuron (with axon associated with the) Perforant Path; HCC, Hilar Interneuron (with axon associated with the) Commissural/Associational Path; IS, Interneuron-Specific Interneuron; MCPP, medial Perforant Path; NGFC, neurogliaform cell; MC, mossy cell; GC, granule cell](Raikov and Soltesz, unpublished data). ( d ) Neurodata Without Borders (NWB) provides a robust, extensible, and maintainable software ecosystem for standardized description, storage, and sharing of the diversity of experimental subjects, behaviors, experimental designs, data acquisition systems, and measures of neural activity exemplified in a – c .

Article Snippet: Appendix 3 provides a more detailed overview of the extension workflow as part of the NDX Catalog. Several extensions have been registered in the Neurodata Extensions Catalog , including extensions to support the storage of the cortical surface mesh of an electrocorticography experiment subject, storage of fluorescence resonance energy transfer (FRET) microscopy data, and metadata from an intracellular electrophysiology acquisition system.

Techniques: Imaging, Microscopy, Activity Assay, Membrane, Software