Integrated Open-Source Software for Multiscale Electrophysiology

Abstract

16The methods for electrophysiology in neuroscience have evolved tremendously over the recent 17 years with a growing emphasis on dense-array signal recordings. Such increased complexity and 18 augmented wealth in the volume of data recorded, have not been accompanied by efforts to 19 streamline and facilitate access to processing methods, which too are susceptible to grow in 20 sophistication. Moreover, unsuccessful attempts to reproduce peer-reviewed publications 21 indicate a problem of transparency in science. This growing problem could be tackled by 22 unrestricted access to methods that promote research transparency and data sharing, ensuring 23 the reproducibility of published results. 24 Here, we provide a free, extensive, open-source software that provides data-analysis, data-25 management and multi-modality integration solutions for invasive neurophysiology. Users can 26 perform their entire analysis through a user-friendly environment without the need of 27 programming skills, in a tractable (logged) way. This work contributes to open-science, analysis 28 standardization, transparency and reproducibility in invasive neurophysiology. 29 30 31 32 33

SpikeInterface, a unified framework for spike sorting

“…Recordings can be loaded and analyzed from six different file formats: Blackrock, Ripple, Plexon, Intan, NWB, and Tucker Davis Technologies. is available on GitHub ( https://github.com/brainstorm-tools/brainstorm3 ; Nasiotis et al, 2019b ) and its functionality is documented ( https://neuroimage.usc.edu/brainstorm/e-phys/Introduction ). does not include the latest spike sorting software ( Rossant et al, 2016 ; Yger et al, 2018 ; Chung et al, 2017 ; Jun et al, 2017b ; Pachitariu et al, 2018 ; Hilgen et al, 2017 ) ( does include instructions on how to import data that has been spike sorted by a non-supported spike sorter), and it does not support any post-sorting analysis such as quality metric calculation, automated curation, or sorting output comparison.…”

Towards a Computer Vision System for Monitoring and Stimulation of Rodents

“…Among the various works in this line, we find three specifically that deal with similar problems. The first two focus on aspects of computer vision for the quantitative determination of behavior tests [3], while the last one shows an electrophysiological recording software in rodents [10].…”

SpikeInterface, a unified framework for spike sorting

“…Most recently, Nasiotis et al [56] implemented IN-Brainstorm, a MATLAB-based GUI designed for the analysis of invasive neurophysiology data. IN-Brainstorm allows users to run three spike sorting packages, (Wave clus [19], UltraMegaSort2000 [37], and Kilosort [59]).…”

“…Previous work to standardize the field has focused on developing open-source frameworks that make extracellular analysis and spike sorting more accessible [26,16,35,29,33,13,45,14,57,43,48,15,61,76,56]. While useful tools in their own right, these frameworks only implement a limited suite of spike sorting technologies since their main focus is to provide entire extracellular analysis pipelines (spike trains, LFPs, EEG, and more).…”