Neurophysiological analytics for all! Free open-source software tools for documenting, analyzing, visualizing, and sharing using electronic notebooks.
Neurophysiology requires an extensive workflow of information analysis routines, which often includes incompatible proprietary software, introducing limitations based on financial costs, transfer of data between platforms, and the ability to share. An ecosystem of free open-source software exists to fill these gaps, including thousands of analysis and plotting packages written in Python and R, which can be implemented in a sharable and reproducible format, such as the Jupyter electronic notebook. This tool chain can largely replace current routines by importing data, producing analyses, and generating publication-quality graphics. An electronic notebook like Jupyter allows these analyses, along with documentation of procedures, to display locally or remotely in an internet browser, which can be saved as an HTML, PDF, or other file format for sharing with team members and the scientific community. The present report illustrates these methods using data from electrophysiological recordings of the musk shrew vagus-a model system to investigate gut-brain communication, for example, in cancer chemotherapy-induced emesis. We show methods for spike sorting (including statistical validation), spike train analysis, and analysis of compound action potentials in notebooks. Raw data and code are available from notebooks in data supplements or from an executable online version, which replicates all analyses without installing software-an implementation of reproducible research. This demonstrates the promise of combining disparate analyses into one platform, along with the ease of sharing this work. In an age of diverse, high-throughput computational workflows, this methodology can increase efficiency, transparency, and the collaborative potential of neurophysiological research.
Biobehavioral Oncology Program, University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania; Department of Neuroscience, University of Pittsburgh, Pittsburgh, Pennsylvania;
David M
0000-0002-0005-4151
DM
Rosenberg
Biobehavioral Oncology Program, University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania; Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; and Center for Neuroscience, University of Pittsburgh, Pittsburgh, Pennsylvania chorn@pitt.edu.
Charles C
0000-0002-5587-3912
CC
Horn
D000344:Afferent Pathways / Q000502:physiology*; D000818:Animals; D001794:Blood Pressure / Q000502:physiology; D001921:Brain / Q000502:physiology*; D003299:Cooperative Behavior; D004558:Electric Stimulation; D033181:Information Dissemination / Q000379:methods*; D008297:Male; D009482:Neurophysiology; D012788:Shrews; D012984:Software; D013270:Stomach / Q000294:innervation*; D014630:Vagus Nerve / Q000502:physiology; D057188:Workflow
IPython; Jupyter; Python; electronic notebook; electrophysiology; neurophysiology; open source; reproducible research