Boulay, C. | Search bioRxiv

bioRxiv2024

The Lab Streaming Layer for Synchronized Multimodal Recording

Accurately recording the interactions of humans or other organisms with their environment and other agents requires synchronized data access via multiple instruments, often running independently using different clocks. Active, hardware-mediated solutions are often infeasible or prohibitively costly to build and run across arbitrary collections of input systems. The Lab Streaming Layer (LSL) framework offers a software-based approach to synchronizing data streams based on per-sample time stamps and time synchronization across a common local area netowrk (LAN). Built from the ground up for neurophysiological applications and designed for reliability, LSL offers zero-configuration functionality and accounts for network delays and jitters, making connection recovery, offset correction, and jitter compensation possible. These features can ensure continuous, millisecond-precise data recording, even in the face of interruptions. In this paper, we present an overview of LSL architecture, core features, and performance in common experimental contexts. We also highlight practical considerations and known pitfalls when using LSL, including the need to take into account input device throughput delays that LSL cannot itself measure or correct. The LSL ecosystem has grown to support over 150 data acquisition device classes and to establish interoperability between client software written in several programming languages including C/C++, Python, MATLAB, Java, C#, JavaScript, Rust, and Julia. The resilience and versatility of LSL have made it a major data synchronization platform for multimodal human neurobehavioral recording, now supported by a wide range of software packages including major stimulus presentation tools, real-time analysis envirnoments, and brain-computer interface applications. Beyond basic science, research, and development, LSL has been used as a resilient and transparent back-end in deployment scenarios including interactive art installations, stage performances, and commercial products. In neurobehavioral studies and other neuroscience applications, LSL facilitates the complex task of capturing organismal dynamics and environmental changes occurring within and across multiple data streams on a common timeline.

neuroscience↗

bioRxiv2018

Lead-DBS v2: Toward a comprehensive pipeline for deep brain stimulation imaging

Deep brain stimulation (DBS) is a highly efficacious treatment option for movement disorders and a growing number of other indications are investigated in clinical trials. To ensure optimal treatment outcome, exact electrode placement is required. Moreover, to analyze the relationship between electrode location and clinical results, a precise reconstruction of electrode placement is required, posing specific challenges to the field of neuroimaging. Since 2014 the open source toolbox Lead-DBS is available, which aims at facilitating this process. The tool has since become a popular platform for DBS imaging. With support of a broad community of researchers worldwide, methods have been continuously updated and complemented by new tools for tasks such as multispectral nonlinear registration, structural / functional connectivity analyses, brain shift correction, reconstruction of microelectrode recordings and orientation detection of segmented DBS leads. The rapid development and emergence of these methods in DBS data analysis require us to revisit and revise the pipelines introduced in the original methods publication. Here we demonstrate the updated DBS and connectome pipelines of Lead-DBS using a single patient example with state-of-the-art high-field imaging as well as a retrospective cohort of patients scanned in a typical clinical setting at 1.5T. Imaging data of the 3T example patient is co-registered using five algorithms and nonlinearly warped into template space using ten approaches for comparative purposes. After reconstruction of DBS electrodes (which is possible using three methods and a specific refinement tool), the volume of tissue activated is calculated for two DBS settings using four distinct models and various parameters. Finally, four whole-brain tractography algorithms are applied to the patients preoperative diffusion MRI data and structural as well as functional connectivity between the stimulation volume and other brain areas are estimated using a total of eight approaches and datasets. In addition, we demonstrate impact of selected preprocessing strategies on the retrospective sample of 51 PD patients. We compare the amount of variance in clinical improvement that can be explained by the computer model depending on the method of choice.\n\nThis work represents a multi-institutional collaborative effort to develop a comprehensive, open source pipeline for DBS imaging and connectomics, which has already empowered several studies, and may facilitate a variety of future studies in the field.

neuroscience↗