Analysis of spike and local field potential (LFP) data is an essential part of neuroscientific research. Today there exist many open-source toolboxes for spike and LFP data analysis implementing various functionality. Here we aim to provide a practical guidance for neuroscientists in the choice of an open-source toolbox best satisfying their needs. We overview major open-source toolboxes for spike and LFP data analysis as well as toolboxes with tools for connectivity analysis, dimensionality reduction and generalized linear modeling. We focus on comparing toolboxes functionality, statistical and visualization tools, documentation and support quality. To give a better insight, we compare and illustrate functionality of the toolboxes on open-access dataset or simulated data and make corresponding MATLAB scripts publicly available.
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http://dx.doi.org/10.3389/fninf.2019.00057 | DOI Listing |
Neuroimage
December 2024
Department of Radiology and Biomedical Research Imaging Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States. Electronic address:
Functional magnetic resonance imaging (fMRI) has been increasingly employed to investigate functional brain activity. Many fMRI-related software/toolboxes have been developed, providing specialized algorithms for fMRI analysis. However, existing toolboxes seldom consider fMRI data augmentation, which is quite useful, especially in studies with limited or imbalanced data.
View Article and Find Full Text PDFEJNMMI Phys
December 2024
Department of Information Engineering, University of Padova, Padova, Italy.
Purpose: PET imaging is a pivotal tool for biomarker research aimed at personalized medicine. Leveraging the quantitative nature of PET requires knowledge of plasma radiotracer concentration. Typically, the arterial input function (AIF) is obtained through arterial cannulation, an invasive and technically demanding procedure.
View Article and Find Full Text PDFJ Am Soc Mass Spectrom
December 2024
Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria.
Top-down mass spectrometry (MS) enables comprehensive characterization of modified proteins and nucleic acids and, when native electrospray ionization (ESI) is used, binding site mapping of their complexes with native or therapeutic ligands. However, the high complexity of top-down MS spectra poses a serious challenge to both manual and automated data interpretation, even when the protein, RNA, or DNA sequence and the type of modification or the ligand are known. Here, we introduce FAST MS, a user-friendly software that identifies, assigns and relatively quantifies signals of molecular and fragment ions in MS and MS/MS spectra of biopolymers with known sequence and provides a toolbox for statistical analysis.
View Article and Find Full Text PDFPhys Med Biol
December 2024
Department of Medical Physics and Bioengineering, University College London, Gower Street, London, WC1E 6BT, UNITED KINGDOM OF GREAT BRITAIN AND NORTHERN IRELAND.
Transcranial ultrasound is used in a variety of treatments, including neuromodulation, opening the blood-brain barrier (BBB), and high intensity focused ultrasound (HIFU) therapies. To ensure safety and efficacy of these treatments, numerical simulations of the ultrasound field within the brain are used for treatment planning and evaluation. This study investigates the accuracy of numerical modelling of the propagation of focused ultrasound through cranial bones.
View Article and Find Full Text PDFPhys Med Biol
December 2024
Radiology and Physics, The University of British Columbia, 6224 Agricultural Rd, Vancouver, British Columbia, V6T 1Z4, CANADA.
Objective: Modeling of the collimator-detector response (CDR) in SPECT reconstruction enables improved resolution and accuracy, and is thus important for quantitative imaging applications such as dosimetry. The implementation of CDR modeling, however, can become a computational bottleneck when there are substantial components of septal penetration and scatter in the acquired data, since a direct convolution-based approach requires large 2D kernels. This work proposes a 1D convolution and rotation-based CDR model that reduces reconstruction times but maintains consistency with models that employ 2D convolutions.
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