Explore how MATLAB can help in your neuroscience projects:

Brain Mapping

Brain mapping approaches provide a macroscopic view of brain activity or structure. They span a wide range of physical imaging and recording modalities including:

• Magnetic (MRI)
• Electrical (EEG/ECoG)
• X-ray (CT)
• Nuclear (PET/SPECT)
• Optical (NIRS)

Neuroscientists must overcome many challenges with brain mapping data. They need algorithms and workflows to carefully separate signal from noise, to localize signal sources, to ascertain functional connectivity, and to determine signal components related to the subject’s task.

Neuroscientists use MATLAB^®, and they create, use, and build upon many widely-used MATLAB based tools for brain mapping studies. They process raw data signals, produce brain images from multidimensional data sets, interpret and visualize brain mapping data sets, perform higher-order analyses of brain activity and connectivity, and much more.

Community Tools on File Exchange

• Brainstorm: Open-source application for MEG/EEG analysis
• EEGLAB: A widely used toolbox for processing electrophysiological data
• FieldTrip: The MATLAB software toolbox for MEG and EEG analysis
• Statistical Parametric Mapping (SPM): Free and open-source software for the analysis of brain imaging data sequences

Examples and How To

Cellular Neuroscience

Cellular neuroscience researchers seek insights into brain structure (neuroanatomy) and function  (neurophysiology) at the microscopic scale of individual neurons and synapses. Neuroscientists use techniques such as:

• Electrophysiology
• Electron microscopy
• Optical microscopy
• Optogenetics

They collect recordings, image sets, timestamps, and other raw data from biological neural networks, and even from whole brains in the case of simple organisms. Recent advances in probe densities, recording speeds, microscopic resolution and fields of view, and integration with behavior and psychophysics are confronting neuroscientists with increased data complexity and data volumes.

Neuroscientists use and create MATLAB^® based workflows and tools for cellular neuroscience. For applications such as multichannel recordings, tissue section imaging, and in vivo optical neurophysiology, they use MATLAB for performing and automating experiments and analysis. They can also combine techniques using MATLAB as a shared platform.

Community Tools on File Exchange

• Axon Segmentation: Original axon segmentation toolbox
• CellSort: Toolbox for automated sorting of cellular calcium signals from optical imaging data
• Deconvolution and Demixing…: Source extraction and deconvolution from calcium imaging data
• Kilosort: Fast and accurate spike sorting toolbox
• Suite2P: Fast, complete two-photon pipeline

Search “neuroscience” on File Exchange to see more.

Behavior and Psychophysics

Neuroscientists perform experiments to understand the correlations and causal links between neural function, sensory inputs (psychophysics), and experimental subject outputs (behavior). These experiments provide a window into the principles of nervous system function, including cognitive function and even consciousness. Neuroscientists must produce controlled sensory stimuli as cues and quantifiable inputs. They must quantify speech, motion, and other behaviors. These experiments demand increasing levels of precision and automation.

Neuroscientists use MATLAB^® and MATLAB based tools for studies involving behavior and psychophysics. MATLAB is used to track experimental subjects in streaming and motion-capture video, identify and classify behavioral features and events, control and record sensory inputs, coordinate complex multistate experiments, and much more.

Community Tools on File Exchange

• MonkeyLogic: A toolbox for the design and execution of psychophysical tasks with high-temporal precision
• Psychophysics Toolbox: A toolbox for neuroscience stimulus presentation and response collection
• Stage: Visual stimulus system

Search “neuroscience” on File Exchange to see more.