Peter_MS13_171206_132039_concat

The behavior model is a module in datasets that is used to describe the behavior occuring in a dataset. The behavior is described by the involved subjects, the experimental setup, and a behavioral paradigm. Both the experimental setup and the behavioral paradigm are private attributes and must be defined separately. You must create both before filling in the behavior form. The private attributes belong to group(s) that must be shared with one of a dataset's associated projects.

Fields

• Dataset: The project name must be unique across BrainSTEM (required).
• Subjects: A rich text description of the project (required).
• Experimental setup: List of related publication IDs formatted as strings (required).
• Behavioral paradigm: Allows you to add additional fields to the project. The values can be strings or numeric values (required).
• Description: Determines if the project is publicly available or accessible only through the private portal.

Permissions

A behavior inherits permissions from the dataset associated with it. For more information on permissions, please visit the permissions page.

Behavior API Access

The API allows for programmable access to behaviors, enabling you to read, edit, and delete behaviors through the API. For details about the behavior's fields and data structure, refer to the API documentation of the Behavior API endpoint.

Experiment data encompasses the diverse range of data types acquired during scientific experiments. These data types are crucial for understanding the complex workings of the brain and nervous system, offering insights into neural function, structure, behavior, and the effects of various interventions. Experiment data types share relationships, but fields are tailored to the various data-types.

Types of Experiment data:

• Audio: Recordings of sounds or vocalizations, used in studies examining auditory processing, communication, and the effects of auditory stimuli on behavior or neural activity.
• Behavioral Tracking Monitoring and recording the movements or behaviors of subjects in response to specific conditions or stimuli. This data is essential for understanding the neural basis of behavior, learning, and memory.
• Computed tomography (CT): A computed tomography scan (CT scan; formerly called computed axial tomography scan or CAT scan) is a medical imaging technique used to obtain detailed internal images of the body.
• Electroencephalography (EEG): A method to record an electrogram of the spontaneous electrical activity of the brain. The biosignals detected by EEG have been shown to represent the postsynaptic potentials of pyramidal neurons in the neocortex and allocortex. It is typically non-invasive, with the EEG electrodes placed along the scalp (commonly called "scalp EEG") using the International 10–20 system, or variations of it. Electrocorticography, involving surgical placement of electrodes, is sometimes called "intracranial EEG". Clinical interpretation of EEG recordings is most often performed by visual inspection of the tracing or quantitative EEG analysis.
• Electroneurogram (ENG): An electroneurogram is a method used to visualize directly recorded electrical activity of neurons in the central nervous system (brain, spinal cord) or the peripheral nervous system (nerves, ganglions). The acronym ENG is often used. An electroneurogram is similar to an electromyogram (EMG), but the latter is used to visualize muscular activity.
• Confocal Microscopy: Most frequently confocal laser scanning microscopy (CLSM) or laser scanning confocal microscopy (LSCM), is an optical imaging technique for increasing optical resolution and contrast of a micrograph by means of using a spatial pinhole to block out-of-focus light in image formation. Capturing multiple two-dimensional images at different depths in a sample enables the reconstruction of three-dimensional structures (a process known as optical sectioning) within an object.
• Extracellular Electrophysiology: In extracellular electrophysiology, the cells' electrical signals are recorded using electrodes outside the cell. The primary advantages of an extracellular unit recording are: The ease of obtaining recordings. The ability to record from numerous neurons simultaneously. Its capability to record over days and weeks.
• Fiber Photometry: A calcium imaging technique that captures 'bulk' or population-level calcium (Ca2+) activity] from specific cell-types within a brain region or functional network in order to study neural circuits.
• Functional Magnetic Resonance Imaging (fMRI): Functional magnetic resonance imaging or functional MRI (fMRI) measures brain activity by detecting changes associated with blood flow. This technique relies on the fact that cerebral blood flow and neuronal activation are coupled.
• Functional Ultrasound Imaging (fUS): A medical ultrasound imaging technique of detecting or measuring changes in neural activities or metabolism, for example, the loci of brain activity, typically through measuring blood flow or hemodynamic changes. The method can be seen as an extension of Doppler imaging.
• General time-series:
• Intracellular Electrophysiology: Intracellular recording is an electrophysiology technique that inserts a glass microelectrode into a single cell (usually a neuron) to precisely measure its electrical activity (voltages across or currents passing through the cellular membranes).
• Light Field Microscopy: Light field microscopy (LFM) is a scanning-free 3-dimensional (3D) microscopic imaging method based on the theory of light field. This technique allows sub-second (~10 Hz) large volumetric imaging ([~0.1 to 1 mm]3) with ~1 μm spatial resolution in the condition of weak scattering and semi-transparence, which has never been achieved by other methods. Just as in traditional light field rendering, there are two steps for LFM imaging: light field capture and processing. In most setups, a microlens array is used to capture the light field.
• Magnetic Resonance Imaging (MRI): A medical imaging technique used in radiology to form pictures of the anatomy and the physiological processes inside the body. MRI scanners use strong magnetic fields, magnetic field gradients, and radio waves to generate images of the organs in the body. MRI does not involve X-rays or the use of ionizing radiation, which distinguishes it from computed tomography (CT) and positron emission tomography (PET) scans.
• Magnetoencephalography (MEG): A functional neuroimaging technique for mapping brain activity by recording magnetic fields produced by electrical currents occurring naturally in the brain, using very sensitive magnetometers. Arrays of SQUIDs (superconducting quantum interference devices) are currently the most common magnetometer, while the SERF (spin exchange relaxation-free) magnetometer is being investigated for future machines./li>
• Miniscope Microscopy: Head-mounted, miniature microscopes that allow imaging of large populations of neural activity in freely-behaving mice and rats. This is possible due to their small size, as they are light enough for a mouse or rat to easily carry without interfering greatly with behavior. Researchers couple miniscopes with implanted gradient-refractive-index (GRIN) lenses or cortical windows that enable deep and superficial brain imaging.
• Positron Emission Tomography (PET): A functional imaging technique that uses radioactive substances known as radiotracers to visualize and measure changes in metabolic processes, and in other physiological activities including blood flow, regional chemical composition, and absorption. Different tracers are used for various imaging purposes, depending on the target process within the body.
• Single-photon emission computed tomography (SPECT): A nuclear medicine tomographic imaging technique using gamma rays. It is very similar to conventional nuclear medicine planar imaging using a gamma camera (that is, scintigraphy), but is able to provide true 3D information.
• Single-Photon Microscopy: An imaging technique that allows for the visualization of cellular and subcellular structures in living tissue with high spatial resolution, using single-photon excitation.
• Three-Photon Microscopy: A high-resolution fluorescence microscopy based on nonlinear excitation effect. Different from two-photon excitation microscopy, it uses three exciting photons. The fluorescent dyes then emit one photon whose energy is (slightly smaller than) three times the energy of each incident photon. In addition, three-photon microscopy employs near-infrared light with less tissue scattering effect. This causes three-photon microscopy to have higher resolution than conventional microscopy.
• Two-Photon Microscopy: A fluorescence imaging technique that is particularly well-suited to image scattering living tissue of up to about one millimeter in thickness. Unlike traditional fluorescence microscopy, where the excitation wavelength is shorter than the emission wavelength, two-photon excitation requires simultaneous excitation by two photons with longer wavelength than the emitted light.

Fields

• Dataset: the dataset of the Experiment data (required).
• Type: the type of Experiment data (required).
• Actions: The Actions the Experiment data was acquired with (required).
• Installations: The Installations used to acquire the data with (required).
• Image: An image of the Experiment data.
• Description: Description of the Experiment data.
• Hardware device: Hardware device used to perform the Experiment data.
• Type details: Each type has a list of details tailed to describe the experimental data.

Permissions

Experiment data inherits permissions from projects via the dataset associate with the entry. For more information on permissions, please visit the permissions page.

Experiment data API Access

The API allows for programmable access to Experiment data, enabling you to read, edit, and delete entries through the API. For details about the Experiment data fields and data structure, refer to the API documentation of the Experiment data API endpoint.

Manipulations refers to various methods and techniques used to alter, control, or influence neural activity, brain functions, or behaviors in experimental settings. These manipulations are crucial for understanding the mechanisms underlying neural processes, the effects of various stimuli or interventions on the brain, and the development of potential therapies for neurological conditions. Manipulations are tied to a dataset and to a subject through actions.

• Deep brain stimulation (DBS): A neurosurgical procedure that involves implanting electrodes in specific areas of the brain to deliver electrical impulses. It's used to treat a variety of neurological conditions, including Parkinson's disease and essential tremor.
• Electromagnetic field stimulation: Involves the use of magnetic or electric fields to modulate neuronal activity. This non-invasive method can influence brain function and is studied for therapeutic potential in psychiatric and neurological disorders.
• Electrical stimulation: The application of electrical currents to neurons or neural tissues to activate or inhibit neural activity. This broad category can include invasive methods like intracortical microstimulation or non-invasive approaches like transcranial direct current stimulation (tDCS).
• Liquid perturbation: Introduces liquids into the brain environment to study the effects of various substances or to physically disrupt brain activity. This can include the injection of drugs, solutions, or other compounds.
• Micro perfusion: A technique that allows the localized delivery of substances directly to a targeted area of the brain through a fine cannula, enabling the study of the effects of drugs or other agents on specific brain regions.
• Optogenetical stimulation: Uses light to control neurons that have been genetically modified to express light-sensitive ion channels. This precise method enables the activation or inhibition of specific neuronal populations with high temporal resolution.
• Pharmacological inhalation: Involves the administration of drugs in vapor form so that they are inhaled and absorbed through the lungs, affecting the brain. This method is used to study the effects of inhaled substances on neural activity and behavior.
• Pharmacological injection: The direct injection of drugs or other substances into the body or directly into brain tissue to study their effects on neural activity, brain function, or behavior.
• Pharmacological superfusion: A technique where drugs are applied directly to neural tissues or cells in a controlled manner, often using a perfusion system, allowing for the study of drug effects on neural activity in vitro.
• Sound stimulation: The use of auditory stimuli to influence brain activity and study the neural mechanisms of hearing, perception, and cognition, as well as the therapeutic effects of sound.
• Thermal perturbation: The application of heat or cold to neural tissue to study the effects of temperature changes on neural activity, function, or structural integrity.
• Transcranial Electrical Stimulation: A non-invasive method that applies electrical currents through the scalp and skull to modulate neuronal activity in the brain, used for research and therapeutic purposes.
• Transcranial Magnetic Stimulation (TMS): A non-invasive technique that uses magnetic fields to induce electrical currents in the brain, capable of modulating neural activity and used for both research and treatment of various neurological and psychiatric conditions.
• Ultra sound stimulation: Utilizes high-frequency sound waves to non-invasively modulate neural activity. This method has potential applications in both research and clinical settings for mapping brain function and treating neurological disorders.

Fields

• Type: the type of manipulation (required).
• Dataset: the type of manipulation (required).
• Actions: The subject the manipulation was performed on (required).
• Description: Description of the manipulation.
• Hardware device: Hardware device used to perform the manipulation.
• Type details: These are type specific fields.

Permissions

Manipulations inherit permissions from projects via the dataset associate with the entry. For more information on permissions, please visit the permissions page.

Manipulation API Access

The API allows for programmable access to manipulations, enabling you to read, edit, and delete manipulations through the API. For details about the manipulation's fields and data structure, refer to the API documentation on the Manipulation API endpoint.