Sessions
A session is a modular construction that provides flexible and standardized descriptions of various aspects of experiments. The session has a number of direct fields, but is primarily described by the module below. There are dedicated tabs with further details on the modules: Behaviors, Data acquisition, and Manipulations.
Session modules:
- Behavior: Description of the behavior the animal subject(s) is doing during the collection of the session. A behavior is described by two personal attributes: the Setup and the Behavioral paradigm.
- Data acquisition: Description of the data acquisition files. The Data acquisition module is highly flexible and can be used to describe many types of experimental data, such as Extracellular and Intracellular Electrophysiology, 2-photon microscopy, Miniscope, Audio Recordings, and Behavioral Video Recordings. Details are tailored to each experiment type.
- Manipulations: Description of any manipulations performed during an experiment. This is a crusial module as manipulations alters the physiological conditions of a recording. The Manipulations module is flexible and can describe many types of manipulations, such as Optogenetic Stimulation, Micro Perfusion, Pharmacological Injection, Thermal Perturbation, Transcranial Electrical Stimulation, and Ultrasound Stimulation. A manipulation is described by a manipulation protocol, typically consisting of a description of the manipulation profile, its power, duration, duty cycle, and the number of repetitions.
- Epochs: Temporal aspects of a session. An epoch is characterized by a name, a start and end time relative to the start of the session. The other modules (Data acquisition, Manipulations, and Behavior) can be linked to epochs, allowing for temporal segmentation of a session.
Two-Part Form with Autosave
The submission form consists of two parts. First, you fill in the required fields. Once you click "Create and continue," the project entry is created, and you can continue editing it on the second part of the form, which contains all the fields.
The second part of the form automatically keeps track of your changes and saves as you fill out the form.
Session fields:
- Name: The session name (required; max length: 100 characters; must be unique; ).
- Projects: You can only select projects for which you have change-permissions. If the project list is empty, you must create a project first on the project page. The selected project also defines which subjects, procedures, and personal attributes you can choose from on the second part of the form (required).
- Description: A text description of the session.
- Date and time: The onset of the session.
- Tags: Tags for the session. Tags are useful for organizational purposes, allowing you to quickly label a subject and use them as filters. Tags are shared among users.
- Data storage: Describes where the data is stored.
- Name used in storage: Optional custom name for the session for data handling. As the session name must be unique across BrainSTEM, this allows for greater flexibility in data handling (string; max length: 200).
- Extra fields: Allows you to add additional fields to the session (The values can be strings or numeric values)s.
- Public repositories: Allows you to to link to a public repository where the data is shared.
Permissions
The session inherits permissions from projects associated with it. Data storage is shared through the project's groups, and you can only add a data storage associated with the same groups as the selected projects. The relationships in modules also depend on the selected projects. For more information on permissions, please visit the permissions page.
Session API Access
The API allows for programmable access to sessions. For detailed information about the sessions' fields and data structure, please refer to the API documentation on the Session API endpoint.
Behaviors
The behavior model is a module in sessions that is used to describe the behavior occuring in a session. The behavior is described by the involved subjects, the setup, and a behavioral paradigm. Both the 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 session's associated projects.
Fields
- Session: The project name must be unique across BrainSTEM (required).
- Subjects: List of subjects (required).
- Setup: Related setup (required).
- Behavioral paradigm: Allows you to add additional fields to the project. The values can be strings or numeric values (required).
- Notes: Notes about the behavior.
Permissions
A behavior inherits permissions from the session 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.
Data acquisition
Data acquisition encompasses a diverse range of data types collected during scientific research. These data are crucial for understanding the intricate workings of the brain and nervous system, informing us about neural function, structure, behavior, and the effects of various interventions. While different data types are often interrelated, each category is tailored to capture unique aspects of neural and physiological processes.
Types of Data Acquisition:
Audio and Behavior Tracking
- Audio: Recordings of sounds, vocalizations, or auditory stimuli. These datasets aid in examining how the brain processes sound, supports communication, and integrates auditory information into behavior.
- Behavioral Tracking: Monitoring and quantifying subjects’ movements, actions, and responses under specific conditions. This information is vital for linking neural activity to behavior, learning, memory, and decision-making processes.
Electrophysiology
- Electroencephalography (EEG): Non-invasive recordings of the brain’s electrical activity from electrodes placed on the scalp. EEG helps researchers study large-scale neural dynamics, sleep states, sensory processing, and cognitive functions.
- Electroneurogram (ENG): Direct measurements of electrical activity from nerves or neurons in the central or peripheral nervous system. ENG data elucidate how neural signals propagate and inform on nerve health and function.
- Extracellular Electrophysiology: Recordings of neuronal signals from outside the cells. This method allows for simultaneous long-term monitoring of multiple neurons, providing insight into network dynamics and population coding.
- Intracellular Electrophysiology: High-precision recordings of a single cell’s electrical activity using a microelectrode inserted into the neuron. Intracellular data reveal subthreshold events, synaptic inputs, and intrinsic cellular properties.
Optical Imaging
- Fiber Photometry: A calcium imaging technique capturing population-level neural activity changes via light signals. It is especially useful for studying the dynamics of specific cell types within a brain circuit.
- Miniscope Microscopy: Small, head-mounted microscopes that let researchers visualize large populations of neurons in freely moving animals, bridging the gap between naturalistic behavior and underlying neural activity.
- Confocal Microscopy: An optical imaging technique that uses a pinhole to achieve high-resolution, high-contrast images and 3D reconstructions. Commonly applied to study cellular structures and brain tissue morphology.
- Light Field Microscopy: A scanning-free, 3D imaging method capturing entire light fields, enabling rapid volumetric imaging at micron-scale resolution. Ideal for reconstructing complex neural circuits in three dimensions.
- Single-Photon Microscopy: A fluorescence imaging method utilizing single-photon excitation for detailed observation of cellular and subcellular structures in living tissue.
- Two-Photon Microscopy: A fluorescence imaging technique using near-infrared light for deeper imaging in scattering tissue. It is well-suited for probing functional neuronal activity in intact brain tissue.
- Three-Photon Microscopy: A nonlinear optical method employing three-photon excitation to achieve deeper penetration and higher spatial resolution, allowing imaging of neuronal activity in challenging tissue environments.
Magnetic and Functional Imaging
- Magnetic Resonance Imaging (MRI): Uses magnetic fields and radio waves to generate detailed anatomical images of the brain and other organs, without ionizing radiation. MRI is a cornerstone of structural brain imaging.
- Functional Magnetic Resonance Imaging (fMRI): Measures brain activity indirectly through changes in blood flow. fMRI helps map functional networks, cognitive states, and sensory-motor processing.
- Magnetoencephalography (MEG): Detects the magnetic fields produced by neuronal activity. With excellent temporal resolution, MEG provides insights into real-time brain dynamics and functional connectivity.
Tomography and Ultrasound
- Computed Tomography (CT): An X-ray-based imaging modality that produces cross-sectional images of internal brain structures, aiding in the identification of pathologies and structural abnormalities.
- Positron Emission Tomography (PET): Uses radioactive tracers to visualize metabolic processes and physiological activities. PET is invaluable for studying neurotransmitter systems, blood flow, and metabolic states in the brain.
- Single-Photon Emission Computed Tomography (SPECT): A nuclear imaging technique capturing 3D information on functional processes. SPECT data are often used alongside other imaging modalities for comprehensive analysis.
- Functional Ultrasound Imaging (fUS): Measures changes in blood flow or metabolism related to neural activity. As a non-invasive method with high spatial and temporal resolution, fUS is emerging as a versatile neuroimaging tool.
General and Time-Series Data
- General Time-Series: Any continuous, time-dependent data—such as neural firing rates, physiological signals, or behavioral readouts—used to analyze temporal patterns, rhythms, and dynamics in neural and physiological systems.
Fields
- Session: the session of the Data acquisition (required).
- Type: the type of Data acquisition (required).
- Procedures: The Procedures the Data acquisition was acquired with (required).
- Equipment: The equipment used to acquire the data with (required).
- Image: An image of the Data acquisition.
- Notes: Notes to the Data acquisition.
- Type details: Each type has a list of details tailed to describe the experimental data.
Permissions
Data acquisition inherits permissions from projects via the session associate with the entry. For more information on permissions, please visit the permissions page.
Data acquisition API Access
The API allows for programmable access to Data acquisition, enabling you to read, edit, and delete entries through the API. For details about the Data acquisition fields and data structure, refer to the API documentation of the Data acquisition API endpoint.
Manipulations
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 session and to a subject through procedures.
Types of manipulation methods:
Electrical and Magnetic Stimulation:
- 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.
- 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).
- 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.
- 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.
Optical, Thermal, and Ultrasound Stimulation:
- 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.
- 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.
- Ultrasound 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.
Chemical and Pharmacological Perturbations:
- 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.
- 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.
- 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.
Odor and Sound Stimulation:
- Odor stimulation: The presentation of controlled olfactory stimuli to study sensory processing, neural activity, and behavior influenced by smells.
- 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.
Fields
- Type: the type of manipulation (required).
- Session: the type of manipulation (required).
- Procedures: The subject the manipulation was performed on (required).
- Notes: Notes to 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 session 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.
