Subjects
Subjects provides a comprehensive description of your animal subjects using a set of standard fields. It offers flexibility through a rich text description field, extra fields, and tags. Additionally, the modular construction of Procedures, Subject State Changes, and Subject Logs allows for versatile descriptions of procedures and other activities performed on your subject. Please see the dedicated tabs on Procedures and Subject state changes for more details.
Subject modules:
- Procedures: surgical and procedural techniques performed on the subject, e.g. silicon probe implantations, craniotomies, virus injections, and optic fiber implants.
Two-Part submission form
The submission form consists of two parts. First, you fill in the required fields. Once you click "Create and continue," the subject entry is created, and you can continue editing it on the second part of the form, which contains all fields. The second part has autosave and will automatically save your changes.
Subject fields:
- Name: The subject name (required; maximum 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 new one first on the project page(required).
- Sex: Sex of the animal (required; Male, Female, or Unknown).
- Species & strain: The species and strain of the animal subject. If either is missing, you can submit them for approval on the Species and Strain pages (required).
- Description: A text description of the subject.
- Genetic line: The genetic line of the subject. Could also be wild type (string; maximum length: 100 characters).
- Birth and death dates: Birth date and death date of the animal subject (e.g. "2023-03-22").
- Tags: Tags for the subject. Tags are useful for organizational purposes, allowing you to quickly label a subject and use them as filters. Tags are shared among users
- Name used in repository: Use this field if you have another name of your subject (string; maximum length: 100 characters).
- Extra fields: Allows you to add additional fields to the project. The values can be strings or numeric values.
Permissions
The subject inherits permissions from the projects associated with it. The relationships in procedures, subject state change, and subject logs also depend on the selected projects. For more information on permissions, please see the documentation.
Subject API Access
The API allows for programmable access to subjects, enabling you to read, edit, and delete subjects through the API. For details about the subject's API fields and data structure, refer to the documentation.
Procedures
Neuroscientific procedures encompass a wide range of surgical and experimental techniques designed to study the brain’s structure, function, and responses to various interventions. These procedures are critical for advancing our understanding of how the brain works, developing new treatments for neurological disorders, and exploring the influence of genetic and environmental factors on brain health. While many of these techniques are interconnected, they are often grouped according to their specific methods and goals.
Types of Procedures:
Surgical Procedures:
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Anesthesia:
The administration of anesthetic agents to induce a state of unconsciousness, analgesia, or sedation. This procedure is essential for most surgical interventions, allowing for humane and effective experimental procedures while minimizing stress and discomfort.
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Cranial window:
A surgical technique where a small section of skull is replaced with a transparent window. This allows for direct, long-term optical access to the brain's surface for imaging and other optical investigations.
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Craniectomy:
The surgical removal of a portion of the skull that is not replaced afterward. This approach provides prolonged, direct access to the brain or helps relieve increased intracranial pressure following injury.
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Craniotomy:
A procedure in which part of the skull is temporarily removed to expose the brain. After surgery or research activities are completed, the bone flap is typically replaced, restoring the skull's integrity.
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Headcap:
The attachment of a protective covering over cranial implants. This structure protects the brain and implanted devices while providing access points for experimental manipulations.
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Head fixation:
The immobilization of the animal's head during experiments. This procedure is crucial for ensuring stability during recordings or manipulations, allowing for precise measurements and interventions.
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Headpost implant:
The attachment of a device to the skull that allows for head fixation. This enables stable recordings or manipulations in awake animals.
Implant Procedures:
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Blood pressure sensor implant:
The surgical implantation of a sensor designed to monitor blood pressure continuously. This device provides valuable data on cardiovascular responses during various experimental conditions.
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Breathing sensor implant:
The placement of a sensor that monitors respiratory patterns and rates. This implant helps track breathing changes in response to experimental manipulations or disease progression.
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Catheter implant:
The insertion of a thin, flexible tube into blood vessels or other body cavities. Catheters can be used for drug delivery, fluid sampling, or pressure monitoring.
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ECG implant:
The surgical placement of electrodes to record the electrical activity of the heart (electrocardiography). This allows for continuous monitoring of cardiac function during experiments.
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EEG implant:
The implantation of electrodes on or beneath the skull to record brain electrical activity (electroencephalography). This provides information about large-scale neural activity patterns.
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EMG implant:
The placement of electrodes in or on muscles to record electrical activity (electromyography). This helps monitor muscle activation patterns during behavior.
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Generic implant:
A general category for implantable devices that don't fit into other specific categories but serve experimental purposes.
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GRIN lens implant:
The implantation of a gradient-index lens that allows for deep brain imaging. This optical device enables visualization of neural activity in deep brain structures.
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Nerve cuff implant:
The placement of a cuff electrode around a peripheral nerve. This allows for recording or stimulation of specific nerve fibers.
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Optic fiber implant:
The surgical placement of a tiny optic fiber into brain tissue, commonly used in optogenetics. By delivering or detecting light, researchers can modulate or record neuronal activity in precise brain regions.
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Prism implant:
The insertion of a prism for redirecting light paths in optical imaging. This enables visualization of brain regions that would otherwise be inaccessible.
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Reference electrode implant:
The placement of an electrode that serves as a reference point for other recording electrodes. This improves the signal quality of electrophysiological recordings.
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Silicon probe implant:
The insertion of a silicon-based probe equipped with multiple recording sites. These probes enable high-density recordings from many neurons simultaneously, facilitating detailed studies of neural circuits.
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Single wire electrode:
The implantation of a thin wire electrode into the brain for recording electrical activity or stimulating neurons. This targeted approach aids in understanding single-neuron contributions to brain function.
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Temperature sensor implant:
The placement of a sensor that monitors body or brain temperature. This provides data on thermal regulation or responses to experimental manipulations.
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Tetrode wire electrode:
The introduction of a four-wire electrode (tetrode) bundle into the brain. Tetrodes allow researchers to monitor and differentiate signals from multiple adjacent neurons, greatly enhancing the resolution of neural recordings.
Injection and Infusion Procedures:
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Injection:
The delivery of solutions, often containing genetic or pharmacological agents, directly into targeted brain areas. This method is commonly performed using a small glass capillary and can be used to alter gene expression or modulate neural activity.
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Virus injection:
Similar to the above, but specifically involves injecting viral vectors to introduce or manipulate genetic material in targeted neuronal populations. This approach is key for studying gene function and developing gene therapies.
Brain and Tissue Procedures:
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Brain lesion:
A deliberate injury or destruction of a specific brain region to investigate its role in behavior, cognition, and physiological processes. Lesion studies help map functions to particular brain areas.
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Perfusion fixation:
A tissue-preservation method in which a fixative solution is perfused through the circulatory system, stabilizing the brain's structure for microscopic examination. This technique ensures that cellular and tissue-level details are well-preserved.
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Slice:
The preparation of thin, ex vivo sections of brain tissue for detailed examination. Brain slices can be used for electrophysiological recordings, imaging, and testing pharmacological agents, providing insights into local circuit properties.
Abstract Procedures:
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Behavioral tracking:
The systematic monitoring and recording of an animal's movements and behaviors. This procedure provides quantitative data on behavioral patterns, responses to stimuli, and changes in activity over time or in response to experimental manipulations.
Fields
- Type: the type of procedure (required).
- Subject: The subject the procedure was performed on (required).
- Notes: Notes of the procedure.
- Date and time: Date and time the procedure was performed.
- Consumable stock: Consumable stock used in the procedure.
- Hardware device: Hardware device used to perform the procedure.
- Brain region: Target brain region where the procedure was performed.
- Coordinates system: The Coordinate system - see a description of the options below.
- Coordinates: Where the procedure is performed. Learn more about the specific values on the documentation website.
- Type details: Each type has a number of specific fields for that procedure type.
Coordinates systems
- Stereotaxic Bregma-Based Absolute Coordinates: Utilizes the Bregma point as a primary reference for absolute positioning within the skull. This system includes anteroposterior (AP), mediolateral (ML), and dorsoventral (DV) coordinates, along with their corresponding angles, enabling precise targeting and measurement from the Bregma landmark.
- Stereotaxic Bregma-Based Surface Coordinates with Depth: Measures coordinates from the surface of the brain at the Bregma point, incorporating depth and rotation adjustments. This system is particularly useful for applications where interventions or measurements need to accommodate the curvature of the brain's surface.
- Stereotaxic Lambda-Based Absolute Coordinates: Anchors measurements to the Lambda, a secondary cranial landmark, providing a set of absolute coordinates. Like the Bregma system, it includes AP, ML, and DV coordinates and their angles, offering an alternative reference point for varied setups.
- Stereotaxic Lambda-Based Surface Coordinates with Depth: Similar to the Bregma brain surface system, but using Lambda as the reference. It includes coordinates adjusted to the brain's surface at Lambda, depth, and rotation, useful for targeting specific areas near the occipital part of the brain.
- Common Coordinate Framework XYZ Absolute Coordinates: A comprehensive three-dimensional coordinate system based on the Common Coordinate Framework developed by the Allen Institute, using X, Y, and Z coordinates along with their corresponding angles. This system allows for precise localization within the reference frame, supporting complex brain mapping.
- External XYZ Coordinates with Angles: A three-dimensional Cartesian coordinate system using absolute positions relative to an external reference point. It includes specific coordinates (X, Y, Z) and angles (X angle, Y angle, Z angle) to describe orientation and position in space, making it ideal for precise, global positioning tasks in research and clinical settings.
Please visit the documentation to learn more about the coordinate systems.
Permissions
Procedures inherits permissions from projects via the subject associate with the entry. For more information on permissions, please see the documentation.
Procedure API Access
The API allows for programmable access to Procedures, enabling you to read, edit, and delete procedures through the API. For details about the procedure's fields and data structure, refer to the documentation.
