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 Actions, 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 Actions and Subject state changes for more details.
Subject modules:
- Actions: Surgical procedures and other actions performed on the subject, e.g. silicon probe implantations, virus injections, and optic fiber implants.
- Subject State Changes: Any state change performed on the subject, e.g. brain perfusion, lesion, creation of brain slices.
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 must be unique across BrainSTEM (required).
- 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).
- 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.
- Birth and Death Dates: Birth date and death date of the animal subject.
- 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
- 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 actions, subject state change, and subject logs also depend on the selected projects. For more information on permissions, please visit the permissions page.
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 API Documentation of the Subject API endpoint.
Actions
Actions encompasses a range of surgical and procedural techniques employed to study the brain's structure, function, and response to various interventions. These actions are critical for advancing our understanding of neural mechanisms, developing treatments for neurological disorders, and exploring the effects of genetic and environmental factors on brain health. The types of actions share relationships, but fields are tailored to type.
Types of Actions:
- Brain lesion: A surgical procedure that intentionally damages or destroys brain tissue to study the functions of specific brain areas. Lesions can help identify the roles of different brain regions in behavior and cognition.
- Craniectomy: Involves the surgical removal of a portion of the skull to access the brain, without replacing the skull bone afterward. This procedure is often used in cases requiring prolonged brain access or to alleviate pressure after brain injury.
- Craniotomy: A surgical procedure where part of the skull is temporarily removed to expose the brain for surgery or research purposes. The removed bone is typically replaced after the procedure, making it a temporary opening.
- Optic fiber implant: Involves the surgical implantation of an optic fiber into the brain, often used in optogenetics research to manipulate or record neuronal activity with light..
- Brain perfusion fixation: A technique for preserving brain tissue where a fixative solution is pumped through the circulatory system to stabilize and preserve tissue structure. This method is essential for preparing brain specimens for microscopic examination.
- Single wire electrode: Refers to the implantation of a single wire electrode into the brain, used for recording electrical activity from or stimulating specific neurons or brain areas.
- Silicon probe implant: Involves the implantation of a silicon probe, a device equipped with multiple recording sites, into the brain. Silicon probes are used for high-density recording of neural activity..
- Brain slice: Refers to ex vivo preparations obtained by sectioning brain tissue into thin slices. These slices are used for various types of experiments, including electrophysiological recordings and pharmacological studies.
- Tetrode wire electrode: The implantation of a tetrode, a device made of four intertwined wire electrodes, into the brain. Tetrodes allow for the recording of electrical signals from multiple neurons simultaneously.
- Virus injection: Involves injecting a virus into the brain, typically to deliver genetic material for research purposes, such as gene therapy experiments or to manipulate gene expression in specific brain regions. Typically performed with a small glass capillary.
Fields
- Type: the type of action (required).
- Subject: The subject the action was performed on (required).
- Description: Description of the action.
- Date and time: Date and time the action was performed.
- Consumable: Consumable used in the action.
- Hardware device: Hardware device used to perform the action.
- Brain region: Target brain region where the action was performed.
- Coordinates system: The Coordinate system - see a description of the options below.
- Coordinates: Where the action is performed. Learn more about the specific values on the documentation website.
- Type details: Each type has a number of specific fields for that action type.
Coordinates systems
- 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.
- 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 experimental 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.
- Stereotaxic XYZ Absolute Coordinates: A comprehensive three-dimensional coordinate system based on stereotaxic principles, using X, Y, and Z coordinates along with their corresponding angles. This system allows for precise navigation and localization within a stereotaxic frame, supporting complex brain mapping and intervention tasks.
- Stereotaxic Surface XY Surface Coordinates with Depth: Focuses on two-dimensional positioning on the brain's surface, using X and Y coordinates and their angles. It also includes depth and rotation measurements, suitable for experiments requiring lateral and anteroposterior precision without full three-dimensional depth.
Permissions
Actions inherits permissions from projects via the subject associate with the entry. For more information on permissions, please visit the permissions page.
Action API Access
The API allows for programmable access to Actions, enabling you to read, edit, and delete actions through the API. For details about the action's fields and data structure, refer to the API documentation of the Action API endpoint.
Subject state changes
Subject state changes covers surgical procedures and other methods that allows you to track or record from a subject(s). Subject state change types share relationships, but fields are tailored to the various Subject state change-types.
Types of subject state changes:
- Brain lesion: surgical procedure where a lesion is performed to brain tissue. The skull bone is not following a craniotomy
- Craniectomy: a surgical removal a portion of the skull to expose the brain. The skull bone is not replaced following a craniectomy.
- Craniotomy: a surgical removal of part of the bone from the skull to expose the brain. The skull bone is replaced following a craniotomy.
- Optic fiber implant: a surgical implantation of an optic fiber.
- Brain perfusion fixation: Perfusion is the passage of fluid through the blood vessels or natural channels of an organ or organism. In tissue fixation via perfusion, the fixative is pumped into the circulatory system, usually through a needle inserted into the left ventricle.
- Single wire electrode: Implantation of a single wire electrode.
- Silicon probe implant: Implantation of a silicon probe.
- Brain slice: Brain slices are ex vivo preparations obtained by serial sectioning of brain tissue
- Tetrode wire electrode: Implantation of a tetrode wire electrode
- Virus injection: Injection of a virus into the brain. Typically performed with a small glass capillary.
Fields
- Type: the type of subject state change (required).
- Subject: The subject the subject state change was performed on (required).
- Description: Description of the subject state change.
- Date and time: Date and time the subject state change was performed.
- Consumable: Consumable used in the subject state change.
- Hardware device: Hardware device used to perform the subject state change.
- Brain region: Target brain region where the subject state change was performed.
- Coordinates system: The Coordinate system.
- Coordinates: Where the subject state change is performed. Learn more about the types of coordinate systems and specific values on the documentation website.
- Type details: These are type specific fields.
Permissions
Subject state changes inherits permissions from projects via the subject associate with the entry. For more information on permissions, please visit the permissions page.
Subject state change API Access
The API allows for programmable access to Subject state changes, enabling you to read, edit, and delete subject state changes through the API. For details about the subject state change's fields and data structure, refer to the Subject state change API page.
