BrainSTEM API

Subject Public List

Subject Public List

GET /api/public/stem/subject/?format=api&page=2

HTTP 200 OK
Allow: GET, POST, PATCH, DELETE, HEAD, OPTIONS
Content-Type: application/json
Vary: Accept
                  
{
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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:

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.
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.
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.

Implant Procedures:

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.
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.
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.
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:

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.
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:

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.
Brain 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.
Brain 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.

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.