Procedure API endpoint

Table of contents

1. Fields
2. Types of procedure
   1. Surgical Procedures
   2. Implant Procedures
   3. Injection and Infusion Procedures
   4. Brain and Tissue Procedures
3. Coordinates system options
4. List view
5. Add
6. Detail
7. Change
8. Delete

Fields

Field	Description
id	UUID identificator formatted as a string
type	string [required]. See options below
notes	string [max length: 500]
subject	related subject ID formatted as a string [required]
date_time	string containing date (e.g. “2023-03-22”)
consumable	related consumable ID formatted as a string
hardwaredevice	related hardware device ID formatted as a string
brain_region	related brain region ID formatted as a string
details	JSON object. See accepted schemas below
coordinates_system	string [required]. See options below
coordinates_details	JSON object. See accepted schemas below

Types of procedure

Surgical Procedures

• Craniectomy: Craniectomy
• Craniotomy: Craniotomy
• CranialWindow: Cranial window

Implant Procedures

• OpticFiberImplant: Optic fiber implant
• SiliconProbeImplant: Silicon probe implant
• TetrodeWireElectrode: Tetrode wire electrode
• SingleWireElectrode: Single wire electrode

Injection and Infusion Procedures

• Injection: Injection
• VirusInjection: Virus injection

Brain and Tissue Procedures

• BrainLesion: Brain lesion
• PerfusionFixation: Brain perfusion fixation
• Slice: Brain slice

Coordinates system options

These are the available coordinates_system options for Procedure:

• External_XYZ_Absolute: External XYZ Coordinates with Angles
• Stereotaxic_BregmaAbsolute: Stereotaxic Bregma-Based Absolute Coordinates
• Stereotaxic_BregmaBrainSurface: Stereotaxic Bregma-Based Surface Coordinates with Depth
• Stereotaxic_LambdaAbsolute: Stereotaxic Lambda-Based Absolute Coordinates
• Stereotaxic_LambdaBrainSurface: Stereotaxic Lambda-Based Surface Coordinates with Depth
• CCF_XYZ_Absolute: Common Coordinate Framework XYZ Absolute Coordinates

A detailed list of the accepted schemas for the coordinates_details field, related to each coordinates_system, can be found in the Coordinates schemas page.

List view

• Allowed portals: public, private, super
• Request method: GET
• URL: https://www.brainstem.org/api/private/modules/procedure
• Data: None
• Responses: 200 OK; 403 Not allowed; 404 Not found

Use example (using Python API)

resp = client.load_model('procedure')

Response example

{'procedures': [
    {
        'id': 'f79d84c8-6bec-40e3-b18a-5b25e57f4a09',
        'type': 'TetrodeWireElectrode',
        'notes': 'First implant',
        'subject': '0f87c229-6769-4854-83a5-c71e154246b8',
        'date_time': None,
        'consumable': 'a5f29099-2758-4163-a8e4-e5e2898e57b2',
        'hardwaredevice': None,
        'details': {
            'tetrodeCount': 1,
            'nWiresTetrode': 4,
            'wireDiameter': 33.9,
            'wireMaterial': 'tunsgten'
        },
        'brain_region': '15f9aef5-2d46-4ff2-a0db-ac6be759c05c',
        'coordinates_system': 'Stereotaxic_BregmaAbsolute',
        'coordinates_details': {
            'apCoordinate': 1.0
        }
    },
    {
        'id': 'a18dd2b1-6393-468c-9424-1bc77b9e4976',
        'type': 'TetrodeWireElectrode',
        'notes': 'Second implant',
        'subject': '0f87c229-6769-4854-83a5-c71e154246b8',
        'date_time': None,
        'consumable': None,
        'hardwaredevice': None,
        'details': {
            'tetrodeCount': 1,
            'nWiresTetrode': 4,
            'wireDiameter': 33.9,
            'wireMaterial': 'tunsgten'
        },
        'brain_region': '15f9aef5-2d46-4ff2-a0db-ac6be759c05c',
        'coordinates_system': 'Stereotaxic_BregmaAbsolute',
        'coordinates_details': {
            'apCoordinate': 1.0,
            'mlCoordinate': 0.0,
            'dvAngle': 2.0
        }
    }
]}

Add

• Allowed portals: private, super
• Request method: POST
• URL: https://www.brainstem.org/api/private/modules/procedure
• Data: JSON dictionary containing at least the required fields.
• Responses: 201 OK; 400 Bad request; 403 Not allowed; 404 Not found

Use example (using Python API)

resp = client.save_model("procedure",  data={
    "type": "OpticFiberImplant",
    "subject": "0f87c229-6769-4854-83a5-c71e154246b8",
    "notes": "some text",
    "details": {"fiberTipShape": "flat"},
    "coordinates_system": "Stereotaxic_BregmaAbsolute",
    "coordinates_details": {
                "apCoordinate": 1.0,
                "mlCoordinate": 2.0,
                "dvCoordinate": 3.0,
                "apAngle": 4.0,
                "mlAngle": 5.0,
                "dvAngle": 6.0
            }
    }
)

Response example

{'procedure': {
    'id': 'd37c9255-d5ae-47d9-b6e1-4ec760c200fb',
    'type': 'OpticFiberImplant',
    'notes': 'some text',
    'subject': '0f87c229-6769-4854-83a5-c71e154246b8',
    'date_time': None,
    'consumable': None,
    'hardwaredevice': None,
    'details': {'fiberTipShape': 'flat'},
    'brain_region': None,
    'coordinates_system': 'Stereotaxic_BregmaAbsolute',
    'coordinates_details': {
                "apCoordinate": 1.0,
                "mlCoordinate": 2.0,
                "dvCoordinate": 3.0,
                "apAngle": 4.0,
                "mlAngle": 5.0,
                "dvAngle": 6.0
            }
    }
}

Detail

• Allowed portals: public, private, super
• Request method: GET
• URL: https://www.brainstem.org/api/private/modules/procedure/<id>/
• Data: None
• Responses: 200 OK; 403 Not allowed; 404 Not found

Use example (using Python API)

resp = client.load_model('procedure', id='d37c9255-d5ae-47d9-b6e1-4ec760c200fb')

Response example

{'procedure': {
    'id': 'd37c9255-d5ae-47d9-b6e1-4ec760c200fb',
    'type': 'OpticFiberImplant',
    'notes': 'some text',
    'subject': '0f87c229-6769-4854-83a5-c71e154246b8',
    'date_time': None,
    'consumable': None,
    'hardwaredevice': None,
    'details': {'fiberTipShape': 'flat'},
    'brain_region': None,
    'coordinates_system': 'Stereotaxic_BregmaAbsolute',
    'coordinates_details': : {
                "apCoordinate": 1.0,
                "mlCoordinate": 2.0,
                "dvCoordinate": 3.0,
                "apAngle": 4.0,
                "mlAngle": 5.0,
                "dvAngle": 6.0
            }
    }
}

Change

• Allowed portals: private, super
• Request method: PATCH
• URL: https://www.brainstem.org/api/private/modules/procedure/<id>/
• Data: dictionary containing the fields to be updated
• Responses: 200 OK; 400 Bad request; 403 Not allowed; 404 Not found

Use example (using Python API)

resp = client.save_model("procedure", id="d37c9255-d5ae-47d9-b6e1-4ec760c200fb", data={"notes": "new text"})

Response example

{'procedure': {
    'id': 'd37c9255-d5ae-47d9-b6e1-4ec760c200fb',
    'type': 'OpticFiberImplant',
    'notes': 'new text',
    'subject': '0f87c229-6769-4854-83a5-c71e154246b8',
    'date_time': None,
    'consumable': None,
    'hardwaredevice': None,
    'details': {'fiberTipShape': 'flat'},
    'brain_region': None,
    'coordinates_system': 'Stereotaxic_BregmaAbsolute',
    'coordinates_details': : {
                "apCoordinate": 1.0,
                "mlCoordinate": 2.0,
                "dvCoordinate": 3.0,
                "apAngle": 4.0,
                "mlAngle": 5.0,
                "dvAngle": 6.0
            }
    }
}

Delete

• Allowed portals: private, super
• Request method: DELETE
• URL: https://www.brainstem.org/api/private/modules/procedure/<id>/
• Data: None
• Responses: 204 OK; 403 Not allowed; 404 Not found

Use example (using Python API)

resp = client.delete_model("procedure", id="d37c9255-d5ae-47d9-b6e1-4ec760c200fb")