Optic fiber implant

The selected type controls the additional structured fields shown in the form. The descriptions below follow the same groups and order as the Type dropdown.

Anesthesia, Drug and Fluid Administration

Administration of anesthetics, sedatives, analgesics, antibiotics, anti-inflammatories, fluids and other substances to a subject, whether as clinical care or as the experimental treatment.

• Analgesic: The administration of a pain-relieving agent, such as buprenorphine or meloxicam. Use this for systemic analgesia given before, during, or after a potentially painful intervention. Structured fields: administered volume, administration route (required), and indication. The body-weight dose is recorded on the active-agent material row.
• Anesthesia: The administration of anesthetic agents to induce unconsciousness, analgesia, or sedation. This entry captures anesthetic protocol details and can stand alone or support a larger procedure episode. Structured fields: anesthetic depth, end time, total duration, recovery time, monitoring, and supportive care. Induction, maintenance, top-ups, reversal and emergence are recorded as stages, each with its route, delivery method, gas concentration, volume, rate and duration; the agents sit inside their stage.
• Anti-inflammatory: The administration of a corticosteroid, NSAID, or another agent to reduce inflammation. Structured fields: administered volume, administration route (required), indication, and administration role. The agent and its body-weight dose are recorded on the active-agent material row.
• Antibiotic: The administration of an antimicrobial agent, whether given preventively, as treatment, or as the experimental manipulation itself. Structured fields: administered volume, administration route (required), and indication (required). The body-weight dose is recorded on the active-agent material row.
• Drug administration (other): Use this catch-all only for medication that does not fit a dedicated type, such as a hormone, reversal agent, antidote, or supplement. File by why the drug was given, not by what the drug is: meloxicam for pain is an analgesic, not a drug administration. Structured fields: purpose (required), administration role, administered volume, and administration route (required). The body-weight dose is recorded on the active-agent material row.
• Fluid therapy: The administration of a physiological solution, such as saline or Ringer's solution, for hydration or volume support. Record the total procedure-level volume and the clinical problem it addressed; state the delivery profile rather than leaving the rate empty to imply a bolus. Structured fields: total administered volume (required), volume per body mass, administration route (required), delivery profile, infusion rate, number of sites, fluid temperature, and fluid indication. The fluid itself is named on the administered-fluid material row.
• Local anesthetic: A site-directed nerve block, infiltration, or topical application, such as bupivacaine at an incision line. Use Analgesic instead for systemic pain relief. Structured fields: placement technique (required), administered volume, application site, laterality, guidance method, topical dwell time, and block effectiveness.
• Sedative: A sedative or anxiolytic given for non-surgical restraint, imaging, or transport, as distinct from full anesthesia. Record the level the animal actually reached, which may be deeper than the level intended. Structured fields: administration route (required), delivery profile, administered volume, infusion rate, gas concentration, sedation level, task enabled, sedation duration, recovery time, and tables for monitoring and supportive care. The body-weight dose is recorded on the active-agent material row.

Surgical Procedures

Surgical steps on the skull and head, such as burr holes, craniotomies, cranial windows, head fixation, headposts, headcaps and baseplating.

• Baseplating: Documents fixing a baseplate to the skull or headcap to dock a head-mounted miniature microscope, typically over a previously implanted GRIN lens or prism.
• Burr hole: A small hole drilled in the skull to provide access for electrode placement, cannula insertion, injection, or another targeted action while otherwise maintaining skull integrity. Structured fields: hole diameter, drill speed, purpose, and cooling method.
• Cranial window: A section of skull opened and fitted with a transparent window for direct, often long-term optical access to the brain surface. Creates an Experimental interface (Cranial window) when saved. Structured fields: surgical method, window shape, dimensions, and orientation.
• Craniectomy: Removal of a portion of the skull that is left open: the bone is not replaced and the opening is not sealed again. Use Craniotomy when the opening is closed afterwards. Structured fields: surgical method, shape, dimensions, orientation, and whether the action was fatal.
• Craniotomy: Opening of the skull to expose the brain, after which the opening is sealed again, by replacing the bone flap or covering it with a window, cement or another seal. Use Craniectomy when the bone is removed and the opening left open. Structured fields: surgical method, shape, dimensions, orientation, and whether the action was fatal.
• Head fixation: Immobilization of the subject's head for stable recordings, manipulations, or imaging. Use Headpost for the separate action of attaching the device used for fixation. Structured fields: fixation methods, alignment, and fixation details.
• Headcap: Attachment of a protective covering over cranial implants while retaining any required experimental access points. Creates an Experimental interface (Headcap) when saved. Structured fields: material, shape, construction method, attachment method, Faraday shielding, skull preparation, and headcap ID.
• Headpost: Attachment of a device to the skull that enables later head fixation, including during experiments with awake subjects. Creates an Experimental interface (Headpost) when saved. Structured fields: material, shape, construction method, attachment method, skull preparation, and headpost ID.

Implant Procedures

Placement of a device in or on the subject, such as recording electrodes, probes, optical implants, cannulas, catheters and physiological sensors; saving one creates an experimental interface for the implanted device.

• Blood pressure sensor implant: Surgical placement of a sensor intended to monitor blood pressure continuously or repeatedly. Creates an Experimental interface (Blood-pressure sensor) when saved. Structured fields: sensor type (required), implant site, catheter material, anchoring method (required), and sterilization method.
• Breathing sensor implant: Placement of a sensor used to monitor respiratory patterns or rate. Creates an Experimental interface (Respiratory sensor) when saved. Structured fields: sensor type (required), implant site, wire or lead material, anchoring method (required), signal transmission, and sterilization method.
• Cannula implant: Implantation of a guide or infusion cannula for targeted delivery, sampling, microdialysis, or cerebrospinal-fluid access. Creates an Experimental interface (Injection cannula) when saved. Structured fields: target site (required), cannula type, gauge, length, laterality, purpose, fixation method, obturator use, and sterilization method.
• Catheter implant: Insertion of a flexible tube into a vessel or body cavity for delivery, sampling, drainage, or pressure monitoring. Creates an Experimental interface (Catheter) when saved. Structured fields: target site (required), catheter type, material, purpose, fixation method, external port, and catheter ID.
• ECG implant (Electrocardiography): Placement of electrodes used to record the electrical activity of the heart. Creates an Experimental interface (ECG) when saved. Structured fields: wire count, wire material, insulation type, implant site, anchoring method (required), and sterilization method.
• EEG implant (Electroencephalography): Placement of electrodes on or beneath the skull to record large-scale brain electrical activity. Creates an Experimental interface (EEG) when saved. Structured fields: wire count, electrode type, electrode material, and anchoring method (all required), plus referencing scheme, Faraday shielding, and sterilization method.
• ECoG implant (Electrocorticography): Placement of a flexible grid or strip array of contacts on the brain surface, above or beneath the dura, or on thinned skull, to record without penetrating the tissue. The array itself is recorded as the required ECoG array material row, sourced from your ECoG array stock or catalog. Creates an Experimental interface (ECoG) when saved. Structured fields: placement layer (epidural, subdural or epicranial), dura handling, skull preparation, how the array itself was held to the surface, ground and reference placement and whether they were tied, anchoring method, and fatal outcome. The array, its reference and ground electrodes, connector, adhesive and anchors are recorded as materials; the array's center and rotation go in the coordinates block.
• EMG implant (Electromyography): Placement of electrodes in or on muscles to record muscle electrical activity. Creates an Experimental interface (EMG) when saved. Structured fields: wire count and implant method (required), wire material, insulation type, target muscles, anchoring method, and sterilization method.
• GRIN (Gradient Index) lens implant: Implantation of a gradient-index lens to provide optical access to deep tissue for imaging. Creates an Experimental interface (GRIN lens) when saved. Structured fields: lens tip type, lens ID, sterilization method, and mounting method.
• Nerve cuff implant: Placement of a cuff electrode around a peripheral nerve for recording or stimulation. Creates an Experimental interface (Nerve cuff) when saved. Structured fields: cuff type and anchoring method (required), target nerve, cuff and electrode materials, wire exit route, signal transmission, and sterilization method.
• Optic fiber implant: Placement of an optical fiber for delivering or collecting light, such as in optogenetic stimulation or fiber photometry. Creates an Experimental interface (Optic fiber) when saved. Structured fields: fiber tip shape, fiber ID, and sterilization method.
• Prism implant: Placement of a prism that redirects the optical path to make a difficult-to-access tissue plane visible. Creates an Experimental interface (Prism) when saved. Structured fields: prism ID, sterilization method, and mounting method.
• Reference electrode implant: Placement of an electrode that supplies a reference signal for other recording electrodes. Creates an Experimental interface (Reference electrode) when saved. Structured fields: electrode count and material (required), impedance, diameter, placement site, anchoring method, and sterilization method.
• Silicon probe implant: Insertion of a silicon probe with one or more recording sites, chronic or acute. The probe itself is recorded as the required Silicon probe material row, sourced from your probe stock or catalog. Creates an Experimental interface (Silicon probe) when saved. Structured fields: probe ID and sterilization method.
• Single wire electrode implant: Implantation of a single wire electrode for neural recording or stimulation. Creates an Experimental interface (Single wire electrode) when saved. Structured fields: wire count (required), diameter, material, impedance, and sterilization method.
• Temperature sensor implant: Placement of a sensor used to monitor body or tissue temperature. Creates an Experimental interface (Thermal probe) when saved. Structured fields: sensor type and anchoring method (required), wire or lead material, signal transmission, power source, and sterilization method.
• Tetrode wire electrode implant: Implantation of a four-wire electrode bundle used to distinguish activity from nearby neurons. Creates an Experimental interface (Tetrode) when saved. Structured fields: tetrode count (required), wires per tetrode, dura handling, insertion rate, ground and reference placement (a reference tetrode counts as "in the bundle"), ground and reference tied, fixation method, and fatal outcome. The wire's material and diameter come from the Tetrode assembly material row's catalog entry. The coordinate depth is where the bundle sat when the surgery ended; the Tetrode adjustment log counts from there.
• Generic implant: Use this only when an implantation action does not fit any specific implant type above. Describe the implanted item and purpose clearly in the structured details and notes. Creates an Experimental interface (Generic interface) when saved. Structured fields: implant type (required), name or description, anchoring method, signal transmission, power source, and sterilization method.

Injection and Infusion Procedures

Targeted delivery of solutions or viral vectors into the brain or body, with target coordinates where relevant.

• Injection: Delivery of a solution to a defined anatomical site. Use this for pharmacological agents, tracers, cells, or other injected materials that are not viral vectors. Structured fields: injection volume, rate, solution concentration, method, injection profile, and laterality.
• Virus injection: Injection of a viral vector to introduce or manipulate genetic material in a target population. Describe each vector and its material-specific volume in Material usage when a total injection contains more than one material. Structured fields: total injection volume, injection rate, virus-solution titer, and injection profile.

Sample Collection Procedures

Collection of blood or tissue samples from a living or dead subject for downstream analysis.

• Blood collection: Collection of blood from a defined anatomical site for hematology, serum or plasma preparation, biochemistry, pharmacokinetics, genotyping, or another analysis. Structured fields: collection site (required), collection method, sample volume, purpose, terminal status, and storage conditions.
• Tissue collection: Collection of non-brain tissue, such as a tail tip, ear punch, biopsy, or excised tissue. Use the structured details to record the site, method, amount, preservation, purpose, and terminal status where applicable. Structured fields: collection site (required), collection method, sample length or mass, purpose, preservation method, and terminal status.

Brain and Tissue Procedures

Procedures that lesion, fix or remove brain tissue, including brain lesions, perfusion fixation and brain extraction.

• Brain extraction: Removal of the brain following an endpoint procedure for subsequent histological, molecular, physiological, or other analysis. Structured fields: extraction method and preservation method (required), time to extraction, brain weight, fixation duration, and storage conditions.
• Brain lesion: Deliberate injury or destruction of a defined brain region to investigate its functional contribution. Structured fields: lesion method, lesion volume, and whether the action was fatal.
• Brain perfusion fixation: Perfusion of fixative through the circulatory system to preserve the brain and other tissues. This remains a Procedure because it is performed on the subject. Structured fields: vascular access route, perfusion scope, drive and pressure, whether the heart was still beating at the start, the signs of completion, any failure modes, and how death was confirmed. Individual perfusion phases, each with its own volume, rate, duration and temperature, are recorded as an ordered table in the Procedure's own details.

Endpoint Procedures (Euthanasia)

Methods used to euthanize a subject, such as barbiturate or inhalant overdose, CO₂ exposure, cervical dislocation and decapitation.

• Cervical dislocation: A physical method involving separation of the cervical vertebrae. Structured fields: dislocation method and confirmation of death (both required).
• Decapitation: A rapid physical endpoint method, including contexts where tissue must be collected immediately. Structured fields: decapitation method (required).
• CO₂ chamber euthanasia: Euthanasia using controlled exposure to carbon dioxide in a chamber. Structured fields: CO₂ concentration, exposure duration, and confirmation of death (required), plus flow rate, time to unconsciousness, chamber prefilling and volume, and gradual introduction.
• Barbiturate injection: Euthanasia by administration of a barbiturate solution using an appropriate route. Structured fields: administration route and confirmation of death (required), plus concentration, dosage, administered volume, and time to unconsciousness.
• Inhalant overdose: Euthanasia using an overdose of an inhalant anesthetic. Structured fields: concentration, oxygen flow rate, delivery method, exposure duration, time to unconsciousness, and confirmation of death.

The initial add form asks for the Type, Subject, and required type-specific details. Materials can also be entered before the Procedure is first saved. Select Create and continue to open the full form and complete its optional context, coordinate information, and related entries.

Type of procedure Required Choice

Select the action recorded by this row. The selection controls the Procedure details and which coordinate, region, equipment, and material options are relevant. The type cannot be changed after Material usage entries have been added because the type determines the valid material policy.

Subject Required Single selection

Select the subject on which the action was performed. The choices are limited to subjects in projects where you can make changes, and the selected subject determines the Procedure's project permission context.

Procedure details Varies by type Structured details

Structured fields defined by the selected Procedure type. Required fields, choices, units, and conditional fields vary by type. Use these fields for information that should be searchable and comparable; use Notes only for relevant information that has no structured field.

Coordinate system Required when shown Choice

Select how the Procedure location is referenced. Available systems may be restricted by the Procedure type. The selected system controls the fields shown under Coordinates.

Coordinates When applicable Structured details

Enter the position and orientation of the action using the selected coordinate system. Coordinates may be hidden when they do not apply to the selected Procedure type.

Status Choice

Performed is the default and means this record describes what was done. Planned means the procedure is prepared ahead of time and nothing has happened yet: the page carries a banner, the title says "Planned", and the row is left out of counts, exports and API listings unless asked for. Mark it as performed from the banner once it has happened; the subject must be enrolled first. Cancelled keeps a dropped plan for the record.

Date and time of the procedure Date and time

Record the onset date and time of this individual action. The Procedure episode, when used, provides the broader intervention timing.

Procedure episode Single selection

Associate the action with its broader intervention and compliance episode. The episode and Procedure must refer to the same Subject.

Equipment When applicable Multiple selections

Setup is an optional form-only filter for this field; it is not stored on the Procedure. Select reusable Equipment used to perform the action. Only setups you can change and the Equipment they contain are offered. Equipment describes the working apparatus; materials used or installed belong in Material usage.

Target regions When applicable Multiple selections

Atlas is an optional form-only filter for this field; it is not stored as another Procedure relationship and starts from your preferred atlas. Select the anatomical regions targeted by the action from the active Atlas. This field may be hidden when an anatomical target does not apply to the selected Procedure type.

Licenses Multiple selections

Select the authorizations that cover this particular Procedure. You can add licenses for which you have change access; existing selections remain visible when editing older entries.

Protocol Single selection

Select the written method, SOP, or other documented protocol followed for this action. This is a reference only: it does not populate Procedure fields; use a Procedure template when form values should be reused. Only Protocols classified for Procedures are shown. A Protocol restricted to particular Procedure types is available only when it includes the selected type, while a Protocol without type restrictions can be used for any Procedure type. You can select Protocols you have change access to; a Protocol already recorded on an older entry stays available when you edit it, even if your access has since changed.

Performed by Single selection

Identify the person who physically performed the Procedure, which can differ from the user who entered the information. Eligible users come from the subject's project context; the current user is suggested when no performer has been recorded.

Notes Text · 500 characters

Record complications, adverse events, deviations, or other relevant detail that is not captured by the structured fields.

Material usage Ordered list

Add ordered entries for the materials actually used, such as a stock lot, catalog consumable, or manual material. Each row stores that material's contribution to the action; an overall measure can remain in Procedure details. See the Material usage tab for all source, type, ordering, association, and permission fields.

Stages When the type declares them Ordered list

Some types divide the action into ordered stages: an anesthetic has an induction and a maintenance stage, a perfusion fixation a flush and a fixation stage. Each material row then names the stage it took part in, so the stage's shared conditions are recorded once and the agents point at it. Stages and their materials are edited together on the Materials tab.

Choose the system that matches how the position was measured. An absolute system stores three position axes in one fixed frame. A surface coordinates with depth system stores two surface-plane coordinates and a depth measured from a local surface. Angle fields describe the approach and rotation around the insertion axis.

External coordinates

• External XYZ Coordinates with Euler Orientation: Uses X, Y, and Z positions plus ordered fixed-frame X, Y, and Z rotations. Name the external frame and define its origin, positive axes, handedness, and unrotated pose.
• External XYZ Coordinates with Quaternion Orientation: Uses the same physical XYZ frame plus a canonical Hamilton W/X/Y/Z quaternion for device orientation. Choose it for software- or sensor-derived poses where Euler angles are unsuitable.

Stereotaxic coordinates

• Stereotaxic Bregma-Based Absolute Coordinates: Uses AP, ML, and DV coordinates and their angles in a fixed Bregma-referenced frame. Choose it when DV is an absolute coordinate rather than a surface-zeroed depth.
• Stereotaxic Bregma-Based Surface Coordinates with Depth: Uses Bregma-referenced AP and ML coordinates, depth from the brain surface, AP and ML angles, and insertion-axis rotation. Choose it when depth was zeroed at the brain surface.
• Stereotaxic Lambda-Based Absolute Coordinates: Uses AP, ML, and DV coordinates and their angles in a fixed Lambda-referenced frame. Choose it when Lambda is the origin and DV is an absolute coordinate.
• Stereotaxic Lambda-Based Surface Coordinates with Depth: Uses Lambda-referenced AP and ML coordinates, depth from the brain surface, AP and ML angles, and insertion-axis rotation. Choose it when Lambda is the origin and depth is surface-zeroed.

Landmark-referenced coordinates

• Landmark-Referenced AP/ML/DV Absolute Coordinates: Uses AP, ML, and DV coordinates and their angles relative to a selected landmark. Choose it when the origin is not fully covered by the Bregma or Lambda systems, and describe custom landmarks.
• Landmark-Referenced AP/ML Surface Coordinates with Depth: Uses landmark-referenced AP and ML coordinates, depth from a selected surface, AP and ML angles, and insertion-axis rotation. Choose it when the landmark and depth surface are separate references.

Spinal coordinates

• Spinal RC/ML/DV Absolute Coordinates: Uses rostrocaudal (RC), mediolateral (ML), and dorsoventral (DV) coordinates and their angles in a spinal frame. Choose a spinal segment, vertebral level, or custom origin and identify the level.
• Spinal RC/ML Surface Coordinates with Depth: Uses spinal RC and ML coordinates, depth from a selected surface, RC and ML angles, and insertion-axis rotation. Choose it when depth was zeroed at the dura, pia, cord, or a custom surface.

Standardized reference spaces

• Allen Mouse CCFv3 XYZ Absolute Coordinates: Uses physical distance from the CCFv3 anterior-superior-left boundary: X increases posteriorly, Y inferiorly or ventrally, and Z rightward. Values are physical coordinates, not voxel indices.
• Waxholm Space Rat Brain Atlas v4 XYZ Absolute Coordinates: Uses physical distance from the Waxholm Space origin in its RAS frame: X increases rightward, Y anteriorly, and Z superiorly. AP and ML angles describe the ordered approach tilts, followed by rotation around the insertion axis. Values are physical coordinates, not voxel indices.
• MNI152 ICBM 2009c Human XYZ Absolute Coordinates: Uses physical distance from the MNI anterior-commissure origin in its RAS frame: X increases rightward, Y anteriorly, and Z superiorly. AP and ML angles describe the ordered approach tilts, followed by rotation around the insertion axis.
• NIMH Macaque Template v2 XYZ Absolute Coordinates: Uses physical distance from ear bar zero in the NMT v2 stereotaxic frame: X increases rightward, Y anteriorly, and Z superiorly. AP and ML angles describe the ordered approach tilts, followed by rotation around the insertion axis.
• Brain/MINDS Marmoset Atlas 2.0 XYZ Absolute Coordinates: Uses physical millimetres from the BMA 2.0 atlas origin, which lies between the commissures and is not ear bar zero: X increases rightward, Y anteriorly, and Z superiorly. AP and ML angles describe the ordered approach tilts, followed by rotation around the insertion axis.
• mapzebrain Larval Zebrafish XYZ Absolute Coordinates: Uses physical micrometre distance from the mapzebrain standard-brain volume corner: X increases rightward, Y posteriorly, and Z superiorly. Y and X angles describe the ordered approach tilts, followed by rotation around the insertion axis. Values are physical coordinates, not voxel indices.
• JRC2018 Unisex Fly Brain XYZ Absolute Coordinates: Uses physical micrometre distance from the JRC2018 unisex template volume corner: X increases toward the fly's left, Y ventrally, and Z posteriorly. Z and X angles describe the ordered approach tilts, followed by rotation around the insertion axis. Values are physical coordinates, not voxel indices.

For anatomical reference points and stereotaxic axis and angle conventions, see the detailed coordinate-system documentation .