An Experimental interface is one physical access, sensing, delivery, or
stimulation point on a Subject or a Specimen set. It describes the thing
that remains in place — the probe, fiber, window, cannula, or sensor — not
the action that installed it, so the same interface can be referenced by
many Procedures, Data acquisitions, and Manipulations.
Interfaces created by a Procedure
Many interfaces are not created here at all. Procedure types that establish an
interface create one automatically when the Procedure is saved as performed, and
that Procedure remains the source of its type, subject, installation date,
coordinates, target regions, equipment, and copied materials. Those fields are
locked on this form and a panel at the top names the Procedure and says whether
the interface still matches it; change them on the Procedure. Name, persistence,
removal time, details, and notes belong to the interface. Notes start as a copy of
the Procedure's notes and are not overwritten afterwards. Create an interface
directly on this form when there was no such Procedure — for example an acute
probe lowered for one session, an ex-vivo interface on a specimen set, or a
configured stimulator that was never surgically implanted.
A material added directly to an interface is kept, even when the creating
Procedure is edited later. If the creating Procedure is deleted, the interface
keeps its values and becomes editable like any other.
Interface types
The selected type controls the structured fields shown under the
interface details. Most types include an identifier field so a
particular physical item can be traced across entries. No detail field
is required. The descriptions below follow the same groups and order as
the Type dropdown.
Electrophysiology
Electrodes, arrays and pipettes that record electrical activity from neurons, nerves, muscle or heart, together with the ground and reference electrodes these recordings need.
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Silicon probe:
A silicon-based probe carrying many recording sites, often on several shanks.
Structured fields: probe ID, channel count, shank count, and reference configuration.
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Tetrode:
A four-wire bundle used to separate nearby single units.
Structured fields: tetrode ID, tetrode count, and wire material.
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Single wire electrode:
One insulated wire electrode used for recording or stimulation.
Structured fields: electrode ID, wire material, and impedance.
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Tungsten microelectrode:
A sharpened metal microelectrode, typically for acute single-unit recording.
Structured fields: electrode ID, impedance, tip diameter, shaft diameter, and reference configuration.
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Multi-electrode array (MEA):
A planar or grid array of electrodes, common for ex-vivo and surface recording.
Structured fields: array ID, electrode count, electrode pitch and diameter, substrate type, and reference configuration.
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Patch pipette:
A glass pipette sealed to a cell for intracellular recording.
Structured fields: pipette ID, patch configuration, pipette and seal resistance, and internal solution.
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EEG:
Electrodes recording large-scale activity on or beneath the skull.
Structured fields: electrode layout and channel count.
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ECoG:
A grid or strip array of contacts installed on the dura, on the brain surface, or on thinned skull. Created by an ECoG implant procedure; the array's design (contact count, pitch, substrate) lives on the ECoG array material row and its catalog entry.
Structured fields: device identifier, placement layer (epidural, subdural or epicranial), and the reference configuration as wired at install.
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EMG:
Electrodes in or on muscle.
Structured fields: muscle and electrode layout.
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ECG:
Electrodes recording cardiac electrical activity.
Structured fields: lead configuration and electrode layout.
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Nerve cuff:
A cuff placed around a peripheral nerve to record or stimulate.
Structured fields: nerve, contact count, and cuff size.
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Reference electrode:
Supplies the reference potential the recording channels are measured against.
Structured fields: electrode ID and reference site.
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Ground electrode:
Ties the preparation to circuit ground. Keep it separate from the reference electrode even when one screw serves both, and say so in Notes.
Structured fields: electrode ID and ground site.
Physiological monitoring
Sensors that monitor the subject's physiological state, such as respiration and blood pressure.
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Blood-pressure sensor:
Represents a sensor that monitors the subject's blood pressure, such as an implanted telemetry catheter or an arterial pressure transducer.
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Respiratory sensor:
Represents a sensor that monitors the subject's breathing, such as a nasal thermistor, thermocouple, pressure sensor or plethysmograph.
Optical
Optical access and light-path hardware, such as cranial windows, GRIN lenses, prisms, optic fibers, objectives, miniscopes and widefield macroscopes.
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Optic fiber:
A fiber delivering or collecting light, typically for optogenetics.
Structured fields: fiber ID, core diameter, and numerical aperture.
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GRIN lens:
A gradient-index lens giving optical access to deep tissue.
Structured fields: lens ID, diameter, and length.
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Prism:
Redirects the optical path to reach a plane a straight lens cannot.
Structured fields: prism ID, angle, and dimensions.
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Microscope objective:
The objective through which the preparation is imaged, when it is worth recording as a target-facing interface.
Structured fields: objective ID, magnification, numerical aperture, and working distance.
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Miniscope:
A head-mounted miniature microscope, usually imaging above a GRIN lens.
Structured fields: miniscope ID, field of view, and frame rate.
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Widefield macroscope:
A large field-of-view imaging path for cortex-wide imaging.
Structured fields: macroscope ID, objective magnification, field of view, excitation and emission wavelength, frame rate, and fluorescent indicator.
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Cranial window:
A transparent window giving optical access to the brain surface.
Structured fields: window ID, window material, and diameter.
Assemblies
Structural hardware fixed to the skull that holds, protects or connects other interfaces, such as headposts and headcaps.
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Headcap:
The assembled cap protecting cranial implants and carrying their connectors. It is the assembly rather than any single device, so its components are recorded as its materials.
Structured fields: headcap ID, final shape or design, shielding configuration, and connector and port configuration.
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Headpost:
Represents a headpost or head plate fixed to the skull for head fixation.
Behavioral and Environmental
Sensors that observe the subject or its surroundings without contacting tissue, such as cameras, microphones and tracking systems.
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Camera:
A camera trained on the subject or preparation as a fixed observation point.
Structured fields: camera ID, view, and frame rate.
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Microphone:
A microphone positioned to capture sound from the preparation.
Structured fields: microphone ID, placement, and sample rate.
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Tracking system:
A configured tracking arrangement observing the subject.
Structured fields: tracking system ID, tracking method, and tracked markers.
Delivery
Lines, cannulas, catheters, pumps and perfusion systems through which drugs or solutions reach the subject or tissue.
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Injection cannula:
A cannula for delivering a substance to a defined site.
Structured fields: cannula ID, gauge, and delivery target.
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Microperfusion line:
A fine line exchanging solution locally at the target.
Structured fields: line ID, flow rate, and solution.
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Bath perfusion:
The bath that superfuses a preparation, normally on a specimen set.
Structured fields: bath ID, flow rate, solution, and temperature.
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Drug delivery line:
A line delivering an agent from an external source.
Structured fields: line ID, route, and dead volume.
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Catheter:
A tube in a vessel or cavity for delivery, sampling, or monitoring.
Structured fields: catheter ID, route, and gauge.
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Osmotic pump:
An implanted pump delivering an agent continuously without external control.
Structured fields: pump ID, nominal flow rate, reservoir volume, delivery duration, and delivery agent.
Stimulation
Devices that deliver electrical, optical, magnetic, thermal or ultrasound stimulation, or present auditory, odor, tactile and visual stimuli.
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Stimulating electrode:
An electrode used to deliver current rather than to record.
Structured fields: electrode ID, contact count, and stimulation mode.
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LED array:
An array of LEDs for patterned optical stimulation.
Structured fields: array ID, wavelength, LED count and pitch, maximum power per LED, and target opsin.
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Ultrasound transducer:
A transducer delivering focused ultrasound to the target.
Structured fields: transducer ID, center frequency, and focus.
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Thermal probe:
A probe heating or cooling the target.
Structured fields: probe ID, temperature range, and contact site.
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TMS coil:
A coil inducing currents in tissue without contact.
Structured fields: coil ID, coil type, and placement.
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Auditory stimulator:
The configured arrangement presenting sound to the subject.
Structured fields: stimulus types, delivery method, stimulation context, and paradigm description.
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Visual stimulator:
The configured arrangement presenting visual stimuli.
Structured fields: stimulus types, presentation device, stimulus position, stimulation context, and paradigm description.
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Tactile stimulator:
The configured arrangement applying mechanical stimuli.
Structured fields: stimulation types, stimulation site, delivery method, stimulation context, and paradigm description.
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Olfactometer:
The configured arrangement presenting odors.
Structured fields: delivery method, stimulation context, and paradigm description.
Generic
A fallback for interface hardware that no specific interface type covers.
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Generic interface:
Use this only when no specific type above applies. Describe what the interface is and how it contacts the target in the configuration notes, because the type name will tell another user nothing.
Structured fields: interface ID and configuration notes.
Interface fields
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Target type
Required · create only
Choice
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Choose whether the interface targets an in-vivo
Subject or an ex-vivo
Specimen set. It is selectable only while
creating the interface: on the change form the target type is
shown but can no longer be switched. It also decides which
coordinate systems are offered.
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Subject
Required for a subject target
Single selection
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The subject carrying this interface. Exactly one of Subject or
Specimen set must be set; the form clears the other one for
you. You can still move the interface to a different subject
later, but not convert it to a specimen-set interface.
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Specimen set
Required for a specimen target
Single selection
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The specimen set this interface applies to, used for ex-vivo
work such as slice recording or bath perfusion.
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Target specimens
Specimen targets only
Multiple selections
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Narrows the interface to particular specimens within the set.
Leave it empty when the interface applies to the whole set.
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Name
Required
Text
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How this interface is identified in selectors elsewhere. An
interface created by a Procedure is named from its subject and
procedure type; rename it if your lab identifies it
differently.
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Type
Required
Choice
-
What kind of interface this is. It controls the structured
detail fields, and it cannot be changed once materials are
associated with the interface, because the type determines
which materials are valid.
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Persistence
Required
Choice
-
How long the interface remains in place: chronic
for something implanted and left in, session
for something present for one session, and
transient for something briefly positioned.
This describes duration only — it says nothing about whether
the target is a subject or a specimen.
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Coordinate system
Required
Choice
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How the interface's position is expressed. The available
systems depend on the target type and are validated on save. A
subject interface offers the external, stereotaxic,
landmark-referenced, spinal, and standardized-space systems. A
specimen-set interface offers external coordinates plus
specimen systems (surface XY, surface XY with depth, volume
XYZ) and container systems (grid row/column, container-local
XY).
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Coordinates
When applicable
Structured details
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The position and orientation of the interface in the selected
system. When a Procedure created the interface, these values
come from that Procedure, are refreshed when it changes, and are
locked here.
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Target regions
Multiple selections
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Atlas is an optional form-only filter for this
field; it is not stored on the interface and starts from your
preferred atlas. Select the anatomical regions the interface
reaches.
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Equipment
Multiple selections
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Setup is an optional form-only filter for this
field; it is not stored on the interface. Select the reusable
instruments used with this interface. All selected Equipment
must belong to the same Setup.
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Installed at / Removed at
Date and time
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The interface's own lifecycle, independent of any single
Procedure or Session. Setting a removal time is how you record
that an interface is no longer available without deleting its
history.
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Materials
Ordered list
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What the interface is made of — the device itself plus its
components. Materials copied from a creating Procedure are
marked From procedure, are refreshed when that Procedure
changes, and cannot be edited or removed here; materials you add
here are kept. Supplies merely consumed during installation belong
on the Procedure, not here.
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Notes
Text · 500 characters
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Context the structured fields do not capture, such as
placement compromises or later damage.
A subject interface is offered the same systems as a Procedure. A
specimen-set interface is offered the external, specimen, and container
systems instead. The reference below covers the specimen-set side; see the
Procedure help for the anatomical systems.
Coordinate systems
These systems describe positions relative to an external frame,
specimen, or container. Choose the system that matches how the
position was measured. For specimen and container systems, document
the origin and orientation whenever another user could not infer them.
Subject-targeted anatomical systems are described in the Procedure
coordinate reference.
External coordinates
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External XYZ Coordinates with Euler Orientation:
Uses X, Y, and Z positions plus ordered fixed-frame X, Y, and Z
rotations. Name the frame and define its origin, positive axes,
handedness, and unrotated pose.
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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.
Specimen coordinates
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Specimen Surface XY Coordinates:
Uses surface-plane X and Y, rotation, an XY origin, and specimen
orientation. Choose it for a position on a slice or section when
depth is not needed.
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Specimen Surface XY Coordinates with Depth:
Adds non-negative insertion depth along the final depth axis from
the selected surface at the XY entry point.
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Specimen Volume XYZ Coordinates:
Uses X, Y, and Z positions, an angle around each axis, an origin,
and specimen orientation. Choose it for a position within a
three-dimensional specimen rather than on a surface.
Container coordinates
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Container Grid Well Coordinates:
Uses one canonical well identifier such as A1 and optional X/Y
offsets from its center. Positive offsets point right and back.
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Container-Local XYZ Coordinates:
Uses physical local X, Y, and Z, an origin, and container
orientation. Choose it for a dish, chamber, or other container
without named grid positions.
For anatomical reference points and stereotaxic axis and angle
conventions, see the
detailed coordinate-system documentation
.
Permissions
An Experimental interface inherits its access through the projects of its
Subject or Specimen set. You need change access through at least one of those
projects to add or edit it. Its materials inherit permissions through the
interface, while catalog and inventory entries keep their own rules.
API access
Experimental interfaces can be read and written through
/api/private/modules/experimentalinterface/. The corresponding
public route is read-only. Type-specific values use details,
while position data keeps the field names coordinates and
coordinates_json — unlike Procedure and Equipment, this route
does not rename them. The type stays writable until a material is associated
with the interface.
Materials are returned with the record as materials
(material_usages keeps the bare ids). A create request may
include a material_collection object holding items,
applied after the interface itself is created and rolled back with it if
rejected; an interface has no stages. To read or replace the collection of
an existing interface, use GET or PUT on
/api/private/modules/experimentalinterface/{id}/materials/; a
template's planned materials are copied on with
POST /api/private/modules/experimentalinterface/{id}/apply-material-template/.
Experimental interface documentation
Material usage
A material usage describes one material used by a procedure,
specimen procedure, or experimental interface. It is the relationship
between the experimental entry and its material source, together with the
use-specific details.
How materials fit together
- Consumable: A shared catalog product or material definition.
- Consumable stock: A particular inventory stock or batch of a catalog consumable.
- Material usage: A material actually used by an experimental entry.
- Material usage template: A reusable planned material attached to a parent template.
Choosing a source
Select exactly one source:
- Inventory stock: Use when the specific lot or batch is known. Provenance is recorded with the usage.
- Catalog consumable: Use when the product is known but no stock lot is available.
- Manual material: Use when the material is not represented in the catalog.
Type and use details
The material type determines the structured detail fields.
The parent type controls which material types are available. Details belong
to this individual material use; the parent retains the overall or primary
measure for the event.
For example, a procedure may record a total volume of 150 µL,
while two virus usages record their respective 100 µL and
50 µL contributions.
Associations and order
A material may optionally be linked to one stage. This keeps shared
stage-level conditions from being repeated on every material. For specimen
work, target specimens can narrow the usage to part of the set. Use
Order to control presentation and Notes
for information that does not fit the structured fields.
Material fields
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Source
Required · one of three
Single selection
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Where this material came from. Choose exactly one: an
inventory stock lot when you know the batch, a catalog
consumable when you know the product but not the lot, or a
manual name when it is in neither. A stock-backed row also
stores a provenance snapshot, so the record stays readable
even if the inventory entry changes later.
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Type
Required
Choice
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What role this material plays, which controls the structured
detail fields below. The available types come from the parent's
type policy, so a Procedure type that does not declare a
material role will not offer it. Choices are grouped by family
to keep a long list scannable.
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Details
Varies by type
Structured details
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This material's own contribution — its volume, dose, count, or
dimensions. The parent keeps the overall measure: a Procedure
may record 150 µL in total while two virus rows
record their 100 µL and 50 µL shares.
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Order
Required
Number
-
Where this row appears among the parent's other materials. Use
it when the sequence is meaningful, such as the order reagents
were applied.
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Stage
When the procedure type declares stages
Single selection
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The stage of the procedure this material took part in, such
as a fixation bath, a primary incubation, or an anesthetic
induction. The editor lists the materials inside their
stages; a stage created in the same edit can be linked right
away, and the collection is saved together.
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Target specimens
Specimen procedures
Multiple selections
-
Narrows this material to part of the specimen set, when it was
applied only to some items. Leave it empty when the material
applies to everything the parent targets.
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Notes
Text · 500 characters
-
Anything about this particular use that the structured fields
do not carry, such as a substitution or a quality problem.
Data integrity and permissions
Material usage entries inherit permissions from their parent procedure,
specimen procedure, experimental interface, or corresponding template.
The parent relationship cannot be changed after creation. Once a parent
has materials, its type is also fixed because that type defines the valid
material policy.
API access
Material usages are available at
/api/private/modules/materialusage/.
Parent and source selections are validated against the current user's
permissions on writes.
