A Subject is one animal, and the anchor for everything done to it: the
Procedures performed on it, the Subject logs tracking it over time, the
Sessions it took part in, and the Experimental interfaces implanted in it.
Subject modules
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Procedures: the technical, experimental, and clinical actions performed on the subject —
implantations, craniotomies, injections, endpoint procedures. See the Procedures tab.
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Subject logs: repeated observations over time — weight and welfare monitoring, consumption,
deprivation, training, housing. See the Subject logs tab.
The distinction is one-off versus recurring. Something done once, at a
particular moment, is a Procedure. Something measured repeatedly is a Subject
log with dated entries.
Subject fields
The add form asks for the name, projects, sex, species and strain, and
status. Select Create and continue to open the full
form, which autosaves as you work.
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Name
Required
Text · 100 characters
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The animal's identifier in BrainSTEM. It must be unique across
the system, so a purely local convention such as "M1" will
often collide — prefix it with something that belongs to your
lab or project.
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Projects
Required
Multiple selections
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The projects this animal belongs to. Only projects where you
are at least a Contributor are offered. These supply the
permission context for the subject and for every Procedure,
log, and interface attached to it. If the list is empty, create
a project first.
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Sex
Required
Choice
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Female, Male, or Unknown.
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Species
Required
Single selection
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The subject's species. It is stored directly so animals without a defined strain are represented
accurately. If the species is missing, submit it on the Species page for approval.
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Strain
Optional
Single selection
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A defined strain belonging to the selected species. Leave this blank when no strain applies;
do not create a species-name or "unspecified" placeholder strain.
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Status
Required
Choice
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Where the animal stands: planned, active, inactive,
transferred, deceased, or unknown. Keep it current — this is
what colleagues check before assuming an animal is available.
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Description
Rich text
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Anything about this animal that the structured fields do not
carry.
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Birth date / Death date
Date
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Used to compute age at any procedure or session, which is why
a birth date is worth recording even when approximate. Setting
a death date does not change the status; update both.
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Breeding
Single selection
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The breeding this animal came from, when it was bred in-house.
This is what links an animal to its parents.
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Genetic line / Genotype
Text · 100 characters
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The line the animal belongs to, including wild type, and its
genotype as determined. Where genotyping was performed and
recorded, a Genotyping subject log holds the result and the
assay; this field holds the conclusion.
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Subject identifier / Supplier
Text · single selection
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The external identifier the animal arrived with — an ear tag,
a vendor ID, a facility number — and who supplied it. Record
these for bought-in animals so a record here can be matched to
the facility's own.
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Licenses
Multiple selections
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The authorizations covering work on this animal. Individual
Procedures and Procedure episodes carry their own licences too;
this records the ones that apply to the animal as a whole.
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Tags
Multiple selections
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Free labels for filtering, shared across all users.
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Name used in storage / Extra content
Text · structured details
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The animal's directory name in your file storage when it
differs from the name above, and any additional key/value
details the standard fields do not cover.
Permissions
A Subject inherits its access from the Projects it belongs to. You need change
access through at least one of them to add or edit it, and the same access
governs its Procedures, logs, and interfaces. Removing a project from a
subject removes that route in for everyone who had access only through it.
API access
Subjects can be read and written through
/api/private/stem/subject/. The corresponding public route is
read-only and exposes subjects in public projects.
Subject documentation
Procedures
A Procedure describes one technical, experimental, or clinical action
performed on one Subject. Use separate Procedure entries when actions have
different types or type-specific details, even when they occur during the
same intervention.
Grouping procedures and creating interfaces
Related Procedures can optionally be grouped in a
Procedure episode. The episode provides the broader,
auditable intervention and compliance context, including responsible
personnel, applicable protocols and licenses, timing, classified severity,
recovery outcome, and follow-up. Each Procedure continues to describe one
action within that intervention.
Procedure types that establish an interface automatically create the
corresponding Experimental interface when the Procedure
is saved as performed; a planned Procedure creates it when it is marked
performed. The Procedure documents the action performed at a particular
time; the Experimental interface describes the resulting probe, cannula,
window, sensor, or other interface that remains available for later
experimental use. The creating Procedure remains the source for the
interface type, installation date, coordinates, target regions, and
equipment: later changes to those values on the Procedure update the
Experimental interface, and they cannot be edited on the interface itself.
Notes are copied once, when the interface is created, and belong to the
interface afterwards. The subject of a Procedure that created an interface
is fixed.
The Experimental interfaces panel at the top of this page
lists every interface linked to the Procedure and says whether it still
matches. After a save, a message names the interface that was created or
the values that were updated. If an interface differs from the Procedure,
for example because it was recorded before this sync existed, use
Update interface in the panel. Deleting the Procedure
leaves its interface in place with the values it had; from then on it is
edited directly.
The interface also receives a copy of the installed materials: the device
the Procedure installed, plus any material whose type the interface itself
accepts. Materials that were merely consumed during the action, such as
adhesives or irrigation, stay on the Procedure. Copied materials are
replaced whenever the Procedure's materials change, so on the interface
they are marked From procedure and cannot be edited or removed
there. A material added directly to the Experimental interface is kept.
Procedure types
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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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Cervical dislocation:
A physical method involving separation of the cervical vertebrae.
Structured fields: dislocation method and confirmation of death (both required).
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Decapitation:
A rapid physical endpoint method, including contexts where tissue must be collected immediately.
Structured fields: decapitation method (required).
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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.
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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.
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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.
Procedure fields
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.
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Type of procedure
Required
Choice
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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.
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Subject
Required
Single selection
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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.
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Procedure details
Varies by type
Structured details
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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.
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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.
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Coordinates
When applicable
Structured details
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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.
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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.
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Date and time of the procedure
Date and time
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Record the onset date and time of this individual action. The
Procedure episode, when used, provides the broader intervention
timing.
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Procedure episode
Single selection
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Associate the action with its broader intervention and compliance
episode. The episode and Procedure must refer to the same Subject.
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Equipment
When applicable
Multiple selections
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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.
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Target regions
When applicable
Multiple selections
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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.
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Licenses
Multiple selections
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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.
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Protocol
Single selection
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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.
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Performed by
Single selection
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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.
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Notes
Text · 500 characters
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Record complications, adverse events, deviations, or other relevant
detail that is not captured by the structured fields.
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Material usage
Ordered list
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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.
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Stages
When the type declares them
Ordered list
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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.
Coordinate systems
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
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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 external 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.
Stereotaxic coordinates
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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.
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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.
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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.
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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
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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.
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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
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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.
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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
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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.
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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.
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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.
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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.
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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.
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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.
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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
.
Permissions
A Procedure inherits its access through the projects associated with its
Subject. The form limits Subjects and related entries to choices the
current user is permitted to use. Material usages inherit their permissions
through this Procedure, while inventory entries retain their own permission rules.
API access
Procedures can be read and written through
/api/private/modules/procedure/. The corresponding public
route is read-only. Structured Procedure data uses details,
and coordinate data uses coordinates_system and
coordinates_details.
Materials and stages are returned with the Procedure. A create request
may include a material_collection object holding
items and stages, which is applied after the
Procedure itself is created; if the collection is rejected, the whole
request is rolled back. To read or replace the collection of an existing
Procedure, use GET or PUT on
/api/private/modules/procedure/{id}/materials/. Both paths are
validated against the Procedure type's material and stage policy and your
permissions.
Procedure documentation
Subject logs
A Subject log is a named stream of repeated observations for one Subject.
Create the stream once, then add dated entries to it over time. Start a
separate log when the type, subject, protocol, or monitoring purpose
changes.
The stream and its entries
This is the distinction that matters most here. The log
holds what stays the same across the whole series: which subject, what kind
of observation, the method followed, and a description of why the series
exists. Each entry holds one dated observation: when it
happened, who performed it, and the measured values for that occasion.
The log's type fixes the fields every one of its entries will offer, so
choose it before you start recording. Entries are added and edited from the
log's own page rather than from this form.
When a log is linked to a Procedure episode, an entry can
also be placed in an episode phase — baseline, pre-procedure, induction,
during, recovery, post-procedure, or follow-up. That keeps perioperative
observations on the episode's timeline without creating a second log system.
Log types
The type controls the structured fields on every entry in the stream.
The descriptions below follow the same groups and order as the Type
dropdown.
Consumption Logs
-
Food consumption log:
How much food the subject ate on each occasion.
Entry fields: food amount.
-
Water consumption log:
How much water the subject drank on each occasion.
Entry fields: water amount.
Deprivation Logs
-
Food deprivation log:
A period of restricted food access. Record the responsible person
and the authorising protocol, since restriction is normally a
regulated activity.
Entry fields: responsible person (name and
phone number) and protocol.
-
Water deprivation log:
A period of restricted water access, most often supporting a
motivated behavioural task.
Entry fields: responsible person (name and
phone number) and protocol.
Experimental Preparation Logs
-
Habituation log:
Sessions acclimatising the subject to the apparatus, handling, or
restraint before the experiment proper.
Entry fields: method of habituation.
-
Handling log:
Sessions in which the subject was handled to reduce stress. Use
Habituation when the subject is being acclimatised to equipment
rather than to people.
Entry fields: method of handling.
-
Training session log:
Task training sessions and how the subject performed.
Entry fields: task, setup, reinforcement
type, and performance level.
Genetic Logs
-
Genotyping log:
Genotyping results for the subject, including which sample and
assay produced them.
Entry fields: genotype result, sample, assay
or panel name, QC or confidence, and per-locus calls.
Housing Logs
-
Housing log:
Where and how the subject was housed, and when that changed.
Entry fields: location, cage ID, cage type,
light cycle, and enrichment.
Observation Logs
-
Von Frey mechanical sensitivity test:
Mechanical withdrawal thresholds measured with calibrated
filaments.
Entry fields: stimulus location, stimulus
force, response score (0–3), and repetitions.
-
Hargreaves thermal sensitivity test:
Thermal withdrawal latency measured with a radiant heat source.
The cutoff latency records the limit set to avoid injury.
Entry fields: stimulus location, withdrawal
latency, cutoff latency, response score (0–3), and
repetitions.
-
Generic observation:
Use this when a recurring observation does not fit a dedicated
type. Name what is being observed in the observation type field,
because the log type alone will not tell another user what the
series measures.
Entry fields: observation type, observation,
and repetitions.
Physical and Health Logs
-
Monitoring log:
Routine measurement of body weight, intake, and condition. This is
the type to use for ordinary weight tracking. Each entry must
record at least one of its values — an entry that measures nothing
is rejected.
Entry fields: weight, food consumed, water
consumed, body condition score (1–5), and health
observations.
-
Welfare check:
A structured welfare assessment against defined endpoint criteria.
Use this rather than Monitoring when the point of the check is
clinical judgement and humane endpoints.
Entry fields: clinical signs, actions taken,
condition and demeanour (0–4), monitoring plan, pain scoring
method and score, procedure or wound site type, site
observation, endpoint criterion, and whether humane endpoint
criteria were met.
-
Weighing log:
A weight-only stream.
Deprecated: use Monitoring for new weight
records.
Legacy entry field: weight.
-
Wellness log:
A free-text health stream.
Deprecated: use Welfare check for new health
records.
Legacy entry field: wellness.
Log fields
The initial add form asks only for the type and subject. Select
Create and continue to add the protocol and
description, and to start recording entries.
-
Type
Required
Choice
-
What this stream records. It fixes the structured fields every
entry in the log will offer, so a stream cannot mix two kinds
of observation — start a second log instead.
-
Subject
Required · fixed after creation
Single selection
-
The subject this stream belongs to. It supplies the log's
project permission context, and it becomes read-only once the
log exists, so a series of observations can never be
reattributed to a different animal.
-
Protocol
Single selection
-
The documented method followed for entries in this stream.
Only Protocols classified for subject logs are offered, and a
Protocol restricted to particular log types appears only when
it covers the selected type. You can select Protocols you have
change access to.
-
Description
Text
-
What this series is for and how to read it — the measurement
context shared by every entry. Per-occasion remarks belong in
the entry's own notes.
Each entry then records its own date and time
(required), the person who performed it, an optional episode phase,
free-text notes, and the structured values defined by the log's type.
Permissions
A Subject log inherits its access through the projects associated with its
Subject. You need change access through at least one of those projects to add
or edit the log and its entries.
API access
Subject logs can be read and written through
/api/private/modules/subjectlog/. The corresponding public route
is read-only. Individual observations are exposed as the log's related
entries rather than as a separate top-level collection.
Subject log documentation
