Animal-behavior rigs and enclosures

Arenas, mazes, head-fixation hardware, spouts and ports, and the extrusion frames that carry them.

Dimensions come from the protocol, not from this file

Behavioral apparatus dimensions are not standardised. They are set by the published protocol the experiment replicates, and they differ between species, strains, ages, and labs. An elevated plus maze sized for rats is wrong for mice; an open field sized from one paper will not reproduce another paper's results.

Ask which protocol or paper the rig replicates, and take the dimensions from it. If the user does not have one, say plainly that the geometry is a design choice affecting comparability, and get their sign-off on the numbers before modelling. Do not supply "standard" maze dimensions from memory — there is no such standard, and a plausible-looking wrong number is worse here than an admitted gap, because it silently breaks comparison with prior work.

What this file does cover is the engineering that is common across rigs.

Regulatory and welfare context

Any apparatus that contacts animals falls under the institution's approved protocol. Before fabrication:

• The design must be consistent with the approved IACUC (or local equivalent) protocol. A geometry change — a narrower arm, a different head-plate, a new restraint — may require an amendment. Flag this; it is not the modeller's call to make.
• Materials must be non-toxic and non-irritant, including after repeated cleaning.
• No entrapment or pinch geometry: no gaps that can catch a limb, tail, or head; no wedge- shaped gaps that narrow into a trap. Break sharp edges everywhere an animal can reach.
• Anything load-bearing over an animal needs a real margin, not a printed part at minimum wall.

Raise these actively rather than waiting to be asked.

Materials and cleaning

This dominates material choice, and it eliminates most of the obvious options:

• Cleaning agents are the constraint. Ethanol (70%) crazes many plastics; quaternary ammonium and chlorine dioxide disinfectants attack others; autoclaving distorts anything with a low glass transition temperature. PLA in particular softens well below autoclave temperature and should be treated as single-use.
• Porosity carries odour. FDM parts are porous by construction, hold odour cues between animals, and cannot be reliably disinfected. Odour is a genuine confound in behavior work. Prefer a non-porous process, or seal the surface, or treat FDM parts as consumable and per-cohort.
• Chew resistance. Rodents will chew anything reachable. Printed polymer at an exposed edge will be destroyed and, worse, ingested. Put metal, glass, or a hard sacrificial edge wherever an animal can bite, and keep printed material out of reach where possible.
• Uncured resin is cytotoxic and an irritant. SLA parts that contact animals need full post- cure and thorough washing. See references/fabrication-limits.md.

Video tracking and optics

Most rigs are recorded, and the geometry either helps or fights the tracking:

• Contrast: match the surface to the animal's coat so the tracker can segment it. Matte white or light grey floors for dark animals, matte dark for albino. Matte, not gloss — specular highlights are tracked as objects.
• Avoid shadow-casting geometry near the floor. Deep walls at low camera angles create shadow bands that trackers segment as the animal.
• Infrared: if illumination is IR, remember that many "opaque" black plastics transmit IR, and that IR-transparent floors change the apparent image. Verify with the actual camera, not by assumption.
• Leave a clear, unobstructed camera line to the whole arena, and model the camera mount as part of the rig so the field of view is checked before fabrication, not after.

T-slot extrusion frames

Most rigs are built on aluminium extrusion. The critical fact: slot width is not implied by profile size.

A 20 mm profile from one supplier takes a 6 mm slot nut; from another, 5 mm. Measure the slot, or get the part number. A bracket modelled for the wrong slot is scrap.

Design notes:

• Slot the bracket's mounting features along the extrusion axis. That is the whole point of extrusion — position is continuously adjustable, and a fixed hole throws that away.
• Extrusion faces are the datum. Design brackets to register flat against a face and, where possible, into the slot, so the part cannot rotate under load.
• Printed brackets carrying a camera or a heavy component should be treated as prototypes. Polymer creeps under sustained load and the camera will slowly droop out of alignment.

Head fixation

The highest-consequence geometry in this file, and entirely lab-specific.

• The head-plate or head-post interface must come from the actual implant the lab uses, as a drawing or a measurement. There is no standard. Get the part.
• The kinematic requirement is to constrain the implant repeatably and without play, with clamping force that does not deflect the plate. Play translates directly into imaging or recording motion artefact.
• Fixation hardware must be quick to release, both for routine handling and in an emergency.
• Printed clamps flex. For any part carrying head-fixation load, recommend machined metal and present the printed version as a fit-check prototype only. Say this explicitly — it is a welfare issue as well as a data-quality one.

Spouts, ports, and reward delivery

• Spout material must be non-toxic and cleanable; stainless steel tubing is the usual choice, held by a printed carrier that never itself contacts the animal's mouth.
• Position is a calibrated experimental variable. Make spout position adjustable and readable, and record it in the manifest, so it can be reproduced across sessions and animals.
• Model the reward line's dead volume — the delay between valve and spout is an experimental parameter. See the dead-volume formula in references/microfluidics.md.
• If lick detection is capacitive, keep conductive material away from the sensing element and give the wire a defined, strain-relieved route in the model.

Checks to run

python scripts/gen.py arena_model.py --outdir out/
python scripts/check.py facts out/arena.step
python scripts/check.py clearance out/arena.step out/camera_mount.step --min 1.0
python scripts/snapshot.py out/arena.step --out out/arena.png

Confirm in the snapshot:

1. No gap an animal can get a limb, tail, or head into.
2. All animal-reachable edges broken; no sharp corners.
3. Camera has an unobstructed view of the whole floor.
4. Extrusion mounting features are slotted, and on the faces you can actually reach with a tool.
5. Nothing printed sits where it will be chewed.

Sources

Deliberately none for dimensions. Arena, maze, and head-fixation geometry must come from the protocol being replicated or from the physical implant, not from a general reference. The material, cleaning, tracking, and extrusion guidance above is general engineering practice.