5 min read
Updated October 9, 2025
In a mouse or rat the constraints repeat. The target is small, the trajectory is short, and the animal cannot carry much. Silicon arrays answer those constraints by making geometry a design parameter rather than an outcome of assembly.
Research use only. NeuroNexus products and the procedures described here are for non-clinical research use, and must not be used in human or veterinary medical procedures.
Why fabricated geometry matters in a cohort#
A wire bundle is hand-made, so every animal gets a slightly different electrode. A silicon array is lithographic, so site spacing and shank geometry are identical across the cohort.
That is the argument in one sentence: between-animal variance comes from the biology and the surgery, not from the electrode. For a study powered on differences between groups, removing one source of variance is worth more than any single-recording improvement.
"Since NeuroNexus began fabricating probes with high reliability and reasonable costs, we virtually stopped using wire electrodes and monitor electrical activity with silicon probes. It is a one-way process: once one begins to record with silicon probes, he/she never goes back to wires."
— Dr. György Buzsáki, New York University
What these arrays reach#
Small-animal designs record cortical and deep structures to about 10 mm of insertion depth, which covers the rodent brain — and which is where the catalog is concentrated: 198 designs have shanks of 10 mm or less, and only thirteen reach further. Beyond that depth the mechanics change and a supported design is needed — see Deep Brain Targets with Vector Arrays.
The same silicon platform is used outside the brain. Spinal circuits, cardiac tissue and peripheral nerve are live application areas with their own packages. Not every neural target is a brain, and the array selection differs accordingly.
Choosing a geometry#
The layouts and what each costs you are set out once, in NeuroNexus Silicon Probes: Overview. Two of those trades change shape in a small animal, and they are the ones that decide a rodent study.
Shank pitch is anatomy, not preference. It is fixed at fabrication, and the same probe means different things in different species: two shanks 200 µm apart sit within one cortical column in a rat and across two in a mouse. Pick the pitch from the target's dimensions in the species you are actually using.
Site spacing has to come from the layer you need to resolve, not from the densest option available. In a mouse the structures are smaller but the layers are not proportionally thinner, so the densest design is often not the right one.
Choosing a package#
The package determines the connector, and therefore the headstage, the cable and the weight on the animal. The acute-versus-chronic comparison is in Reference Guide: Acute vs Chronic Probes; what follows is the part that is specific to a small animal.
Weight is a hard constraint in a mouse, and it is a package decision. Channel count, connector size and cable stiffness all add to it, and an implant the animal cannot carry produces no behaviour worth recording. A 30 g mouse is not a small rat: the same headcap that a rat tolerates for months will change a mouse's gait. Budget the weight at selection, alongside the geometry — not after the package has been chosen.
The package is committed at implant. A chronic package cannot be revisited, so it is decided before ordering rather than discovered during surgery.
Site coating#
Where units are small or the protocol includes microstimulation, Z-Coat™ lowers site impedance on supported designs. Coating support is a property of the design; check it at selection time. See Z-Coat.
Acute or chronic#
Decided before ordering, and not revisitable. In short: chronic if the measurement needs the same neurons on more than one day, or if the animal has to move; acute otherwise, because it is faster, cheaper, and it tells you what to build the chronic study around. The full criteria are in Reference Guide: Acute vs Chronic Probes.
Custom designs#
Where no catalog geometry fits, NeuroNexus designs to specification: site layout, shank count and length, thickness, materials and packaging. The fabrication process is the catalog's own.
Consider it in three cases. The target's dimensions match no standard spacing. One insertion has to reach two structures. A catalog design is close, but the shank is the wrong length.
Ordering#
Designs, site counts, spacings, package options and lead times are catalog data. Read them from the product catalog, and confirm probe, package, headstage and acquisition system agree before ordering.