Silicon Probes: Setup, Handling, Cleaning and Care

A silicon probe is set up in five steps before a session — inspect, measure impedance in saline, mount by the package, connect the headstage, verify in saline — and cleaned in four after it — rinse at once, enzyme, rinse, then alcohol. Most first-session failures are set up before the probe reaches the animal, and most probes are destroyed by something that dried on them, something that touched the sites, or something that pulled on a reference wire.

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.

Six rules#

These are stated in full where they belong below; they are repeated here because each one ends a probe.

Handle only by the package, never the shank. Never touch sites with metal instruments or bare hands.

Do not let biological material dry on the probe: this is the single most consequential rule in this guide. Rinse in distilled water as soon as the probe is out of the tissue. A probe rinsed within a minute usually recovers; one left until the end of the session often does not.

In cleaning, the sequence matters more than any individual step, because alcohol before enzyme fixes protein onto the sites permanently. Alcohol applied to a probe that still has protein on it fixes that protein to the sites, and the impedance change that follows is not reversible.

Never use an ultrasonic cleaner. Cavitation damages sites, substrate and bond wires; the damage is often invisible and shows up as an impedance change.

Never autoclave. Steam and pressure degrade polymer components and adhesives and change electrical characteristics permanently. Use the alcohol step for sterilization.

For the ground and reference wires: support the wire rather than the joint, with no tension, no repeated bending and as little manipulation as the procedure allows. A damaged ground or reference wire does not produce an obvious failure; it produces a noisy recording that looks like an environmental problem.

Setup takes about thirty minutes, done in this order. Cleaning takes minutes of attention and up to four hours of soaking. The two are one procedure because a probe that is cleaned well sets up quickly next time, and the impedance measured at setup is the record that tells you whether cleaning worked.

What you need#

The silicon probe, in its case. The matching headstage, and any adapter the package ↗ requires. Cables, and the acquisition system powered and running. A dissecting microscope with a cold light source. Saline, and an impedance meter or the acquisition software's impedance check. For cleaning: distilled and deionized water, an enzymatic detergent such as Tergazyme, and 70% isopropyl alcohol.

Handle the probe#

Handle the probe only by its package, never by the shank or the cable. Never touch the sites with metal instruments or bare hands. The shank must not take a lateral load at any point: when the probe is lifted, mounted, connected or cleaned, the force goes into the package and the shank hangs free. The ground and reference wires are handled by their own rule below.

Inspect the probe#

Take the probe out by its package. Under magnification, check that the shank is straight, the sites are clear, and the ground and reference wire joints are intact. A bent shank or a damaged site found now costs a few minutes; found during surgery it costs the session. If the probe has been used, confirm it was cleaned by the sequence below — enzyme before alcohol, never ultrasonic, never autoclave.

Measure impedance#

Measure every site in saline, before mounting, and compare against the probe's own baseline — the factory record on first use, your last measurement afterwards — rather than a nominal figure. For a 177 µm² site the typical value is 200 kΩ to 1 MΩ at 1 kHz, and what matters is the distribution: a tight cluster is a good probe, a site far above the cluster has a broken trace, an open bond, a contaminated surface or a dried residue, and a site far below has a short. A channel well outside its baseline is a failed channel, and knowing which one before you record is the difference between excluding a channel and mistrusting a result. Impedance ↗ explains what the number means.

Mount the probe#

Mount the probe on the manipulator or holder by its package. The shank must hang free, with no lateral load on it. Check the manipulator's trajectory through its full travel before the probe is anywhere near tissue.

Connect the headstage#

Attach the headstage to the probe connector while supporting the probe; the insertion force on a connector is more than a shank tolerates through a lever arm. If an adapter is in the path, get its channel map now and fold it into the site map — site 1 is rarely channel 1 through an adapter. Route the cable so that nothing pulls on the probe as the manipulator moves, and strain-relieve it at a fixed point.

Verify before the animal#

Connect to the acquisition system and confirm four things: every channel present, impedance as measured above, the noise floor at its baseline, and no mains peak. Do this with the probe in saline, not in air. A probe in air looks quiet because nothing is connected to anything.

Clean the probe, in order#

The sequence matters more than any individual step, because alcohol before enzyme fixes protein onto the sites permanently.

Rinse immediately. Rinse in distilled water as soon as the probe is out of the tissue, immersing and withdrawing gently to dislodge loose material. Do not let biological material dry on the probe: this is the single most consequential rule in this guide. A probe rinsed within a minute usually recovers; one left until the end of the session often does not. Use fresh distilled water each time.

Dissolve protein with an enzyme. Tergazyme is the usual choice; a contact-lens cleaning solution or a diluted surgical-instrument detergent also works. Immerse the shank only and keep the circuit board dry. Soak at room temperature, up to four hours.

Rinse thoroughly. Deionized water, with repeated immersion and withdrawal or gentle stirring, until no detergent remains. Inspect under magnification.

Then, and only then, alcohol. 70% isopropyl alcohol, brief contact. Alcohol applied to a probe that still has protein on it fixes that protein to the sites, and the impedance change that follows is not reversible. Confirm the enzyme step has finished before this step begins.

Never do these two things#

Never use an ultrasonic cleaner. Cavitation damages sites, substrate and bond wires; the damage is often invisible and shows up as an impedance change.

Never autoclave. Steam and pressure degrade polymer components and adhesives and change electrical characteristics permanently. Use the alcohol step above for sterilization.

Handle the ground and reference wires#

These wires are thin and flexible by design, so that they disturb as little tissue as possible, and that same property makes them the most fragile part of the assembly. A damaged ground or reference wire does not produce an obvious failure; it produces a noisy recording that looks like an environmental problem, and laboratories lose days to the wrong diagnosis. Support the wire rather than the joint, with no tension, no repeated bending and as little manipulation as the procedure allows. Plan the routing before surgery and use strain relief at every point where the wire crosses from one fixed thing to another. During cleaning, work on the shank, do not manipulate the wire joints, and inspect them afterwards.

Store the probe#

Store in the original shipping box, in a clean, dry place at room temperature, away from temperature swings and humidity. Keep connector covers on chronic packages — CM series, Hybrid series and any long-term package — to prevent contamination and protect the connector mechanically. Keep the probe's identification documents with the probe: the design name and channel map are what let you plan the next experiment, and a probe with no paperwork is a probe you cannot cite.

Track condition over time#

Measure impedance before each use and compare to the value at first use. The trend is the signal: a steady rise means the sites are degrading, a jump means something mechanical happened. Inspect visually under magnification — shank straightness, site appearance, wire joints — and log each cleaning cycle. Probes do not fail on a schedule; a probe with a long cleaning history and a rising impedance trend is one to retire before it costs an experiment. With this care, an acute probe is reused across many sessions, and a Vector array across fifty or more.

When cleaning does not work#

Material remains after the enzyme step: fresh solution, a longer soak within the four-hour limit, then a soft brush used gently. If it persists, contact support rather than escalating the mechanical effort. Impedance is higher after cleaning than before: compare against the pre-cleaning values. A uniform rise across sites usually means residue; a rise on some sites usually means damage. If the noise floor rather than the impedance is the problem, Noise Reduction and Troubleshooting is the diagnostic sequence.

Next#

With the probe verified in saline, the surgical procedure is in the acute or chronic surgical guide. Technical questions: support@neuronexus.com · +1.734.913.8858.