Does anybody use a preheated syringe for injecting an agarose mixture during insertion of a Neuropixels probe?

Hi there,

I inject agarose mixture into my cranial window to carefully insert a Neuropixels probe into my brain region of interest. I was wondering if anyone uses a preheated syringe for this?


Hi Selena – for our Neuropixels experiments at the Allen Institute, we place the agarose syringe inside a Falcon tube in a hot water bath. This helps ensure the agarose doesn’t solidify too quickly when applying it to the brain.

Thank you for your response! A few more questions:

  1. After applying the agarose gel to the craniotomy, how long do you wait until probe insertion?
  2. Have you had issues of this agarose gel sticking to the Neuropixels probe?
  3. Is the purpose of the gel to prevent drift?
  4. Why can’t we just use saline on the craniotomy during probe insertion?

I really appreciate you taking the time to answer my questions!

  1. We apply the agarose while the mouse is anesthetized, so we wait 1-2 hours for the mouse to recover before inserting the probes. But the agarose itself completely solidifies within a few minutes, and at that point it’s safe to insert probes through it.
  2. If some agarose dries on the probe (happens very rarely), it can be dipped in warm water to remove it.
  3. Yes, but agarose alone is not enough to stabilize larger craniotomies (3+ mm in diameter). In this case we recommend injecting the agarose under a plastic window to further stabilize the brain.
  4. Agarose (covered with silicone oil) is preferred because it will not evaporate and therefore does not need to be re-applied throughout the recording. If you’d prefer to use a liquid, make sure it’s ACSF instead of PBS to preserve tissue health.

I’d recommend reading through this paper for the full details of our recording protocol.