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:
- After applying the agarose gel to the craniotomy, how long do you wait until probe insertion?
- Have you had issues of this agarose gel sticking to the Neuropixels probe?
- Is the purpose of the gel to prevent drift?
- Why can’t we just use saline on the craniotomy during probe insertion?
I really appreciate you taking the time to answer my questions!
- 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.
- If some agarose dries on the probe (happens very rarely), it can be dipped in warm water to remove it.
- 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.
- 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.