Small animal brain surgery with neither a brain atlas nor a stereotaxic frame

Background: Stereotaxic surgery is a cornerstone in brain research for the precise positioning of electrodes and probes, but its application is limited to species with available brain atlases and tailored stereotaxic frames. Addressing this limitation, we introduce an alternative technique for small animal brain surgery that requires neither an aligned brain atlas nor a stereotaxic frame. New method: The new method requires an ex-vivo high-contrast MRI brain scan of one specimen and access to a micro-CT scanner. The process involves attaching miniature markers to the skull, followed by CT scanning of the head. Subsequently, MRI and CT images are co-registered using standard image processing software and the targets for brain recordings are marked in the MRI image. During surgery, the animal's head is stabilized in any convenient orientation, and the probe's 3D position and angle are tracked using a multi-camera system. We have developed a software that utilizes the on-skull markers as fiducial points to align the CT/MRI 3D model with the surgical positioning system, and in turn instructs the surgeon how to move the probe to reach the targets within the brain. Results: Our technique allows the execution of insertion tracks connecting two points in the brain. We successfully applied this method for neuropixels probe positioning in owls, quails, and mice, demonstrating its versatility. Comparison with existing methods: We present an alternative to traditional stereotaxic brain surgeries that does not require established stereotaxic tools. Thus, this method is especially of advantage for research in non-standard and novel animal models.