Accurate Localization of Linear Probe Electrode Arrays across Multiple Brains

Abstract

We thank the Mouse Imaging Center at The Hospital for Sick Children in Toronto for the MRI of the brains. Rob Campbell for providing technical assistance and maintenance of the SBF2P microscope. Andrew Recknagel, Tiago Ferreira and Jayaram Chandrashekar from the Mouselight team at Janelia for invaluable advice on brain clearing. Tim Harris Lab at Janelia for support with the Neuropixels probe recordings. The vivarium staff at the Janelia Research Campus for excellent animal care. Britton Sauerbrei, Ilana Witten and Sonja Hofer for comments on the manuscript.

A midbrain-thalamus-cortex circuit reorganizes cortical dynamics to initiate movement

“…A small craniotomy (diameter, 0.5 -1 mm) was made over the recording sites one day prior to the first recording session. Extracellular spikes were recorded using Janelia silicon probes (HH-2) with two shanks (32 channels each, 25 mm interval between channel, 250 mm between shanks), or Neuropixels probes (Jun et al, 2017b;Liu et al, 2021;Steinmetz et al, 2021). For the HH-2 probe, 64 channel voltage signals were multiplexed, recorded on a PCI6133 board (National instrument), and digitized at 400 kHz (14 bit).…”

Accurate determination of marker location within whole-brain microscopy images

“…To our knowledge, there has been only a single report of this type of analysis using whole-brain microscopy. Liu et al (2020) 13 used light sheet microscopy to image electrophysiological probes and a semi-automated approach to align the images to an atlas (CCFv3). However, while the accuracy of their approach is comparable to that reported here, it is specific to linear electrophysiological probes and the software is not publicly available.…”

Cortico-thalamo-cortical interactions modulate electrically evoked EEG responses in mice

“…Then each recording channel along the Neuropixels probe (and associated neurons) was assigned to a unique CCFv3 structure. Other studies have reported better than 0.1 mm accuracy for electrode localization following similar methods (Liu et al, 2021).…”

“…Because each CCFv3 coordinate corresponds to a unique brain region, the precision of brain region assignments is determined by the resolution of the CCFv3, which was 25 μm per pixel. For each Neuropixels probe the locations of major structural boundaries along the track was manually aligned with the physiology data (Liu et al, 2021; Siegle et al, 2021). Then each recording channel along the Neuropixels probe (and associated neurons) was assigned to a unique CCFv3 structure.…”