DOI: 10.7272/q6st7n3b
title: High-density single-unit human cortical recordings using the Neuropixels probe

description: This dataset contains the raw broadband and LFP data collected using the
 Neuropixels probe in human participants in the intraoperative setting. The
 Neuropixels probe allows for single-unit recordings simultaneously over
 384 contacts. The experimental design and procedures are explained in
 Chung, Sellers et al (2022), Neuron. Each participant received an
 identifier (e.g. NP##). Multiple blocks of data were collected for some
 participants, denoted by B##. Recordings were started prior to probe
 insertion, to allow for visualization during insertion - thus spike
 sorting should not be conducted on the full duration of these raw
 recordings but rather following termination of insertion artifact.
description: Full methodological details are available in the published paper.
 Reproduced here is the most relevant information: Probe
 preoperative preparation and sterilization Neuropixels
 1.0 NHP-short probes, with 10mm long shanks and metal dovetail caps (IMEC,
 Leuven, Belgium), were used for all recordings. These probes are adapted
 and modified versions of the Neuropixels 1.0 rodent probes (Jun et al.,
 2017) that are electronically identical, with the notable difference of
 increased shank thickness from 24μm to 97μm (Paulk et al., 2022). This
 increased thickness allowed for tolerance of greater mechanical forces for
 larger brain recordings. Two 27G subdermal needle electrodes (Ambu,
 Columbia, MD) were soldered separately to the probe flex-interconnect to
 serve as ground and reference using lead-free solder and two strands of
 twisted 36 AWG copper wire. The connected needle electrodes were
 approximately 20cm long, to allow for insertion into the skin flap
 following probe insertion. No additional modifications were made to the
 Neuropixels probe. Probes with soldered needle electrodes were installed
 into custom CleanCut mounting cards (Oliver Healthcare Packaging, Grand
 Rapids, MI) for storage and transport. The Neuropixels
 probe was secured to the metal cap dovetail probe mount (IMEC, Leuven,
 Belgium). The probe mount was in turn attached to either a Elekta
 microdrive (Elekta, Stockholm, Sweden) or Narishige (Tokyo)
 micromanipulator (MM-3 or M-3333). The manipulator/microdrive was secured
 to the Mayfield skull clamp using an 3-joint mounting arm (Noga NF9038CA)
 and Nano clamp (Manfrotto 386BC-1, Cassola, Italy) assembly attached to
 the primary articulating arm and C-clamp of the Integra Brain Retractor
 System A2012 (Integra, Princeton, NJ). Probes, headstages, interface
 cables, Narishige micromanipulators, screwdrivers, and probe mount with
 metal cap dovetail were all separately sterilized according to standard
 protocols of ethylene oxide sterilization, while the Elekta
 micromanipulators were sterilized using Sterrad prior to use. Probes were
 not reused across participants. Recording site
 selection In all cases, the insertion of Neuropixels
 probes was targeted to cortical tissue that was destined for resection in
 the same procedure based on clinical criteria. In cases where a tumor or
 cavernoma was resected, the recording was targeted to radiographically
 normal tissue (no T2 hyperintensity) which would require resection as part
 of the transcortical approach. In all cases the recorded tissue appeared
 normal intraoperatively. The specific sites were selected to be the crown
 of surface gyri which allowed for direct visualization and monitoring of
 the insertion and penetration through cortical layers. See below for
 post-hoc insertion localization. Probe positioning and
 insertion Each participant was secured with a Mayfield
 skull clamp. A compatible C-clamp was then attached to the skull clamp,
 and in turn, a primary articulating bar was attached to the C-clamp (all
 items contained in Integra Brain Retractor System A2012). A clamp
 (Manfrotto 386BC-1) was used to attach a 3-joint mounting arm (Noga
 NF9038CA) to the articulating bar. The 3-joint mounting arm was connected
 to a micromanipulator (Elekta or Narishige MM-3 or M-3333) which held the
 Neuropixels assembly. All equipment was sterilized according to standard
 protocols using either Sterrad or ethylene oxide sterilization. The
 articulating arms were positioned to place the micromanipulator above the
 target insertion site, and the Neuropixels probe was lowered using the
 micromanipulator to a target depth of 6 to 8 mm from the brain surface, at
 a rate of 50–75 μm/sec. Insertion trajectory was approximately
 perpendicular to the surface. Insertion locations were estimated through a
 combination of intraoperative navigation, intraoperative photos taken
 during the surgery, and histology when available. In some cases, a piotomy
 was performed at the site of insertion, which also reduced the risk for
 probe fracture. We hypothesized this would also increase unit yield,
 although this did not appear to have an effect. Recordings were typically
 started to visualize probe insertion (Video S1).
 Recording Data were collected using a
 custom-constructed rig including a Windows machine, PXI chassis (NI
 PXIe-1071), PXI Multifunction I/O Module (NI PXIe-6341), NI SHC68-68-EPM
 shielded cable, Neuropixels PXIe Acquisition Module, and NI BNC-2110
 Connector Block with SpikeGLX 3.0 (http://billkarsh.github.io/SpikeGLX/)
 acquisition software. In some experiments, speakers were used to present
 auditory stimuli and a microphone was used for recording; these signals
 were also acquired as analog inputs synchronized with the neural data. The
 Neuropixels probe was configured to acquire from 384 channels in a ‘long
 column’ layout, providing the greatest possible depth span of recording
 while acquiring from a contact at each depth. Total recording span was
 7.67mm. Ground and reference needle electrodes were inserted into the
 scalp adjacent to the craniotomy. AP gain was 500 and LF gain was 250.
 During data acquisition, all non-essential equipment in the operating room
 was unplugged or run using battery power in order to reduce electrical
 noise. By iteratively turning off pieces of equipment, when possible, and
 listening to the high-pass filtered signal from a recording channel, we
 found the operative table, electrocautery, and electronics associated with
 intravenous lines should be on direct current, including syringe pumps and
 blood/fluid warmers. Other key environmental sources of noise included
 neuromonitoring and the Brainlab neuronavigation system.
description: Data were acquired using SpikeGLX 3.0. The raw data are stored in
 binary files which can be read into Matlab or Python. Example functions
 provided by SpikeGLX developers are available at https://billkarsh.github.io/SpikeGLX/#post-processing-tools for reading raw data into Matlab and Python.