Recording with a Neuropixels probe

These data were obtained by Nick Steinmetz (nick[dot][e-mail]), in the CortexLab at UCL, and were published in Jun JJ, Steinmetz, NA, Siegle, JH, Denman, DJ, Bauza, M, Barbarits, B, Lee, AK et al. Fully integrated silicon probes for high-density recording of neural activity. Nature 2017.A "Phase3" Neuropixels probe was inserted into the brain of an awake, head-fixed mouse for about an hour. This electrode array recorded 384 channels of neural data at 30 kHz and <7 µV RMS noise levels. The sites are densely spaced in a "continuous tetrode"-like arrangement, so that the probe records from a 3.8 mm span of the brain.The probe recorded from visual cortex, hippocampus, and some parts of thalamus. Data was high-pass filtered at 300 Hz on-probe. After applying common average referencing, the data were spike-sorted automatically by Kilosort (software by M. Pachitariu; using the included master_file.m) and manually by N. Steinmetz using Phy (manual phase; software by C. Rossant). In total 242 well-isolated individual neurons were identified. Example raw data can be seen in visctxRawExample.PNG. The waveform and autocorrelogram of an example neuron can be seen in vixctxNeuronExample.PNG.In addition to neural data, a movie of the eye of the mouse was acquired at 100 Hz and a movie of the frontal aspect (face, forearms, anterior trunk) was recorded at 40 Hz. The mouse's forepaws rested on a wheel that could move left or right, and the movements of this wheel were recorded. Auditory and olfactory information was not recorded and the mouse was not guaranteed to be in silence or in an odor-free environment.The experiments that were runExperiment 1During the first phase of the recording, the mouse was shown visual stimuli (described below) on three monitors placed around the mouse at right angles to each other, covering about +/-135 degrees azimuth and +/-35 degrees elevation.Sparse noise stimuli for receptive field mapping 8 degree squares were displayed at random times for 1/6 of a second on each vertex of a 9x34 grid with 8 degree spacing covering the whole extent of the monitors. Background was grey and squares could be either white or black. The presentation consisted of three repeats of a single five-minute long pattern of squares.Experiment 2During the second phase of the recording, the monitors were turned off and the mouse was in complete or nearly-complete darkness.Loading the dataThe electrophysiology data is in a compressed file named Hopkins_20160722_g0_t0.imec.ap_CAR.cbin (29.6 GB). To decompress it, use mtscomp. This will require the associated metadata file, which has the same name, with extension ".ch" (120 KB). The result of the decompression must have the same name, with extension ".bin".The raw data (".bin" files) are binary files of type int16 and with 385 data rows (see params.py). In Matlab this can be read as follows:fn = 'rawDataSample.bin';fid = fopen(fn, 'r');dat = fread(fid, [385 Inf], '*int16');fclose(fid);chanMap = readNPY('channel_map.npy');dat = dat(chanMap+1,:);figure; imagesc(dat(:,1:30000));The preprocessed data is stored in a set of npy files. These can be loaded with numpy in Python, or you will need the npy-matlab repository to load them in Matlab.You can view the data most easily with Phy, please see specifically this documentation for details about the meaning of the included files.

本数据集由伦敦大学学院（University College London, UCL）皮层实验室的Nick Steinmetz（nick[dot][e-mail]）获取，相关研究成果发表于2017年《Nature》期刊，作者涵盖Jun JJ、Steinmetz NA、Siegle JH、Denman DJ、Bauza M、Barbarits B、Lee AK等，论文题为《Fully integrated silicon probes for high-density recording of neural activity》。

实验采用"Phase3"型神经像素（Neuropixels）探针插入清醒且头部固定的小鼠脑部，采集时长约1小时。该电极阵列以30 kHz的采样率记录384通道神经信号，本底噪声低于7 µV RMS。探针上的电极位点以类似连续四极阵列的方式密集排布，可覆盖大脑3.8 mm的范围，记录区域涵盖视觉皮层、海马体及部分丘脑区域。探针端内置高通滤波，截止频率为300 Hz。

完成公共平均参考（common average referencing）预处理后，数据先由Kilosort（由M. Pachitariu开发，配套使用master_file.m脚本）完成自动尖峰分类，再由N. Steinmetz使用Phy（由C. Rossant开发）进行人工校验。最终共鉴定出242个分离良好的单个神经元。示例原始数据可见visctxRawExample.PNG，示例神经元的波形与自相关图可见vixctxNeuronExample.PNG。

除神经电生理数据外，本数据集还以100 Hz帧率采集了小鼠眼部影像，以40 Hz帧率采集了其前额区域（面部、前肢、躯干前部）的影像。小鼠前爪置于可左右移动的转轮上，实验同步记录了转轮的运动情况。本次实验未采集听觉与嗅觉信号，且无法保证小鼠处于无噪音、无异味的环境中。

实验流程如下：
实验1：在记录的第一阶段，向小鼠展示视觉刺激，刺激呈现在围绕小鼠呈直角排布的三台显示器上，覆盖方位角约±135°、仰角约±35°的视野范围。本次实验使用用于感受野映射的稀疏噪声刺激：在覆盖全部显示器范围的9×34网格（网格间距8°）的每个顶点处，随机呈现8°见方的方块，单次呈现时长为1/6秒，背景为灰色，方块颜色可选白色或黑色。刺激呈现方案为一段时长5分钟的方块图案重复三次。
实验2：在记录的第二阶段，关闭所有显示器，小鼠处于完全或近乎完全的黑暗环境中。

数据加载：
电生理原始数据存储于压缩文件Hopkins_20160722_g0_t0.imec.ap_CAR.cbin（大小29.6 GB）。需使用mtscomp工具进行解压缩，该过程需要配套的元数据文件（同名，扩展名为.ch，大小120 KB）。解压缩后的文件需保留原文件名，仅将扩展名改为.bin。
原始数据（.bin文件）为int16类型的二进制文件，共包含385个数据行（详见params.py）。在Matlab中可按如下方式读取：
fn = 'rawDataSample.bin';
fid = fopen(fn, 'r');
dat = fread(fid, [385 Inf], '*int16');
fclose(fid);
chanMap = readNPY('channel_map.npy');
dat = dat(chanMap+1,:);
figure; imagesc(dat(:,1:30000));
预处理后的数据存储于一系列npy文件中。可使用Python的numpy库加载，若在Matlab中加载则需安装npy-matlab工具库。
最便捷的可视化方式为使用Phy软件，详细的配套文件含义请参阅其官方文档。

搜集汇总

背景与挑战

背景概述

该数据集包含使用Neuropixels探针在小鼠大脑中记录的神经活动数据，覆盖视觉皮层、海马体和部分丘脑。数据包括高密度神经信号记录、眼动和面部视频，以及前爪运动数据，并附有视觉刺激实验的详细信息。