20191010_L544

If you use these data in a paper, please cite Dalgleish et al. 2020 (eLife) and reference the figshare dataset DOI. This dataset contains the processed imaging data (Suite2p – ROIs, traces, metadata), photostimulation protocols, opsin expression data and synchronisation data from a single “number of neurons” psychometric curve behavioural session (1 animal, 1 day, 1 - 1.5 hours). Experiments are in L2/3 barrel cortex of mice. Imaging is of GCaMP6s at 920 nm (~50 mW) across 4 planes (using an ETL) at ~27 Hz frame rate, ~7 Hz volume rate. Photostimulation is of C1V1-Kv2.1 (somatically restricted) at 1030 nm. This an Emx1-Cre;CaMKIIa-tTA;Ai94 GCaMP6s transgenic mouse injected with AAV2/9-CaMKII-C1V1(t/t)-mRuby2-Kv2.1. Code for import, analysis and figure plotting can be found here: https://github.com/alloptical/Dalgleish-eLife-2020 Fall.mat – Suite2p output (ROIs, traces etc.) in standard format for Python Suite2p’s MATLAB output (see Suite2p documentation for details). ROIs have been manually curated (NB to use curated ROIs use the iscell label). targets – photostimulation target data. Each *_Points.mat file returns a points variable with fields X, Y, Z and Zum corresponding to XY co-ordinate in pixels, Z co-ordinate in plane number and Z co-ordinate in µm respectively. Each file corresponds to a different stimulus type (number of neurons targeted) used during the experiment (see number of elements in the above fields). The *_VarFile_*.mat file contains the training photostimulation protocol. This can be synced with the *_Points.mat files (see above) and *_paq_analysis.mat file (see below) via code in the Dalgleish et al. 2020 Github repo. cellPose – C1V1 expression images and cellpose-identified C1V1-expressing neurons. *.tif files are acquired expression images of C1V1-mCherry (765nm). *_cellPoseCentroids.mat files contain co-ordinates of C1V1-expressing neurons (NB this has a similar format to the target *_Points.mat files described above). Other files are raw output from the Cellpose algorithm (see Cellpose documentation for details). *_paqanalysis.mat – synchronisation data recording the timing of all features of the experiment. Fields should be self-explanatory. Returns variable pa with relevant fields: frames: imaging frames stims: stimulus times as a structure array where each instance records timing for a given stimulus channel (see NB below). Two trigger types: “in” are sent from the behavioural control hardware (i.e. “deliver photostimulation”); “out” are sent from the microscope photostimulation hardware (i.e. “photostimulation delivered”). Where possible use “out” for the most accurate timing information (e.g. for Go stimulus trials). NB Catch trials only have “in” triggers as no photostimulation was delivered. licks: lick times rewards: reward delivery times running: rotary encoder reading from linear treadmill NB that there are two “stimulus types” in our experiment and thus two relevant stimulus channels: Go trials, with photostimulation, delivered via channel 7 referenced via pa.stims(7), and Catch trials, with no stimulus, delivered via channel 6 referenced via pa.stims(6). Go trials have 7 different trial types, or variations/var, corresponding to different numbers of neurons stimulated. These are: 1: 200 neurons 2: 100 neurons 3: 75 neurons 4: 50 neurons 5: 25 neurons 6: 10 neurons 7: 5 neurons若将本数据集用于学术论文，请引用Dalgleish等人2020年发表于《eLife》的研究，并标注figshare数据集的DOI编号。 本数据集包含来自单一场“神经元数量”心理测量曲线行为实验（1只小鼠，1天实验时长，1~1.5小时）的处理后成像数据（Suite2p——感兴趣区(Regions of Interest, ROIs)、钙信号轨迹、元数据）、光刺激范式、视蛋白(opsin)表达数据以及同步数据。实验位点为小鼠L2/3级桶皮层。成像采用920 nm（~50 mW）激发的GCaMP6s钙指示剂，通过电控可调透镜(Electrical Tunable Lens, ETL)采集4层平面的图像，帧频约27 Hz，体频约7 Hz。光刺激采用1030 nm激发的C1V1-Kv2.1（体细胞限制性）光遗传通道蛋白。实验所用小鼠为Emx1-Cre;CaMKIIa-tTA;Ai94 GCaMP6s转基因小鼠，并注射了AAV2/9-CaMKII-C1V1(t/t)-mRuby2-Kv2.1（腺相关病毒(Adeno-associated virus, AAV)血清型2/9携带CaMKII-C1V1(t/t)-mRuby2-Kv2.1载体）。 用于数据导入、分析及图像绘制的代码已开源，地址为：https://github.com/alloptical/Dalgleish-eLife-2020 Fall.mat：采用Python版Suite2p的MATLAB输出标准格式存储的Suite2p输出结果（包含感兴趣区、钙信号轨迹等，详见Suite2p官方文档）。所有感兴趣区均经过人工筛选（注：若需使用筛选后的感兴趣区，请调用iscell标签）。 targets文件夹：存储光刺激靶点数据。每个*_Points.mat文件包含points变量，其字段X、Y、Z和Zum分别对应像素坐标系下的XY坐标、平面编号Z坐标以及以微米为单位的Z坐标。每个文件对应实验中使用的一种刺激类型（即靶向激活的神经元数量，可通过上述字段的元素数量判断）。*_VarFile_*.mat文件包含训练阶段的光刺激范式，可通过Dalgleish等人2020年开源的GitHub仓库中的代码，与上述*_Points.mat文件及下文提及的*_paq_analysis.mat文件完成时间同步。 cellPose文件夹：存储C1V1视蛋白表达图像以及通过Cellpose算法(Cellpose)识别的C1V1阳性神经元坐标。*.tif文件为765 nm激发下采集的C1V1-mCherry表达图像。*_cellPoseCentroids.mat文件包含C1V1阳性神经元的空间坐标（注：该文件格式与上述targets文件夹中的*_Points.mat文件类似）。其余文件为Cellpose算法的原始输出结果（详见Cellpose官方文档）。 *_paqanalysis.mat：存储记录实验全流程时序信息的同步数据，各字段含义直观易懂。该文件返回变量pa，其包含以下核心字段： frames：成像帧序列 stims：刺激时序结构体数组，每个元素记录对应刺激通道的触发时间（详见下文注记）。本实验包含两类触发信号：“in”信号由行为控制硬件发送（即“启动光刺激”指令）；“out”信号由显微镜光刺激硬件发送（即“光刺激已完成”确认）。若条件允许，建议使用“out”信号以获取最精准的时序信息（如Go任务试次）。注：Catch试次仅包含“in”触发信号，因该试次未施加光刺激。 licks：舔舐动作发生时刻 rewards：奖励发放时刻 running：线性跑步机配套旋转编码器的读数 注：本实验包含两类刺激类型，对应两个刺激通道：①Go试次：施加光刺激，对应通道7（可通过pa.stims(7)调用）；②Catch试次：不施加刺激，对应通道6（可通过pa.stims(6)调用）。Go试次共包含7种试次变体（var），分别对应不同数量的被激活神经元，具体如下： 1：200个神经元 2：100个神经元 3：75个神经元 4：50个神经元 5：25个神经元 6：10个神经元 7：5个神经元