20191125_OG424

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 a wild-type (C57/BL6) mouse injected with AAV1-Syn-GCaMP6s-WPRE-SV40 and AAV2/9-CaMKII-C1V1(t/t)-mScarlett-Kv2.1. Code for import, analysis and figure plotting can be found here: https://github.com/alloptical/Dalgleish-eLife-2020<b> </b><b>Fall.mat</b> – 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 <i>iscell</i> label). <b>targets</b> – photostimulation target data. Each <i>*_Points.mat</i> file returns a <i>points</i> 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 <i>*_VarFile_*.mat</i> file contains the training photostimulation protocol. This can be synced with the <i>*_Points.mat</i> files (see above) and <i>*_paq_analysis.mat </i>file (see below) via code in the Dalgleish et al. 2020 Github repo. <b>cellPose</b> – C1V1 expression images and cellpose-identified C1V1-expressing neurons. <i>*.tif </i>files are acquired expression images of C1V1-mCherry (765nm). <i>*_cellPoseCentroids.mat</i> files contain co-ordinates of C1V1-expressing neurons (NB this has a similar format to the target <i>*_Points.mat</i> files described above). Other files are raw output from the Cellpose algorithm (see Cellpose documentation for details). <b>*_paqanalysis.mat</b> – synchronisation data recording the timing of all features of the experiment. Fields should be self-explanatory. Returns variable <i>pa</i> with relevant fields: <i>frames:</i> imaging frames<i>stims:</i> 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.<i>licks:</i> lick times<i>rewards:</i> reward delivery times<i>running:</i> 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 <i>pa.stims(7)</i>, and Catch trials, with no stimulus, delivered via channel 6 referenced via <i>pa.stims(6)</i>. Go trials have 7 different trial types, or variations/var, corresponding to different numbers of neurons stimulated. These are:1: 200 neurons2: 100 neurons3: 75 neurons4: 50 neurons5: 25 neurons6: 10 neurons7: 5 neurons

若您在论文中使用本数据集，请引用Dalgleish等人2020年发表于《eLife》的研究，并标注figshare数据集的DOI。本数据集包含经过预处理的成像数据（Suite2p——感兴趣区（ROIs）、信号轨迹、元数据）、光刺激协议、视蛋白表达数据，以及来自单次"神经元数量"心理测量曲线行为实验的同步数据（实验动物为1只小鼠，单天实验，时长1至1.5小时）。实验部位为小鼠的L2/3层桶状皮层。成像采用GCaMP6s指示剂，激发波长920 nm，功率约50 mW，通过ETL实现4层平面成像，帧频约27 Hz，体素帧率约7 Hz。光刺激采用体细胞限制性视蛋白C1V1-Kv2.1，激发波长1030 nm。实验所用小鼠为野生型（C57/BL6），通过注射AAV1-Syn-GCaMP6s-WPRE-SV40与AAV2/9-CaMKII-C1V1(t/t)-mScarlett-Kv2.1构建模型。用于数据导入、分析与绘图的代码可在以下仓库获取：https://github.com/alloptical/Dalgleish-eLife-2020

**Fall.mat**：符合Python版Suite2p的MATLAB输出标准格式的结果文件，包含ROIs、信号轨迹等数据（详细格式请参见Suite2p官方文档）。已对ROIs进行人工校正，若需使用校正后的ROIs，请调用`iscell`标签。

**targets**：光刺激靶点数据。每个`*_Points.mat`文件将返回名为`points`的变量，其包含`X`、`Y`、`Z`、`Zum`四个字段，分别对应像素坐标XY、平面编号Z、以微米为单位的Z轴坐标。每个文件对应实验中使用的一种刺激类型（即靶向的神经元数量，可通过上述字段的元素数量判断）。`*_VarFile_*.mat`文件包含训练用的光刺激协议，可通过Dalgleish等人2020年开源仓库中的代码，与`*_Points.mat`文件及`*_paq_analysis.mat`文件进行同步。

**cellPose**：C1V1表达成像图与Cellpose识别的C1V1阳性神经元。`*.tif`文件为C1V1-mCherry的表达成像图（激发波长765 nm）。`*_cellPoseCentroids.mat`文件包含C1V1阳性神经元的坐标，格式与前述靶点`*_Points.mat`文件类似。其余文件为Cellpose算法的原始输出（详细格式请参见Cellpose官方文档）。

**`*_paqanalysis.mat`**：记录实验所有事件时序的同步数据，字段含义直观。返回名为`pa`的变量，其关键字段包括：
- `frames`：成像帧时序
- `stims`：以结构体数组形式存储的刺激时刻，每个结构体记录对应刺激通道的时序信息（详见下述注意事项）。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"）。建议优先使用"out"信号获取最精准的时序信息（例如Go任务试次）。注意：Catch试次仅包含"in"触发信号，因为未施加光刺激。
- `licks`：舔舐时刻
- `rewards`：奖励投递时刻
- `running`：线性跑步机的旋转编码器读数

本实验包含两类刺激类型，因此存在两个相关刺激通道：Go试次（施加光刺激）通过通道7发送，对应`pa.stims(7)`；Catch试次（无刺激）通过通道6发送，对应`pa.stims(6)`。Go试次共包含7种不同的试次类型（即变量`var`），对应不同数量的被刺激神经元，分别为：
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