20191010_L542

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，并注明figshare数据集的DOI标识。
本数据集包含经处理的成像数据（Suite2p输出的感兴趣区域（Regions of Interest, ROIs）、信号轨迹与元数据）、光刺激方案、视蛋白表达数据，以及单场"神经元数量"心理测量曲线行为实验的同步数据——实验对象为1只小鼠，单天实验时长1至1.5小时。实验在小鼠的L2/3桶状皮层中开展，采用920 nm、约50 mW的激光对GCaMP6s进行成像，通过电控变焦透镜（Electrically Tunable Lens, ETL）实现4层成像，帧率约27 Hz，体帧率约7 Hz。光刺激采用1030 nm激光对体细胞限制性表达的C1V1-Kv2.1进行调控。实验所用小鼠为Emx1-Cre;CaMKIIa-tTA;Ai94 GCaMP6s转基因小鼠，通过注射AAV2/9-CaMKII-C1V1(t/t)-mRuby2-Kv2.1构建。
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：为Suite2p的MATLAB标准格式输出文件，包含ROIs、信号轨迹等内容（具体格式可参考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文件将返回一个points变量，其包含X、Y、Z与Zum字段，分别对应像素单位的XY坐标、以平面编号计的Z坐标，以及以微米计的Z坐标。每个文件对应实验中使用的一种刺激类型（即靶向的神经元数量，可通过上述字段的元素数量确认）。*_VarFile_*.mat文件包含训练阶段的光刺激方案，可通过Dalgleish等人2020年的GitHub仓库中的代码，与*_Points.mat文件及*_paq_analysis.mat文件（详见下文）进行同步。

cellPose：包含C1V1表达成像结果与经Cellpose算法识别的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（格式与上述targets部分的*_Points.mat文件类似）。其余文件为Cellpose算法的原始输出结果（具体可参考Cellpose官方文档）。

*_paqanalysis.mat：记录实验全流程时序的同步数据文件，变量命名直观易懂。该文件返回pa变量，包含以下核心字段：
- frames：成像帧时序
- stims：以结构体数组形式存储的刺激时间数据，每个元素对应一个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"光刺激已执行"反馈）。若需获取最精准的时序信息，建议优先使用"out"信号（例如Go任务试次）。注意：Catch试次仅包含"in"触发信号，因未施加光刺激。
- licks：舔舐行为发生时序
- rewards：奖励递送时序
- 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"，对应两个刺激通道：
1. Go试次：施加光刺激，通过通道7调控，对应pa.stims(7)
2. Catch试次：不施加光刺激，通过通道6调控，对应pa.stims(6)
Go试次共包含7种试次类型（即不同的刺激变量var），对应不同的靶向神经元数量，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