DOI: 10.6084/m9.figshare.13114193.v1
title: 20191009_L544

description: If you use these data in a paper, please cite Dalgleish et al. 2020 (eLife) and reference the figshare dataset DOI.<br>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<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