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## Introduction ## This repository contains the data used in the paper **A projection specific logic to sampling visual inputs in mouse superior colliculus** **(doi: 10.7554/eLife.50697)**. For details of the different datasets please see instructions below. In addition, code is provided for loading and visualizing single examples of each data type in Matlab. Additional code used in the paper is available at https://github.com/farrowlab. ![enter image description here][1] [1]: http://www.farrowlab.com/wp-content/uploads/2018/08/RabiesRec.png ## RGC Anatomy ## ### Data information ### An excel table of all retinal ganglion cells included in the paper is provided, see **RGC_Table.xlsx**. Here we provide information about which cell type we assigned it to, what circuit it innervates, if we know its molecular identity, its uncorrected x-y position in the retina, its area and whether we have physiological recording of its visual response properties. Specifically, the columns are: - cell: cell identifier from 1 – 658 ID: internal identifier of the cell - cluster#: cluster number as used in the paper. 1 to 14: analysed clusters, 0: non-classifiable, -1 to -11: <1% of all cells and hence not included in the paper - Experiment Type: 1 = Pbg, 2 = LP mol info: 0 = negative, 1 = smi32+, 2 = cart+, 3 = foxp2+, NaN = no data - x-coord: x-coordinate in the retina in um with the optic nerve being 0. <0 is temporal, >0 is nasal - y-coord: y-coordinate in the retina in um with the optic nerve being 0. <0 is ventral, >0 is dorsal - dendritic area: en-face hull area of the dendritic field in um2. - patched: 0 = not patched, 1 = patched The same information is also included in the Matlab file **infoRGC.mat**. ### Data for each cell ### The data for each retinal ganglion cell is in its corresponding Matlab file with the name format of iiii_eeeee_ms_Ccc_nn.mat (**e.g. 0001_00535_1L_C01_01.mat**) with iiii = ID (as found in RGC_Table.xlsx and infoRGC.mat), eeeee = experiment number, m = mouse number in this experiment, s = left (L) or right (R) retina, cc = scan number within this retina, nn = neuron number within this scan. Each file contains the following 4 variables: - Profile: the normalized dendritic profile in z for this cell - profileAxis: the axis for plotting the profile with 0 = ON-ChAT and 1 = OFF-ChAT. - somaCoord: x,y,z coordinate of soma. Z coordinates could not be obtained for all data sets and are only valid if below the dendritic tree. - tree: dendritic tree structure created with TREES toolbox (https://www.treestoolbox.org) including the X, Y, and Z position of each pixel belonging to a given cell. **X and Y are in um, Z in arbitrary units where Z = 0 indicates the ON-ChAT band, Z = 50 the OFF-ChAT band.** ### Visualization ### The ‘tree’ can be plotted using the provided code **plotRGCanatomy.m**. **Important:** While the x and y coordinates of each cell can be consideres as actual um distance within the retina, the z-coordinates are in arbitrary units relative to the ChAT-bands. Due to different degrees of squishing of the retinas, we do not know the actual position in um. **Z = 0 indicates here the ON-ChAT band, Z = 50 the OFF-ChAT band.** ---------- ## RGC Physiology ## ### Data information ### An excel table of all patched retinal ganglion cells included in the paper is provided, see **RGCphysiology_Table.xlsx**. Each row represents one cell, each column a visual stimulus. For each cell and stimulus we indicate if the stimulus induced responses and was used for the paper (2), the stimulus was presented but did not elicit clear responses (1) or if the stimulus was not presented to that particular cell (0). Similar information is included in **infoRGCphysiology.mat**. The additional information provided here is: - date: recording date - molMarker: 0 = negative, 1 = smi32+, 2 = cart+, 3 = foxp2+, NaN = no data - anatomy: whether the cell has been traced ### Data for each cell ### The data for each patched cell is in its corresponding Matlab file with the name format of iiii_eeeee_ms_ccccxxYYYYpppp_spikes.mat as well as the corresponding _StimInfo.mat file **e.g. 0672_00891_2L_0001gbDIMM0001_spikes.mat**) with iiii = ID (same as anatomy if the cell was traced. If only patched, the ID starts with x), eeeee = experiment number, m = mouse number in this experiment, s = left (L) or right (R) retina, cccc = cell patched in this retina, xx = background and stimulus color (g = gray, b = black, x = not applicable), YYYY = stimulus name, pppp = stimulus repetition for this cells. These files contain the following variables: - spikes: occurrence of a spike for each bin (0 = no spike, 1 = spike) sampled at 20 kHz. - StimInfo: {1,1} contains the timing information for different parts of the stimulus (columns) for each repetitions of the stimulus (rows). Time is given in samples. {1,2} contains a description of what each time point in {1,1} represents in terms of stimulus properties. ### Visualization ### The visual responses can be plotted using **plotRGCphysiology.m**. ---------- ## NeuroPixels Data ## ### Data information ### An excel table of all single units recorded using Neuropixels is provided, see **Neuropixels_Table.xlsx**. Specifically, the columns are: - Cell ID: an internal ID number for each cell used in the paper. - Experiment date: date of the recording - Experiment number: an experiment number of the same format as for the retinas - Mouse ID - Experiment type: 1 = Pbg, 2 = LP Plus for 7 stimuli we indicate whether the cell responded (1) or not (0). Similar information is included in **infoNeuropixels.mat**. It further includes ‘stimuliDone’ which indicates which stimuli have been presented to this unit. The index refers to the rows in ‘stimulusInfo’, which is organised in the following way: - stimulusInfo{:,1} contains for each stimulus the relevant timing information of changes in the stimulus organised as cell x timepoint. Time is given in sampling point (30 kHz sampling rate). - simulusInfo{:,2} contains information about each time point indicated in stimulusInfo{:,1}. - stimulusInfo{:,3} contains the stimulus name ### Data for each cell ### The data for each recorded unit is in its corresponding Matlab file with the name format of celliiiii_eeeee_ddddddddd_clnnnnn_spikes.mat (**e.g. cell00398_00845_20180823a_cl00303.mat**) with iiiii = cell ID (can be used to index stimulusInfo{:,1}, eeeee = experiment number, ddddddddd = recording date, nnnnn = corresponding cluster number within this experiment. The files contain only one variable ‘SPIKES’ where each row in column one contains a 1 for each sampling bin (30 kHz) that contains a spike for a given stimulus indicated in column 2. The spike times are organized in stiumulusRepetition x bin. ### Visualization ### The visual responses can be plotted using **plotNeuropixelsData.m**.