# Thiele_attention_gratc_V1_V4_laminar Simultaneous recordings from rhesus macaque V1 and V4 during a selective attention task. These preprocessed data allow reproduction of the main analyses and results reported in the paper "Top-down coordination of local cortical state during selective attention", van Kempen (2020) BioRxiv ([doi: 10.1101/2020.03.26.009365](https://www.biorxiv.org/content/10.1101/2020.03.26.009365v1)). Code can be found [here](https://gitlab.com/JvK/cortical-state-coordination). ## Data organisation & files Data is organised by subject and recording date. The folder `data/processed` contains the files necessary to replicate the main results described in this article. Output from the analyses and the pooled results will be stored in `data/analysed` and `data/population`, respectively. ### Files In each recording folder, you can find the following files: ``` Thiele_attention_gratc_V1_V4_laminar │ LICENCE.txt │ README.md │ datacite.yml │ └─── data │ └─── processed │ └─── J └─── T └─── W └─── 2016-01-21 │ └─── LFPb.mat │ └─── SNR.mat │ └─── V1_Coordinates.mat │ └─── V4_Coordinates.mat │ └─── hash.mat │ └─── pupil.mat │ └─── rf.mat │ └─── stability.mat │ └─── trialdata.mat │ └─── 2016-01-22 │ ... ``` - LFPb.mat : bipolar rereferenced local field potentials - SNR.mat : signal to noise ratios - V1_Coordinates/V4_Coordinates.mat : electrode depth coordinates - hash.mat : population spiking activity, thresholded such that each channel has approximately 100 Hz firing rate - pupil.mat : pupil diameter data - rf.mat : receptive field locations - stability.mat : info about which periods of the recording were stable - trialdata.mat : trial info, events and reaction times etc. ### Coordinates Electrode depth coordinates can be found in the files `V1_Coordinates.mat` and `V4_Coordinates.mat`. Each of these files is a matrix with 3 columns. ```Matlab Coordinates = -0.9404 -6.0000 0.1500 -0.7904 -5.0000 0.3000 -0.6404 -4.0000 0.4500 -0.4904 -3.0000 0.6000 -0.3404 -2.0000 0.7500 -0.1904 -1.0000 0.9000 -0.0404 0 1.0500 0.1096 1.0000 1.2000 0.2596 2.0000 1.3500 0.4096 3.0000 1.5000 0.5596 4.0000 1.6500 0.7096 5.0000 1.8000 0.8596 6.0000 1.9500 1.0096 7.0000 2.1000 1.1596 8.0000 2.2500 1.3096 9.0000 2.4000 ``` - The first column indicates the depth of the contact (in μm), relative to the alignment channel estimated as the input layer (layer IV). The first channel (`Coordinates(1,:)`) is the lowest channel and is inserted first (deepest into the tissue). Thus, the most negative numbers are deepest into the tissue. - The second column indicates the channel index relative to the alignment channel. - The third column indicates the electrode spacing (spaced 150 μm) ### Hash Population activity (hash) was extracted by lowering the spiking threshold such that average firing rates were approximately 100 Hz for each channel. This population activity is stored in `hash.mat`. Inside this file, you'll find the following variables: ```matlab FixAlign: {32×735 cell} StimAlign: {32×735 cell} CueAlign: {32×735 cell} Dim1Align: {32×735 cell} Dim2Align: {32×735 cell} numUnit: 32 unitList: [32×1 double] area: [32×2 char] ``` The fields `...Align` are variables with the data aligned to each of the events. This is a cell array of size (number of channels × number of trials). Each cell contains spike times relative to the event. The variable `unitList` contains the channel number and `area` contains which area a certain channel was recorded from. ### LFPb Bipolar re-referenced local field potential (LFP) activity is stored in `LFPb.mat`. This file contains: ```matlab struct with fields: CueAlign: [1×1 struct] SF: 1017 numUnit: 30 unitList: [30×1 double] area: [30×2 char] ``` The fields `...Align` are variables with the data aligned to each of the events. Each of these is a structure with the following fields: ```matlab struct with fields: TimeStamps: [1×4069 double] Samples: [30×376×4069 double] ``` `TimeStamps` is an array with the times relative to the event. `Samples` is a 3D array of size (number of channels × number of trials × number of time points). The variable `unitList` contains the channel number and `area` contains which area a certain channel was recorded from. Because of the bipolar re-referencing, there are 15 channels in each area (instead of 16). ### Pupil The file `pupil.mat` contains pupil diameter data, aligned to stimulus onset. Pupil diameter was recorded for most recordings (75/83). ```matlab StimAlign = struct with fields: TimeStamps: [1×751 double] Samples: [1×735×751 double] ``` ### SNR The file `SNR.mat` contains the signal-to-noise ratios for each channel, based on the MUAe signal. The file contains only 1 variable: ```matlab SNR: [32×3 table] ``` The variable `SNR` contains a table with the channel number (unitList), the area and maximum signal-to-noise ratio (SNR) in any of the tested time windows for each channel. ```matlab 32×3 table unitList area SNR ________ ____ _______ 1 V1 1.5658 2 V1 3.13 3 V1 13.076 4 V1 12.906 5 V1 26.571 6 V1 38.108 7 V1 45.913 8 V1 52.399 9 V1 96.766 10 V1 33.067 11 V1 34.225 12 V1 21.108 13 V1 11.472 14 V1 5.039 15 V1 0.86814 16 V1 0.53039 17 V4 36.337 18 V4 29.928 19 V4 28.666 20 V4 27.546 21 V4 16.787 22 V4 21.231 23 V4 12.358 24 V4 10.803 25 V4 9.4491 26 V4 11.73 27 V4 11.973 28 V4 10.374 29 V4 14.974 30 V4 4.3474 31 V4 0.99858 32 V4 0.1953 ``` ### Stability Recording stability (during the attention task) was determined by investigating possible drifts in the energy of the activity in the baseline period. The trial selection based on this criteria is stored in `stability.mat`. We selected the longest trial window that showed stable activity across all channels. ```matlab selectedTrialWindow: [354 674] chan2exclude: [1×0 double] ``` In this particular recording, we selected a trial window between 354 and 674, stored in `selectedTrialWindow`. The variable `chan2exclude` contains channels excluded from analyses. ### Trialdata The file `trialdata.mat` contains the metadata about each trial, e.g. the condition number, the events, etc. ```matlab trialdata = 1×803 struct array with fields: eventArray NLX_events cond_num RT_EPP targetDim rfDim positionRF positionOut1 positionOut2 fixbreak ``` - `eventArray`: the events as recorded by The Cortex - `NLX_events`: the events as recorded by Cheetah (Neuralynx) - `cond_num`: the condition number (1 & 4 for attend RF, 2 & 5 for attend away 1, 3 & 6 for attend away 2) - `RT_EPP`: the reaction time - `targetDim`: during which 'dimmming event' (first, second or third) the target changed luminance - `rfDim`: during which 'dimmming event' (first, second or third) changed the grating inside the receptive field (RF) in luminance - `positionRF`: position of grating inside RF - `positionOut1`: position of first grating outside RF - `positionOut2`: position of second grating outside RF - `fixbreak`: boolean indicating whether fixbreak occurred on this trial ## Funding - Wellcome trust, 093104 - MRC, MR/P013031/1 ## Credits - Data collection: Jochem van Kempen and Michael Boyd in the lab of Alexander Thiele, Newcastle University, UK - Data processing: Jochem van Kempen, Michael Boyd and Demetrio Ferro