Simultaneous recordings from rhesus macaque V1 and V4 during a selective attention task

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README.md

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).
Code can be found here.

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.

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:

      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:

  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:

  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).

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:

    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.

  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.

    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.

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
datacite.yml
Title Simultaneous laminar V1 and V4 recordings during selective attention
Authors van Kempen,Jochem;Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom;ORCID:0000-0002-0211-9545
Boyd,Michael;Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
Thiele,Alexander;Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom;ORCID:0000-0003-4894-0213
Description Simultaneous laminar recordings (16-contact silicon probes) in macaque V1 and V4 during a selective attention task.
License Attribution-NonCommercial-ShareAlike 4.0 International (https://creativecommons.org/licenses/by-nc-sa/4.0/)
References van Kempen J, Gieselmann MA, Boyd M, Steinmetz NA, Moore T, Engel T, Thiele A. 2020. Top-down coordination of local cortical state during selective attention, bioRxiv. doi:10.1101/2020.03.26.009365 [doi:10.1101/2020.03.26.009365] (IsDescribedBy)
Ferro D, van Kempen J, Boyd M, Panzeri S, Thiele A. 2020. Directed information exchange between cortical layers in macaque V1 and V4 and its modulation by selective attention. bioRxiv. doi:10.1101/2020.06.09.142190 [doi:10.1101/2020.06.09.142190] (IsDescribedBy)
Funding Wellcome, 093104
MRC, MR/P013031/1
Keywords neuroscience
vision
primary visual cortex (V1)
V4
attention
cortical state
feedforward
feedback
grating
colour
primate
macaque
Resource Type Dataset