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 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.
In each recording folder, you can find the following files:
Thiele_attention_V1_V4_laminar_gratc
│ 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
│ ...
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
Coordinates(1,:)
) is the lowest channel and is inserted first (deepest into the tissue). Thus, the most negative numbers are deepest into the tissue.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.
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).
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]
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
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.
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 CortexNLX_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 timetargetDim
: during which 'dimmming event' (first, second or third) the target changed luminancerfDim
: during which 'dimmming event' (first, second or third) changed the grating inside the receptive field (RF) in luminancepositionRF
: position of grating inside RFpositionOut1
: position of first grating outside RFpositionOut2
: position of second grating outside RFfixbreak
: boolean indicating whether fixbreak occurred on this trial