Public Data/Code

 

Database #1: Orientation tuning data in macaque primary visual cortex.

This database contains the analysis of the tuning curves of 308 neurons in macaque primary visual cortex (M. fascicularis). The database contains all the variables needed to recreate the figures in the article:

D. L. Ringach, R. Shapley and M. J. Hawken, "Orientation Selectivity in Macaque V1: Diversity and Laminar Dependence", J. Neuroscience, 22(13):5639-5651. 
The article describes in detail the methods used in data collection and analysis. The database (distributed as a Matlab .mat file) contains a structure with the following variables:
db.orivar: The circular variance of the orientation tuning curve based on the mean spike rate at each orientation.

db.maxdc: The mean spike rate (in spk/sec) at the optimal orientation

db.mindc: The minimum spike rate (in spk/sec) across all orientations

db.maxfirst: The first harmonic response (in spk/sec) at the optimal orientation.

db.po: The ratio between the response at the orthogonal vs. preferred orientation

db.bw: The orientation bandwidth (in deg) of the tuning curve

db.spont: The spontaneous firing rate of the cell

db.rdepth: The relative cortical depth of the unit. Zero corresponds to the top of the cortex. One to the bottom. The division between the layers in this representation are as follows. Layers 2+3 correspond to [0, 0.422]. Layer 4A corresponds to [0.422, 0.4993]. Layer 4B corresponds to [0.4993, 0.6083]. Layer 4C corresponds to [0.6083, 7736]. Layer 5 corresponds to [0.7736, 0.8846]. Layer 6 corresponds to [0.8846, 1.0].

db.animal: The animal id number

db.unit: The unit id number

db.expt: The experiment id number

db.chan: The electrode channel id number

Acknowledgements: This work has been possible by the support of the following grants: NIH-EY12816 (DLR), NSF-IBN-9720305 (DLR), EY-08300 (MJH) and EY-01472 (RS).

Database #2: Shape of Simple-Cell Receptive Fields in Macaque V1

This database represents the analysis of the shapes of N=93 cells primary visual cortex (M. fascicularis). The database contains the variables needed to recreate the figures in the article:

D. L. Ringach "Spatial structure and symmetry of simple-cell receptive fields in macaque V1". J. Neurophysiol. 88:455-463, 2002. You can download a reprint of this article.

This article describes in detail the methods used in data collection and analysis. Here, we only describe the variables included in the database. The present database is a superset of the data analyzed in the paper (this is the reasons why there are N=93 cells in the database versus N=70 in the paper) where we have added some recent data. 

The database is provided as Matlab MAT file structure. The structure has fields which contain the variables analyzed in the article. The variables included are:

db.nx: The product of the spatial frequency of the carrier and sigma_x (unitless)

db.ny: The product of the spatial frequency of the carrier and sigma_y (unitless)

db.ph: The phase of the carrier with respect to the center of the envelope

db.animal: The animal id number

db.unit: The unit id number

db.expt: The experiment id number

db.chan: The electrode channel id number

Acknowledgements: This work has been possible by the support of the following grants: NIH-EY12816 (DLR), NSF-IBN-9720305 (DLR), EY-08300 (MJH) and EY-01472 (RS). A subset of these data has been collected in the laboratory of Robert Shapley and Michael Hawken.
Database #3: Subregion overlap and F1/F0 in macaque V1
This database represents the analysis of subregion overlap in 300 neurons in macaque primary visual cortex (M. fascicularis). In a subset of neurons, we have also measured the F1/F0 ratio in response to drifting gratings. The database contains all the variables needed to recreate the data figures in the article:

M. L. Mata and D. L. Ringach, R. Shapley and M. J. Hawken, "Spatial overlap of 'on' and 'off' subregions and its relation to response modulation ratio in macaque primary visual cortex", J. Neurophysiology, 2004.
The original describes in detail the methods used in data collection and analysis. Here, we only describe the variables included in the database.

The database is provided as Matlab MAT 'data'. Each column of the matrix represents a different measure. Each row represents a different cell.
data(:,1) Discreteness measure (alpha)
data(:,2) Correlation coefficient (rho)
data(:,3) Normalized distance (delta)
data(:,4) Overlap index (omega)
data(:,5) Relative phase measure
data(:,6) F1/F0 ratio

Acknowledgements: This work has been possible by the support of NIH-EY12816 (DLR) and a Research to Prevent Blindness Grant to the Jules Stein Eye Institute at UCLA.
Model #1: Orientation Tuning
This is the Matlab code implementing the model described in:
M. Carandini and D. L. Ringach, "Predictions of a Recurrent Model of Orientation Selectivity", Vision Res (37)21:3061-71. You can download a reprint of this article. 

Algorithm #1: Hartigan's dip test
These two files implement Hartigan's dip test of bimodality in Matlab. The file HartigansDipTest.m computes the dip statistic, while the second file HartigansDipSignifTest.m provides a boostrap calculation of the p-value.
Algorithm #2: Maximum likelihood estimate of tetrachoric correlation

This file implements maximum likelihood estimation of the tetrachoric correlation coefficient following the method described in G. M. Tallis, The Maximum Likelihood Estimation of Correlation from Contingency Tables, Biometrics, Vol. 18, No. 3. (Sep., 1962), pp. 342-353. The M-file can be downloaded here. However, in order to run this file you also need the numerical integration toolbox.
The use of the tetrachoric correlation coefficient for the analysis of neural data is described in:
J.D. Dorn and D. L. Ringach, "Estimating Membrane Voltage Correlations from Extracellular Spike Trains", J. Neurophysiol. 89:2271-2278, 2003.Data_files/db.matData_files/db_rf.matData_files/overlapdata.matData_files/v1ori5.zipData_files/hartigansdiptest.mData_files/hartigansdipsigniftest.mData_files/tetrachoric.mData_files/nit.zipshapeimage_2_link_0shapeimage_2_link_1shapeimage_2_link_2shapeimage_2_link_3shapeimage_2_link_4shapeimage_2_link_5shapeimage_2_link_6shapeimage_2_link_7