LGN development

    1. Making sure all the files are specified correctly

      1. Generally check to make sure all Intan files are placed correctly

      2. At the level of the experiment directory:

      3. testdirinfo.txt

      4. Within each t0000# directory, make sure the following files are specified correctly:

      5. vhintan_filtermap.txt

      6. vhintan_channelgrouping.txt

    2. Spike sorting

      1. Using RunExperiment panel, useful tools popup menu, "Intan sorting"

    1. Computing and fitting responses to stimuli that we know how to analyze

      1. Call function analyzeferretlgn([dirname],1,1,0,1) % last inputs: 0/1 calculate responses, 0/1 calculate fits, 0/1 plot it as we go, 0/1 save our work

    1. To show the results from the whole study up to now:

      1. Call function lgnandrea_dir_analysis(prefix, expernames) (prefix is the directory where the experiments live, like prefix = '/Volumes/van-hooser-lab/Projects/LGNtraining_Andrea', and expernames is a cell list of experiments, like expernames = {'2017-05-05','2017-05-06'}

Steve/Andrea to-do list:

    1. Computing responses to stimuli

      1. Mixed grating stimuli

      2. Reverse-correlation-type stimuli

    2. Analyzing responses to stimuli (making fits)

      1. Mixed grating stimuli

      2. Reverse-correlation-type stimuli

Plotting orientation and direction selectivity against cortical selectivity from Jared’s paper

Plotting spatial frequency preferences and cut-offs


Function to jointly fit

function [ot_params, sf_params, offset, fitcurve_mesh, fitcurve, err] = joint_ot_sf_fit(angles, sfs, responses)

% JOINT_OT_SF_FIT - joint fit of orientation/direction and spatial frequency




% Performs a joint fit of orientation/direction and spatial frequency.

% R(o,s) = OFFSET + DOG(s, [0 SF_PARAMS]) .* DOUBLE_GAUSSIAN_PLOT([0 OT_PARAMS 180], o, 360)



% Inputs:

% ANGLES are the directions of stimulation in degrees

% SFS are the spatial frequencies presented

% RESPONSES are the responses to each angle and spatial frequency; RESPONSES(i,j) is the

% response to the ith angle (that is, ANGLE(i)) and jth spatial frequency (SFS(j))


% Outputs:

% SF_PARAMS = [ RE SE RI SI ] % parameters of DOG, see help dog

% OT_PARAMS = [ RP OP SIGM RN ] % parameters of DOUBLE_GAUSSIAN_PLOT, see help double_gaussian_plot

% OFFSET = constant offset

% FITCURVE_MESH - a set of angles and spatial frequencies for the fit: meshgrid([0:1:359],logspace(-2,1,100))

% FITCURVE - the fitted responses at FITCURVE_MESH

% ERR - sum of squared error between fit and data