Recruiting different population ratios in V1 using orientation components: a biphoton study

A feature of MotionClouds is the ability to precisely tune the precision of information following the principal axes. One which is particularly relevant for the primary visual cortical area of primates (area V1) is to tune the otirentation mean and bandwidth.

To install the necessary libraries, check out the documentation.

summary of the biphoton protocol

For the biphoton experiment:

  • The refresh rate of the screen is 70Hz and stimulation for 5 times 1s, which makes 350 images.
  • for the spatial frequency 0.125 cyc/deg is optimal (between 0.01 and 0.16).
  • for the temporal frequency 2 cyc/sec is optimal (between 0.8 and 4 sic/sec), we manipulate $B_V$ to get a qualitative estimate.

This is part of a larger study to tune orientation bandwidth.

Let's summarize this:

  • Presentation of stimuli with a circular disk during 250 ms ON then 250ms OFF
  • fixed parameters:

    • mean spatial frequency tuned for optimal neural tuning,
    • spatial frequency bandwidth tuned for optimal neural tuning,
    • temporal frequency bandwidth tuned for optimal neural tuning (TODO),
  • parameters:

    • 12 orientations including cardinals (TO BE DONE AT THE PRESENTATION SOFTWARE LEVEL)
    • 7 orientation bandwidths (infinite, pi/2, pi/4, pi/8, pi/16, pi/32, dirac),
    • 2 bandwidth in speed: dynamic (B_V=.5) or static (STATIC TO BE DONE AT THE PRESENTATION SOFTWARE LEVEL BY TAKING ONE FRAME of the DYNAMIC STIMULUS)
    • 3 different seeds: 42, 1973 and 2015 (completely arbitrary)

Grand total for one block is (12 orientations times 6 BWo + 1) (Dyn / stat) 0.5s :

In [1]:
%%writefile ../files/2017-04-19_biphoton_protocol.py
#!/usr/bin/env python3
# -*- coding: utf-8 -*
import numpy as np
import MotionClouds as mc
import os

viewingDistance = 30 # cm
screen_height_cm = 29 # cm
#un deg / cm
print('visual angle of the screen', 2*np.arctan(screen_height_cm/2/viewingDistance)*180/np.pi, ' degrees')
print('degrees per centimeter', 2*np.arctan(screen_height_cm/2/viewingDistance)*180/np.pi/screen_height_cm)

screen_height_px = 1024 # pixels 
#screen_height_px = 256 # pixels 
deg_per_px = 2*np.arctan(screen_height_cm/2/viewingDistance)*180/np.pi/screen_height_px
print('degrees per pixel', deg_per_px)

fps = 60 # frames per second
T = 1 # duration of one period in second

mc.N_X, mc.N_Y, mc.N_frame = screen_height_px, screen_height_px, int(fps*T)

print('width of these motion clouds (', mc.N_X, ', ', mc.N_Y, ')')
print('width of stimulus in degrees', mc.N_X * deg_per_px)
phi_sf_0 = .06 # Optimal spatial frequency [cpd]
print('Optimal spatial frequency in cycles per degree', phi_sf_0)
print('Optimal spatial frequency in cycles per window = ', phi_sf_0 *  mc.N_X * deg_per_px)
sf_0 = phi_sf_0 * deg_per_px
print('cycles per pixel = ', sf_0)

# Experimental constants 
contrast = 1.
B_sf = 0.1*sf_0 # 0.1   # BW spat. freq.
B_ft = .1 # BW temp. freq.

B_V = B_ft/sf_0     # BW in speed ("plane thickness")
print('B_V = ', B_V)
theta = 0.0   # Central orientation
# generate all files
dry_run = True
dry_run = False

#downscale = 1
fx, fy, ft = mc.get_grids(mc.N_X, mc.N_Y, mc.N_frame)

name = '2017-04-19_biphoton'
vext = '.png'
try:
    os.mkdir(os.path.join(mc.figpath, name))
except:
    pass
print('-'*50)
print('Starting protocol')
print('-'*50)
for B_theta in [0, np.pi/32, np.pi/16, np.pi/8, np.pi/4, np.pi/2, np.inf]:
    if B_theta == np.inf: B_theta_str = 'inf'
    else: B_theta_str = str(int(np.ceil(B_theta*180/np.pi)))
    for seed in [42, 1973, 2015]:
        name_ = name + '_B_theta_' + B_theta_str
        name_ += '_seed_' + str(seed)
        print('Cooking:', name_)
        if not dry_run:
            if  not(os.path.isfile(os.path.join(mc.figpath, name, name_ + vext))):
                mc_i = mc.envelope_gabor(fx, fy, ft, 
                                         V_X=0., V_Y=0., B_V=B_V, 
                                         sf_0=sf_0, B_sf=B_sf, 
                                         theta=0., B_theta=B_theta)
                im = mc.random_cloud(mc_i)
                mc.anim_save(mc.rectif(im, contrast=contrast, verbose=True), os.path.join(mc.figpath, name, name_), T_movie=T, vext=vext)
            else:
                print(' MC ' + os.path.join(mc.figpath, name, name_) + ' already done')
        else:
            print(' MC ' + os.path.join(mc.figpath, name, name_) + ' skipped  (dry run)')
Overwriting ../files/2017-04-19_biphoton_protocol.py
In [2]:
%%writefile  ../files/2017-04-19_biphoton_protocol.sh
#!/usr/bin/env bash
NAME=2017-04-19_biphoton
cd ../files
rm -fr `echo $NAME`_protocol.zip `echo $NAME`
ipython3 `echo $NAME`_protocol.py
zip `echo $NAME`_protocol.zip `echo $NAME`_protocol.* `echo $NAME`_protocol.sh `echo $NAME`/* `echo $NAME`/**/*
rm -fr `echo $NAME`
cd ..
nikola build
nikola deploy
cd files
echo 'done'
Overwriting ../files/2017-04-19_biphoton_protocol.sh
In [3]:
!sh ../files/2017-04-19_biphoton_protocol.sh
]0;IPython: motionclouds.invibe.net/filesvisual angle of the screen 51.592052989  degrees
degrees per centimeter 1.77903630997
degrees per pixel 0.0503828642471
width of these motion clouds ( 1024 ,  1024 )
width of stimulus in degrees 51.592052989
Optimal spatial frequency in cycles per degree 0.06
Optimal spatial frequency in cycles per window =  3.09552317934
cycles per pixel =  0.00302297185482
B_V =  33.0800301169
--------------------------------------------------
Starting protocol
--------------------------------------------------
Cooking: 2017-04-19_biphoton_B_theta_0_seed_42
Before Rectification of the frames
Mean= -4.26825196077e-22 , std= 1.77089064483e-05 , Min= -5.37177628656e-05 , Max= 5.35417131376e-05  Abs(Max)= 5.37177628656e-05
After Rectification of the frames
Mean= 0.5 , std= 0.164832873742 , Min= 0.0 , Max= 0.998361345311
percentage pixels clipped= 0.0
Cooking: 2017-04-19_biphoton_B_theta_0_seed_1973
Before Rectification of the frames
Mean= -3.47129101327e-21 , std= 2.14200732875e-05 , Min= -5.47432955489e-05 , Max= 5.47162028613e-05  Abs(Max)= 5.47432955489e-05
After Rectification of the frames
Mean= 0.5 , std= 0.195641065018 , Min= 0.0 , Max= 0.999752547893
percentage pixels clipped= 0.0
Cooking: 2017-04-19_biphoton_B_theta_0_seed_2015
Before Rectification of the frames
Mean= -2.49288110522e-22 , std= 1.64617842266e-05 , Min= -3.77911365534e-05 , Max= 3.76536678572e-05  Abs(Max)= 3.77911365534e-05
After Rectification of the frames
Mean= 0.5 , std= 0.217799538833 , Min= 0.0 , Max= 0.998181204527
percentage pixels clipped= 0.0
Cooking: 2017-04-19_biphoton_B_theta_6_seed_42
Before Rectification of the frames
Mean= -7.24260947512e-10 , std= 4037672.31132 , Min= -12593009.9986 , Max= 12593214.515  Abs(Max)= 12593214.515
After Rectification of the frames
Mean= 0.5 , std= 0.160311424319 , Min= 8.12010317797e-06 , Max= 1.0
percentage pixels clipped= 0.0
Cooking: 2017-04-19_biphoton_B_theta_6_seed_1973
Before Rectification of the frames
Mean= -6.50288711768e-12 , std= 3070504.68147 , Min= -8244907.4307 , Max= 8194391.53313  Abs(Max)= 8244907.4307
After Rectification of the frames
Mean= 0.5 , std= 0.186206134349 , Min= 0.0 , Max= 0.996936539433
percentage pixels clipped= 0.0
Cooking: 2017-04-19_biphoton_B_theta_6_seed_2015
Before Rectification of the frames
Mean= -6.93641292552e-11 , std= 3067951.60533 , Min= -7477426.92597 , Max= 7481392.70691  Abs(Max)= 7481392.70691
After Rectification of the frames
Mean= 0.5 , std= 0.205038802634 , Min= 0.000265042960179 , Max= 1.0
percentage pixels clipped= 0.0
Cooking: 2017-04-19_biphoton_B_theta_12_seed_42
Before Rectification of the frames
Mean= 4.76936018167e-19 , std= 0.0145012018123 , Min= -0.0459819809002 , Max= 0.0459483197054  Abs(Max)= 0.0459819809002
After Rectification of the frames
Mean= 0.5 , std= 0.157683526551 , Min= 0.0 , Max= 0.999633974068
percentage pixels clipped= 0.0
Cooking: 2017-04-19_biphoton_B_theta_12_seed_1973
Before Rectification of the frames
Mean= -1.67859342601e-18 , std= 0.0137622878287 , Min= -0.0408339884324 , Max= 0.040868242676  Abs(Max)= 0.040868242676
After Rectification of the frames
Mean= 0.5 , std= 0.168373863513 , Min= 0.000419081434988 , Max= 1.0
percentage pixels clipped= 0.0
Cooking: 2017-04-19_biphoton_B_theta_12_seed_2015
Before Rectification of the frames
Mean= -4.29728048574e-20 , std= 0.0126597281082 , Min= -0.0381898825174 , Max= 0.0382695382798  Abs(Max)= 0.0382695382798
After Rectification of the frames
Mean= 0.5 , std= 0.16540215374 , Min= 0.00104072019185 , Max= 1.0
percentage pixels clipped= 0.0
Cooking: 2017-04-19_biphoton_B_theta_23_seed_42
Before Rectification of the frames
Mean= 1.30831297311e-20 , std= 0.000129369665574 , Min= -0.000491440121939 , Max= 0.000501667469229  Abs(Max)= 0.000501667469229
After Rectification of the frames
Mean= 0.5 , std= 0.128939659744 , Min= 0.0101933530851 , Max= 1.0
percentage pixels clipped= 0.0
Cooking: 2017-04-19_biphoton_B_theta_23_seed_1973
Before Rectification of the frames
Mean= 4.85720455691e-22 , std= 0.000119174705452 , Min= -0.000371295656452 , Max= 0.000370521916548  Abs(Max)= 0.000371295656452
After Rectification of the frames
Mean= 0.5 , std= 0.160484917317 , Min= 0.0 , Max= 0.998958054195
percentage pixels clipped= 0.0
Cooking: 2017-04-19_biphoton_B_theta_23_seed_2015
Before Rectification of the frames
Mean= -7.83615766959e-21 , std= 0.000112728883639 , Min= -0.000431846725931 , Max= 0.00039672456326  Abs(Max)= 0.000431846725931
After Rectification of the frames
Mean= 0.5 , std= 0.130519553431 , Min= 0.0 , Max= 0.959334920746
percentage pixels clipped= 0.0
Cooking: 2017-04-19_biphoton_B_theta_45_seed_42
Before Rectification of the frames
Mean= 1.71700637016e-21 , std= 5.20622524427e-05 , Min= -0.000200871801153 , Max= 0.000198257927113  Abs(Max)= 0.000200871801153
After Rectification of the frames
Mean= 0.5 , std= 0.129590744305 , Min= 0.0 , Max= 0.993493676005
percentage pixels clipped= 0.0
Cooking: 2017-04-19_biphoton_B_theta_45_seed_1973
Before Rectification of the frames
Mean= 2.18419798013e-21 , std= 4.46139663833e-05 , Min= -0.000175305805962 , Max= 0.000176355607723  Abs(Max)= 0.000176355607723
After Rectification of the frames
Mean= 0.5 , std= 0.126488652557 , Min= 0.00297637759796 , Max= 1.0
percentage pixels clipped= 0.0
Cooking: 2017-04-19_biphoton_B_theta_45_seed_2015
Before Rectification of the frames
Mean= -7.64094304502e-22 , std= 4.54100375531e-05 , Min= -0.000166230309578 , Max= 0.000186322673525  Abs(Max)= 0.000186322673525
After Rectification of the frames
Mean= 0.5 , std= 0.121858592661 , Min= 0.0539181935491 , Max= 1.0
percentage pixels clipped= 0.0
Cooking: 2017-04-19_biphoton_B_theta_90_seed_42
Before Rectification of the frames
Mean= 3.25054408046e-22 , std= 4.4387031292e-05 , Min= -0.000163282613518 , Max= 0.000192962453377  Abs(Max)= 0.000192962453377
After Rectification of the frames
Mean= 0.5 , std= 0.115014684243 , Min= 0.0769057382403 , Max= 1.0
percentage pixels clipped= 0.0
Cooking: 2017-04-19_biphoton_B_theta_90_seed_1973
Before Rectification of the frames
Mean= 1.65436122511e-23 , std= 4.18306476709e-05 , Min= -0.000154367265254 , Max= 0.000155090427285  Abs(Max)= 0.000155090427285
After Rectification of the frames
Mean= 0.5 , std= 0.134858896204 , Min= 0.00233142058869 , Max= 1.0
percentage pixels clipped= 0.0
Cooking: 2017-04-19_biphoton_B_theta_90_seed_2015
Before Rectification of the frames
Mean= 6.99684507472e-22 , std= 4.3204846181e-05 , Min= -0.000169025074717 , Max= 0.000157482840432  Abs(Max)= 0.000169025074717
After Rectification of the frames
Mean= 0.5 , std= 0.127806025979 , Min= 0.0 , Max= 0.965856443772
percentage pixels clipped= 0.0
Cooking: 2017-04-19_biphoton_B_theta_inf_seed_42
Before Rectification of the frames
Mean= -1.09276073456e-21 , std= 4.25558157156e-05 , Min= -0.000162493496722 , Max= 0.000157546150665  Abs(Max)= 0.000162493496722
After Rectification of the frames
Mean= 0.5 , std= 0.130946211922 , Min= 0.0 , Max= 0.984776787512
percentage pixels clipped= 0.0
Cooking: 2017-04-19_biphoton_B_theta_inf_seed_1973
Before Rectification of the frames
Mean= -1.68413972716e-22 , std= 4.45963719168e-05 , Min= -0.000175975069281 , Max= 0.000175676820571  Abs(Max)= 0.000175975069281
After Rectification of the frames
Mean= 0.5 , std= 0.126712187411 , Min= 0.0 , Max= 0.999152582492
percentage pixels clipped= 0.0
Cooking: 2017-04-19_biphoton_B_theta_inf_seed_2015
Before Rectification of the frames
Mean= -3.04843628413e-22 , std= 4.42769258975e-05 , Min= -0.000181531804854 , Max= 0.00020355580502  Abs(Max)= 0.00020355580502
After Rectification of the frames
Mean= 0.5 , std= 0.108758691242 , Min= 0.054098187384 , Max= 1.0
percentage pixels clipped= 0.0
  adding: 2017-04-19_biphoton_protocol.py (deflated 60%)
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[2017-04-20T11:41:20Z] WARNING: Nikola: Shortcode name conflict: post-list
[2017-04-20T11:41:20Z] WARNING: Nikola: Shortcode name conflict: chart
[2017-04-20T11:41:20Z] WARNING: Nikola: Shortcode name conflict: media
[2017-04-20T11:41:20Z] WARNING: Nikola: Shortcode name conflict: doc
Scanning posts.........done!
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[2017-04-20T11:41:41Z] WARNING: Nikola: Shortcode name conflict: doc
[2017-04-20T11:41:41Z] WARNING: Nikola: Shortcode name conflict: chart
[2017-04-20T11:41:41Z] WARNING: Nikola: Shortcode name conflict: post-list
[2017-04-20T11:41:41Z] WARNING: Nikola: Shortcode name conflict: media
Scanning posts.........done!
[2017-04-20T11:41:42Z] INFO: deploy: => preset 'default'
[2017-04-20T11:41:42Z] INFO: deploy: ==> sh deploy.sh
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[2017-04-20T11:46:45Z] INFO: deploy: Successful deployment
done

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