Retina model

A pin-hole model of fish's retina which transforms bottom-projected stimuli into retinal space

Examples of retina images

Setup

• Install the latest version of Python 3. We are using the Anaconda distribution
• Some additional packages needed:

  • skimage - an open source Python package designed for image preprocessing;

    # Update pip
    python -m pip install -U pip
    # Install scikit-image
    python -m pip install -U scikit-image
    

  • openpyxl - a Python library to read/write Excel 2010 xlsx/xlsm/xltx/xltm files;

    pip install openpyxl      
    

  • pandas - a software library written for the Python programming language for data manipulation and analysis;

    pip install pandas
    

Usage

• Put in parameters for the visual stimuli in the file "eye_model_curve.py" as follow:

  ratio = 1### how big is one axis compared to the other.
  minor_p = 0.225  #minor axis of the dot   (cm)
  major_p = minor_p * ratio #major axis of the dot  (cm)
  dist_to_center =  [0.9]   # distance from the fish's head to the center of the stimulus (cm) 
  angle_to_fish = [20] #angle between Oy and the line connecting the closet point of the ellipse to the fish (deg) 
  angle_ver = [20]  # angle from Oy to the major axis of the ellipse  (deg)
  location = r'WHERE YOU WANT TO SAVE THE OUTPUT DATA FILES'
  labels = "vertical_constant" ##labels of stimulus. Eg: vertical ellipse or horizontal ellipse
  

• If you want to also control for the parameters of the fish's eyes, additional parameters can be adjusted in the file "additional_input.py":

  arena_radius_real = 9.2/2   # (cm)
  distance_xy_right = 0.9  # (cm)
  distance_xy_left = 0.9  # (cm)                                          
  dist_btw_eye = 0.12 # distance between the two eyes        #(cm)
  body_len = 0.5 #the length of the fish's body              #(cm)
  y_leye = 0 # y position of the left eye                    #(cm)
  x_leye = -0.06# x position of the left eye                 #(cm)
  eye_rad = 0.045 # fish eye's radius                         #(cm)
  h = 0.5 # the z position of the fish from the ground      #(cm)
  x_reye = x_leye + dist_btw_eye #x position of  the right eye    #(cm)
  y_reye = y_leye #y position of the right eye               #(cm)
  z_reye = z_leye = h #the z position of the fish from the ground  #(cm)
  angle_retina = 26.5 #angle made btw the normal vector of retina and the horizontal (deg)
  retina_field = 163 (deg)
  

• Then hit the 'Run file' button

Output clarification

• All the output files are saved as excel file (.xlsx)

• Example of output parameters:

  • 'ratio': aspect ratio of the visual stimulus
  • 'minor_p': the length (cm) of the visual stimulus' minor axis
  • 'major_p': the length (cm) of the visual stimulus' major axis
  • 'dist_to_center': the distance (cm) from the center of the visual stimulus to the midpoint of the line segment connecting two eye balls' centers
  • 'angle_to_fish': angle (deg) from the vertical axis (Oy) to the line segment connecting the fish to the visual stimulus's center (clockwise)
  • 'angle_ver' : angle (deg) from the vertical axis (Oy) to the major axis of the visual stimulus (clockwise)
  • 'x_eye_ball_left', 'y_eye_ball_left', 'z_eye_ball_left': are coordinates (cm) of the left/ right eye ball's center
  • 'x_center_retina_left', 'y_center_retina_left' : are coordinates (cm) of the left/right retina center
  • 'eye_rad': eye ball's radius (cm)
  • 

• Example of output data:

  • 'x_point', 'y_point', 'z_point' are coordinates of points on the contour of the visual stimuli
  • 'x_image_right', 'y_image_right', 'z_image_right' are coordinates of points on the contour of the stimuli's retina images on the right retina
  • 'x_image_left', 'y_image_left', 'z_image_left' are coordinates of points on the contour of the stimuli's retina images on the left retina
  • 

• Example of output properties:

  • 'Semi major': the length (cm) of major axis of a stimulus's retina image
  • 'Semi minor': the length (cm) of major axis of a stimulus's retina image
  • 'Image_area': the area (cm2) of the stimulus's retina image
  • 'Aspect ratio': the aspect ratio of the stimulus's retina image
  • 'Distance to retina center': the distance(cm) from the retina center to the stimulus's retina image
  • 'Azimuth': the azimuth angle position of the stimulus's retina image
  • 'Altitude': the altitude angle position of the stimulus's retina image
  •