Feature map statistics

A collection of MATLAB functions for generating and analysing cortical feature maps. All functions were developed and tested with MATLAB R2014b.

This code was used to perform the analyses in the following paper: Cloherty, SL, Hughes, NJ, Hietanen, MA, Bhagavatula, PS, Goodhill, GJ, Ibbotson, MR (2016) "Sensory experience modifies feature map relationships in visual cortex." eLife 2016;5:e13911. doi: 10.7554/eLife.13911.

tests.m contains a collection of tests and examples of the provided functions.

Functions

Map pre-processing and generation

• esd: Performs extended spatial decorrelation. Follows the method described in section 4.5.1 of http://webdoc.sub.gwdg.de/ebook/diss/2003/tu-berlin/diss/2001/schiessl_ingo.pdf
• align_images: Aligns a collection of images to a reference image using spatial translation by maximising linear correlation.

Map statistics and analysis

• orientation_hist: Generates a histogram of orientation preference from an OP map.
• crossing_angle_dist: Calculates a distribution of the crossing-angles between the contours of an OP and an OD map.
• od_op_crossing: Calculates the angle of intersection between all crossings of the contours of an OP and an OD map. Used by crossing_angle_dist.
• pinwod: Calculates a histogram of pinwheel locations in an OP map relative to the accompanying OD map.
• binned_selectivity: Calculates a histogram of orientation selectivity in the same OD bins as used by pinwod.
• pinw_density: Calculates the pinwheel density of an OP map.
• locate_pinwheels: Provides the location of all pinwheels in an OP map. Used by pinw_density.
• fourier_wavelength: Calculates the average wavelength of an OP map using its Fourier spectrum. Used by pinw_density.

Plotting

• op_contours - Calculates the contours of an OP map for pretty plotting.

Other

• corr_matrix: Calculates a shifted cross-correlation matrix. Used by esd.
• lattice_gradient_descent: Performs gradient descent minimisation on a lattice. Used by align_images.