Image Degradation

MATLAB code for reducing spatial resolution of histopathology images. Image datasets used:

• BACH (data here, paper here)
• BreaKHis (data here, paper here)
• PatchCamelyon (data here, paper here)

Functions

• dataset_parameters.m: returns struct called params containing previously determined parameters of imaging system used to capture publicly available datasets. Takes a single required argument:
  • dataset - (required) string, one of 'BreaKHis4X', 'BreaKHis10X', 'BreaKHis20X', 'BreaKHis40X', 'BACH', 'CAMELYON16-UMCU', 'CAMELYON16-RUMC', 'PCam'
  • params struct contains NA_H (original NA of system), M_obj (magnification of objective), M_relay (magnification of any relay used, 1 otherwise, d_pixel (physical size of camera pixel in metres), f (focal length of objective), img_ext (expected extension of image files in dataset), scale_factor (integer number by which to upscale images if necessary, e.g. for PCam)
• NA_estimation.m: code demonstrating process used to estimate NA_H for all datasets. While this calls dataset_parameters, it does not use the stored value of NA_H for that dataset for computation. It is overlaid on the resulting plot to illustrate how the value was obtained for each dataset. Takes the following arguments:
  • dataset - (required) string, one of 'BreaKHis4X', 'BreaKHis10X', 'BreaKHis20X', 'BreaKHis40X', 'BACH', 'CAMELYON16-UMCU', 'CAMELYON16-RUMC', 'PCam'
  • cutoff_min - (optional, default 10) integer, divisor of camera sampling frequency f_s to set minimum cutoff frequency for NA_H estimation
  • show_estimation - (optional, default false) boolean flag of whether to display images during NA estimation (for debugging)
• NA_degradation.m: script for systematically degrading images in a given dataset according to the degraded NA value NA_L based on the system parameters returned by dataset_parameters. Takes the following arguments:
  • dataset - (required) string, one of 'BreaKHis4X', 'BreaKHis10X', 'BreaKHis20X', 'BreaKHis40X', 'BACH', 'CAMELYON16-UMCU', 'CAMELYON16-RUMC', 'PCam'
  • NA_L - (required) positive float, should also be less than NA_H for this script to make sense but this is not currently enforced
  • save_images - (optional, default true) boolean flag of whether to save degraded images to disk
  • sanity_check - (optional, default false) boolean flag of whether to show PSF/MTF of system to ensure things are sensible
  • plot_fft - (optional, default false) boolean flag of whether to show image spectra of original/degraded images to ensure things are sensible
  • Q - (optional, default 10) integer, quantization/padding factor of pupil field size to ensure FFTs are computed correctly

Installation

Tested on Windows 10 using MATLAB R2021a. Requires Image Processing Toolbox to be installed.

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